Skip to content
GitLab
Menu
Projects
Groups
Snippets
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
tsoc
openmm
Commits
8086b201
Commit
8086b201
authored
Mar 17, 2011
by
Peter Eastman
Browse files
Further cleanup to reference platform - mostly deleting lots of unnecessary "default return" values
parent
51475608
Changes
61
Hide whitespace changes
Inline
Side-by-side
Showing
20 changed files
with
146 additions
and
718 deletions
+146
-718
platforms/reference/src/gbsa/ImplicitSolventParameters.cpp
platforms/reference/src/gbsa/ImplicitSolventParameters.cpp
+10
-84
platforms/reference/src/gbsa/ImplicitSolventParameters.h
platforms/reference/src/gbsa/ImplicitSolventParameters.h
+10
-44
platforms/reference/src/gbsa/ObcParameters.cpp
platforms/reference/src/gbsa/ObcParameters.cpp
+10
-37
platforms/reference/src/gbsa/ObcParameters.h
platforms/reference/src/gbsa/ObcParameters.h
+10
-26
platforms/reference/src/gbsa/ObcReadme.txt
platforms/reference/src/gbsa/ObcReadme.txt
+0
-126
platforms/reference/src/gbsa/cpuObcInterface.cpp
platforms/reference/src/gbsa/cpuObcInterface.cpp
+5
-22
platforms/reference/src/gbsa/cpuObcInterface.h
platforms/reference/src/gbsa/cpuObcInterface.h
+4
-12
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceTorsionTorsionForce.cpp
...src/SimTKReference/AmoebaReferenceTorsionTorsionForce.cpp
+0
-2
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceTorsionTorsionForce.h
...e/src/SimTKReference/AmoebaReferenceTorsionTorsionForce.h
+0
-2
plugins/freeEnergy/platforms/reference/src/SimTKReference/ReferenceFreeEnergyLJCoulomb14Softcore.cpp
...SimTKReference/ReferenceFreeEnergyLJCoulomb14Softcore.cpp
+4
-19
plugins/freeEnergy/platforms/reference/src/SimTKReference/ReferenceFreeEnergyLJCoulomb14Softcore.h
...c/SimTKReference/ReferenceFreeEnergyLJCoulomb14Softcore.h
+4
-12
plugins/freeEnergy/platforms/reference/src/SimTKReference/ReferenceFreeEnergyLJCoulombSoftcoreIxn.cpp
...imTKReference/ReferenceFreeEnergyLJCoulombSoftcoreIxn.cpp
+9
-41
plugins/freeEnergy/platforms/reference/src/SimTKReference/ReferenceFreeEnergyLJCoulombSoftcoreIxn.h
.../SimTKReference/ReferenceFreeEnergyLJCoulombSoftcoreIxn.h
+9
-27
plugins/freeEnergy/platforms/reference/src/gbsa/CpuGBVISoftcore.cpp
...eeEnergy/platforms/reference/src/gbsa/CpuGBVISoftcore.cpp
+5
-25
plugins/freeEnergy/platforms/reference/src/gbsa/CpuGBVISoftcore.h
...freeEnergy/platforms/reference/src/gbsa/CpuGBVISoftcore.h
+5
-15
plugins/freeEnergy/platforms/reference/src/gbsa/CpuObcSoftcore.cpp
...reeEnergy/platforms/reference/src/gbsa/CpuObcSoftcore.cpp
+6
-24
plugins/freeEnergy/platforms/reference/src/gbsa/CpuObcSoftcore.h
.../freeEnergy/platforms/reference/src/gbsa/CpuObcSoftcore.h
+4
-12
plugins/freeEnergy/platforms/reference/src/gbsa/GBVISoftcoreParameters.cpp
...y/platforms/reference/src/gbsa/GBVISoftcoreParameters.cpp
+20
-86
plugins/freeEnergy/platforms/reference/src/gbsa/GBVISoftcoreParameters.h
...rgy/platforms/reference/src/gbsa/GBVISoftcoreParameters.h
+16
-38
plugins/freeEnergy/platforms/reference/src/gbsa/ObcSoftcoreParameters.cpp
...gy/platforms/reference/src/gbsa/ObcSoftcoreParameters.cpp
+15
-64
No files found.
platforms/reference/src/gbsa/ImplicitSolventParameters.cpp
View file @
8086b201
...
@@ -173,11 +173,9 @@ RealOpenMM ImplicitSolventParameters::getSolventDielectric( void ) const {
...
@@ -173,11 +173,9 @@ RealOpenMM ImplicitSolventParameters::getSolventDielectric( void ) const {
@param solventDielectric solvent dielectric
@param solventDielectric solvent dielectric
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ImplicitSolventParameters
::
setSolventDielectric
(
RealOpenMM
solventDielectric
){
void
ImplicitSolventParameters
::
setSolventDielectric
(
RealOpenMM
solventDielectric
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -187,7 +185,6 @@ int ImplicitSolventParameters::setSolventDielectric( RealOpenMM solventDielectri
...
@@ -187,7 +185,6 @@ int ImplicitSolventParameters::setSolventDielectric( RealOpenMM solventDielectri
_solventDielectric
=
solventDielectric
;
_solventDielectric
=
solventDielectric
;
_resetPreFactor
();
_resetPreFactor
();
return
SimTKOpenMMCommon
::
DefaultReturn
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -215,11 +212,9 @@ RealOpenMM ImplicitSolventParameters::getSoluteDielectric( void ) const {
...
@@ -215,11 +212,9 @@ RealOpenMM ImplicitSolventParameters::getSoluteDielectric( void ) const {
@param soluteDielectric solute dielectric
@param soluteDielectric solute dielectric
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ImplicitSolventParameters
::
setSoluteDielectric
(
RealOpenMM
soluteDielectric
){
void
ImplicitSolventParameters
::
setSoluteDielectric
(
RealOpenMM
soluteDielectric
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -229,7 +224,6 @@ int ImplicitSolventParameters::setSoluteDielectric( RealOpenMM soluteDielectric
...
@@ -229,7 +224,6 @@ int ImplicitSolventParameters::setSoluteDielectric( RealOpenMM soluteDielectric
_soluteDielectric
=
soluteDielectric
;
_soluteDielectric
=
soluteDielectric
;
_resetPreFactor
();
_resetPreFactor
();
return
SimTKOpenMMCommon
::
DefaultReturn
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -257,11 +251,9 @@ RealOpenMM ImplicitSolventParameters::getElectricConstant( void ) const {
...
@@ -257,11 +251,9 @@ RealOpenMM ImplicitSolventParameters::getElectricConstant( void ) const {
@param electricConstant electric constant
@param electricConstant electric constant
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ImplicitSolventParameters
::
setElectricConstant
(
RealOpenMM
electricConstant
){
void
ImplicitSolventParameters
::
setElectricConstant
(
RealOpenMM
electricConstant
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -271,8 +263,6 @@ int ImplicitSolventParameters::setElectricConstant( RealOpenMM electricConstant
...
@@ -271,8 +263,6 @@ int ImplicitSolventParameters::setElectricConstant( RealOpenMM electricConstant
_electricConstant
=
electricConstant
;
_electricConstant
=
electricConstant
;
_resetPreFactor
();
_resetPreFactor
();
return
SimTKOpenMMCommon
::
DefaultReturn
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -300,11 +290,9 @@ RealOpenMM ImplicitSolventParameters::getProbeRadius( void ) const {
...
@@ -300,11 +290,9 @@ RealOpenMM ImplicitSolventParameters::getProbeRadius( void ) const {
@param probeRadius probe radius
@param probeRadius probe radius
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ImplicitSolventParameters
::
setProbeRadius
(
RealOpenMM
probeRadius
){
void
ImplicitSolventParameters
::
setProbeRadius
(
RealOpenMM
probeRadius
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -313,7 +301,6 @@ int ImplicitSolventParameters::setProbeRadius( RealOpenMM probeRadius ){
...
@@ -313,7 +301,6 @@ int ImplicitSolventParameters::setProbeRadius( RealOpenMM probeRadius ){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
_probeRadius
=
probeRadius
;
_probeRadius
=
probeRadius
;
return
SimTKOpenMMCommon
::
DefaultReturn
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -364,11 +351,9 @@ RealOpenMM ImplicitSolventParameters::getPreFactor( void ) const {
...
@@ -364,11 +351,9 @@ RealOpenMM ImplicitSolventParameters::getPreFactor( void ) const {
@param pi4Asolv probe radius
@param pi4Asolv probe radius
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ImplicitSolventParameters
::
setPi4Asolv
(
RealOpenMM
pi4Asolv
){
void
ImplicitSolventParameters
::
setPi4Asolv
(
RealOpenMM
pi4Asolv
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -377,7 +362,6 @@ int ImplicitSolventParameters::setPi4Asolv( RealOpenMM pi4Asolv ){
...
@@ -377,7 +362,6 @@ int ImplicitSolventParameters::setPi4Asolv( RealOpenMM pi4Asolv ){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
_pi4Asolv
=
pi4Asolv
;
_pi4Asolv
=
pi4Asolv
;
return
SimTKOpenMMCommon
::
DefaultReturn
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -405,11 +389,9 @@ RealOpenMM ImplicitSolventParameters::getKcalA_To_kJNm( void ) const {
...
@@ -405,11 +389,9 @@ RealOpenMM ImplicitSolventParameters::getKcalA_To_kJNm( void ) const {
@param kcalA_To_kJNm probe radius
@param kcalA_To_kJNm probe radius
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ImplicitSolventParameters
::
setKcalA_To_kJNm
(
RealOpenMM
kcalA_To_kJNm
){
void
ImplicitSolventParameters
::
setKcalA_To_kJNm
(
RealOpenMM
kcalA_To_kJNm
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -418,7 +400,6 @@ int ImplicitSolventParameters::setKcalA_To_kJNm( RealOpenMM kcalA_To_kJNm ){
...
@@ -418,7 +400,6 @@ int ImplicitSolventParameters::setKcalA_To_kJNm( RealOpenMM kcalA_To_kJNm ){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
_kcalA_To_kJNm
=
kcalA_To_kJNm
;
_kcalA_To_kJNm
=
kcalA_To_kJNm
;
return
SimTKOpenMMCommon
::
DefaultReturn
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -452,11 +433,9 @@ RealOpenMM* ImplicitSolventParameters::getAtomicRadii( void ) const {
...
@@ -452,11 +433,9 @@ RealOpenMM* ImplicitSolventParameters::getAtomicRadii( void ) const {
@param atomicRadii array of atomic radii
@param atomicRadii array of atomic radii
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ImplicitSolventParameters
::
setAtomicRadii
(
RealOpenMM
*
atomicRadii
){
void
ImplicitSolventParameters
::
setAtomicRadii
(
RealOpenMM
*
atomicRadii
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -469,8 +448,6 @@ int ImplicitSolventParameters::setAtomicRadii( RealOpenMM* atomicRadii ){
...
@@ -469,8 +448,6 @@ int ImplicitSolventParameters::setAtomicRadii( RealOpenMM* atomicRadii ){
_ownAtomicRadii
=
false
;
_ownAtomicRadii
=
false
;
}
}
_atomicRadii
=
atomicRadii
;
_atomicRadii
=
atomicRadii
;
return
SimTKOpenMMCommon
::
DefaultReturn
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -479,11 +456,9 @@ int ImplicitSolventParameters::setAtomicRadii( RealOpenMM* atomicRadii ){
...
@@ -479,11 +456,9 @@ int ImplicitSolventParameters::setAtomicRadii( RealOpenMM* atomicRadii ){
@param atomicRadii array of atomic radii
@param atomicRadii array of atomic radii
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ImplicitSolventParameters
::
setAtomicRadii
(
const
RealOpenMMVector
&
atomicRadii
){
void
ImplicitSolventParameters
::
setAtomicRadii
(
const
RealOpenMMVector
&
atomicRadii
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -512,58 +487,17 @@ int ImplicitSolventParameters::setAtomicRadii( const RealOpenMMVector& atomicRad
...
@@ -512,58 +487,17 @@ int ImplicitSolventParameters::setAtomicRadii( const RealOpenMMVector& atomicRad
for
(
int
ii
=
0
;
ii
<
numberOfAtoms
;
ii
++
){
for
(
int
ii
=
0
;
ii
<
numberOfAtoms
;
ii
++
){
_atomicRadii
[
ii
]
=
atomicRadii
[
ii
];
_atomicRadii
[
ii
]
=
atomicRadii
[
ii
];
}
}
return
SimTKOpenMMCommon
::
DefaultReturn
;
}
}
/**---------------------------------------------------------------------------------------
Set AtomicRadii array
@param atomicRadii array of atomic radii
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
/*
int ImplicitSolventParameters::setAtomicRadii( RealOpenMM* atomicRadii ){
// ---------------------------------------------------------------------------------------
static const char* methodName = "\nImplicitSolventParameters::setAtomicRadii:";
// ---------------------------------------------------------------------------------------
int numberOfAtoms = getNumberOfAtoms();
if( _ownAtomicRadii ){
delete[] _atomicRadii;
_atomicRadii = new RealOpenMM[numberOfAtoms];
} else if( _atomicRadii == NULL ){
_atomicRadii = new RealOpenMM[numberOfAtoms];
_ownAtomicRadii = true;
}
// force kcal/A units
for( int ii = 0; ii < numberOfAtoms; ii++ ){
_atomicRadii[ii] = atomicRadii[ii];
}
return SimTKOpenMMCommon::DefaultReturn;
} */
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
Set AtomicRadii array
Set AtomicRadii array
@param atomicRadii vector of atomic radii
@param atomicRadii vector of atomic radii
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ImplicitSolventParameters
::
setOwnAtomicRadii
(
int
ownAtomicRadii
){
void
ImplicitSolventParameters
::
setOwnAtomicRadii
(
int
ownAtomicRadii
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -572,8 +506,6 @@ int ImplicitSolventParameters::setOwnAtomicRadii( int ownAtomicRadii ){
...
@@ -572,8 +506,6 @@ int ImplicitSolventParameters::setOwnAtomicRadii( int ownAtomicRadii ){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
_ownAtomicRadii
=
ownAtomicRadii
;
_ownAtomicRadii
=
ownAtomicRadii
;
return
SimTKOpenMMCommon
::
DefaultReturn
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -602,11 +534,9 @@ int ImplicitSolventParameters::getFreeArrays( void ) const {
...
@@ -602,11 +534,9 @@ int ImplicitSolventParameters::getFreeArrays( void ) const {
@param freeArrays flag
@param freeArrays flag
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ImplicitSolventParameters
::
setFreeArrays
(
int
freeArrays
){
void
ImplicitSolventParameters
::
setFreeArrays
(
int
freeArrays
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -615,8 +545,6 @@ int ImplicitSolventParameters::setFreeArrays( int freeArrays ){
...
@@ -615,8 +545,6 @@ int ImplicitSolventParameters::setFreeArrays( int freeArrays ){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
_freeArrays
=
freeArrays
;
_freeArrays
=
freeArrays
;
return
SimTKOpenMMCommon
::
DefaultReturn
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -683,8 +611,6 @@ void ImplicitSolventParameters::_resetPreFactor( void ){
...
@@ -683,8 +611,6 @@ void ImplicitSolventParameters::_resetPreFactor( void ){
@param title title (optional)
@param title title (optional)
@return SimTKOpenMMCommon::DefaultReturn always
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
std
::
string
ImplicitSolventParameters
::
getStateString
(
const
char
*
title
)
const
{
std
::
string
ImplicitSolventParameters
::
getStateString
(
const
char
*
title
)
const
{
...
...
platforms/reference/src/gbsa/ImplicitSolventParameters.h
View file @
8086b201
...
@@ -75,11 +75,9 @@ class OPENMM_EXPORT ImplicitSolventParameters {
...
@@ -75,11 +75,9 @@ class OPENMM_EXPORT ImplicitSolventParameters {
@param kcalA_To_kJNm probe radius
@param kcalA_To_kJNm probe radius
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
setKcalA_To_kJNm
(
RealOpenMM
kcalA_To_kJNm
);
void
setKcalA_To_kJNm
(
RealOpenMM
kcalA_To_kJNm
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -87,11 +85,9 @@ class OPENMM_EXPORT ImplicitSolventParameters {
...
@@ -87,11 +85,9 @@ class OPENMM_EXPORT ImplicitSolventParameters {
@param freeArrays flag
@param freeArrays flag
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
setFreeArrays
(
int
freeArrays
);
void
setFreeArrays
(
int
freeArrays
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -167,11 +163,9 @@ class OPENMM_EXPORT ImplicitSolventParameters {
...
@@ -167,11 +163,9 @@ class OPENMM_EXPORT ImplicitSolventParameters {
@param solventDielectric solvent dielectric
@param solventDielectric solvent dielectric
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
setSolventDielectric
(
RealOpenMM
solventDielectric
);
void
setSolventDielectric
(
RealOpenMM
solventDielectric
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -189,11 +183,9 @@ class OPENMM_EXPORT ImplicitSolventParameters {
...
@@ -189,11 +183,9 @@ class OPENMM_EXPORT ImplicitSolventParameters {
@param soluteDielectric solute dielectric
@param soluteDielectric solute dielectric
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
setSoluteDielectric
(
RealOpenMM
soluteDielectric
);
void
setSoluteDielectric
(
RealOpenMM
soluteDielectric
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -222,11 +214,9 @@ class OPENMM_EXPORT ImplicitSolventParameters {
...
@@ -222,11 +214,9 @@ class OPENMM_EXPORT ImplicitSolventParameters {
@param electricConstant electric constant
@param electricConstant electric constant
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
setElectricConstant
(
RealOpenMM
electricConstant
);
void
setElectricConstant
(
RealOpenMM
electricConstant
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -244,11 +234,9 @@ class OPENMM_EXPORT ImplicitSolventParameters {
...
@@ -244,11 +234,9 @@ class OPENMM_EXPORT ImplicitSolventParameters {
@param probeRadius probe radius
@param probeRadius probe radius
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
setProbeRadius
(
RealOpenMM
probeRadius
);
void
setProbeRadius
(
RealOpenMM
probeRadius
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -278,11 +266,9 @@ class OPENMM_EXPORT ImplicitSolventParameters {
...
@@ -278,11 +266,9 @@ class OPENMM_EXPORT ImplicitSolventParameters {
@param pi4Asolv see above
@param pi4Asolv see above
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
setPi4Asolv
(
RealOpenMM
pi4Asolv
);
void
setPi4Asolv
(
RealOpenMM
pi4Asolv
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -300,11 +286,9 @@ class OPENMM_EXPORT ImplicitSolventParameters {
...
@@ -300,11 +286,9 @@ class OPENMM_EXPORT ImplicitSolventParameters {
@param atomicRadii array of atomic radii
@param atomicRadii array of atomic radii
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
virtual
int
setAtomicRadii
(
RealOpenMM
*
atomicRadii
);
virtual
void
setAtomicRadii
(
RealOpenMM
*
atomicRadii
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -312,23 +296,9 @@ class OPENMM_EXPORT ImplicitSolventParameters {
...
@@ -312,23 +296,9 @@ class OPENMM_EXPORT ImplicitSolventParameters {
@param atomicRadii vector of atomic radii
@param atomicRadii vector of atomic radii
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
virtual
int
setAtomicRadii
(
const
RealOpenMMVector
&
atomicRadii
);
virtual
void
setAtomicRadii
(
const
RealOpenMMVector
&
atomicRadii
);
/**---------------------------------------------------------------------------------------
Set AtomicRadii array
@param atomicRadii array of atomic radii
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
//virtual int setAtomicRadii( RealOpenMM* atomicRadii );
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -339,11 +309,9 @@ class OPENMM_EXPORT ImplicitSolventParameters {
...
@@ -339,11 +309,9 @@ class OPENMM_EXPORT ImplicitSolventParameters {
@param ownAtomicRadii flag indicating whether array of atomic radii
@param ownAtomicRadii flag indicating whether array of atomic radii
should be freed
should be freed
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
setOwnAtomicRadii
(
int
ownAtomicRadii
);
void
setOwnAtomicRadii
(
int
ownAtomicRadii
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -351,8 +319,6 @@ class OPENMM_EXPORT ImplicitSolventParameters {
...
@@ -351,8 +319,6 @@ class OPENMM_EXPORT ImplicitSolventParameters {
@param title title (optional)
@param title title (optional)
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
virtual
std
::
string
getStateString
(
const
char
*
title
)
const
;
virtual
std
::
string
getStateString
(
const
char
*
title
)
const
;
...
...
platforms/reference/src/gbsa/ObcParameters.cpp
View file @
8086b201
...
@@ -180,11 +180,9 @@ ObcParameters::ObcType ObcParameters::getObcType( void ) const {
...
@@ -180,11 +180,9 @@ ObcParameters::ObcType ObcParameters::getObcType( void ) const {
@param obcType OBC type (ObcTypeI or ObcTypeII -- Eq. 7 or 8)
@param obcType OBC type (ObcTypeI or ObcTypeII -- Eq. 7 or 8)
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ObcParameters
::
setObcTypeParameters
(
ObcParameters
::
ObcType
obcType
){
void
ObcParameters
::
setObcTypeParameters
(
ObcParameters
::
ObcType
obcType
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -202,8 +200,6 @@ int ObcParameters::setObcTypeParameters( ObcParameters::ObcType obcType ){
...
@@ -202,8 +200,6 @@ int ObcParameters::setObcTypeParameters( ObcParameters::ObcType obcType ){
_gammaObc
=
4.85
f
;
_gammaObc
=
4.85
f
;
}
}
_obcType
=
obcType
;
_obcType
=
obcType
;
return
SimTKOpenMMCommon
::
DefaultReturn
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -311,11 +307,9 @@ RealOpenMM* ObcParameters::getAtomicRadii( void ) const {
...
@@ -311,11 +307,9 @@ RealOpenMM* ObcParameters::getAtomicRadii( void ) const {
@param atomicRadii array of atomic radii
@param atomicRadii array of atomic radii
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ObcParameters
::
setAtomicRadii
(
RealOpenMM
*
atomicRadii
){
void
ObcParameters
::
setAtomicRadii
(
RealOpenMM
*
atomicRadii
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -323,7 +317,7 @@ int ObcParameters::setAtomicRadii( RealOpenMM* atomicRadii ){
...
@@ -323,7 +317,7 @@ int ObcParameters::setAtomicRadii( RealOpenMM* atomicRadii ){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
return
ImplicitSolventParameters
::
setAtomicRadii
(
atomicRadii
);
ImplicitSolventParameters
::
setAtomicRadii
(
atomicRadii
);
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -332,11 +326,9 @@ int ObcParameters::setAtomicRadii( RealOpenMM* atomicRadii ){
...
@@ -332,11 +326,9 @@ int ObcParameters::setAtomicRadii( RealOpenMM* atomicRadii ){
@param atomicRadii vector of atomic radii
@param atomicRadii vector of atomic radii
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ObcParameters
::
setAtomicRadii
(
const
RealOpenMMVector
&
atomicRadii
){
void
ObcParameters
::
setAtomicRadii
(
const
RealOpenMMVector
&
atomicRadii
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -344,7 +336,7 @@ int ObcParameters::setAtomicRadii( const RealOpenMMVector& atomicRadii ){
...
@@ -344,7 +336,7 @@ int ObcParameters::setAtomicRadii( const RealOpenMMVector& atomicRadii ){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
return
ImplicitSolventParameters
::
setAtomicRadii
(
atomicRadii
);
ImplicitSolventParameters
::
setAtomicRadii
(
atomicRadii
);
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -380,11 +372,9 @@ const RealOpenMM* ObcParameters::getScaledRadiusFactors( void ) const {
...
@@ -380,11 +372,9 @@ const RealOpenMM* ObcParameters::getScaledRadiusFactors( void ) const {
@param ownScaledRadiusFactors flag indicating whether scale factors
@param ownScaledRadiusFactors flag indicating whether scale factors
array should be deleted
array should be deleted
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ObcParameters
::
setOwnScaleFactors
(
int
ownScaledRadiusFactors
){
void
ObcParameters
::
setOwnScaleFactors
(
int
ownScaledRadiusFactors
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -393,8 +383,6 @@ int ObcParameters::setOwnScaleFactors( int ownScaledRadiusFactors ){
...
@@ -393,8 +383,6 @@ int ObcParameters::setOwnScaleFactors( int ownScaledRadiusFactors ){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
_ownScaledRadiusFactors
=
ownScaledRadiusFactors
;
_ownScaledRadiusFactors
=
ownScaledRadiusFactors
;
return
SimTKOpenMMCommon
::
DefaultReturn
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -403,11 +391,9 @@ int ObcParameters::setOwnScaleFactors( int ownScaledRadiusFactors ){
...
@@ -403,11 +391,9 @@ int ObcParameters::setOwnScaleFactors( int ownScaledRadiusFactors ){
@param scaledRadiusFactors scaledRadiusFactors
@param scaledRadiusFactors scaledRadiusFactors
@return SimTKOpenMMCommon::DefaultReturn always
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ObcParameters
::
setScaledRadiusFactors
(
RealOpenMM
*
scaledRadiusFactors
){
void
ObcParameters
::
setScaledRadiusFactors
(
RealOpenMM
*
scaledRadiusFactors
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -421,9 +407,6 @@ int ObcParameters::setScaledRadiusFactors( RealOpenMM* scaledRadiusFactors ){
...
@@ -421,9 +407,6 @@ int ObcParameters::setScaledRadiusFactors( RealOpenMM* scaledRadiusFactors ){
}
}
_scaledRadiusFactors
=
scaledRadiusFactors
;
_scaledRadiusFactors
=
scaledRadiusFactors
;
return
SimTKOpenMMCommon
::
DefaultReturn
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -432,11 +415,9 @@ int ObcParameters::setScaledRadiusFactors( RealOpenMM* scaledRadiusFactors ){
...
@@ -432,11 +415,9 @@ int ObcParameters::setScaledRadiusFactors( RealOpenMM* scaledRadiusFactors ){
@param scaledRadiusFactors scaledRadiusFactors
@param scaledRadiusFactors scaledRadiusFactors
@return SimTKOpenMMCommon::DefaultReturn always
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ObcParameters
::
setScaledRadiusFactors
(
const
RealOpenMMVector
&
scaledRadiusFactors
){
void
ObcParameters
::
setScaledRadiusFactors
(
const
RealOpenMMVector
&
scaledRadiusFactors
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -452,8 +433,6 @@ int ObcParameters::setScaledRadiusFactors( const RealOpenMMVector& scaledRadiusF
...
@@ -452,8 +433,6 @@ int ObcParameters::setScaledRadiusFactors( const RealOpenMMVector& scaledRadiusF
for
(
int
ii
=
0
;
ii
<
(
int
)
scaledRadiusFactors
.
size
();
ii
++
){
for
(
int
ii
=
0
;
ii
<
(
int
)
scaledRadiusFactors
.
size
();
ii
++
){
_scaledRadiusFactors
[
ii
]
=
scaledRadiusFactors
[
ii
];
_scaledRadiusFactors
[
ii
]
=
scaledRadiusFactors
[
ii
];
}
}
return
SimTKOpenMMCommon
::
DefaultReturn
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -571,15 +550,12 @@ std::string ObcParameters::getStateString( const char* title ) const {
...
@@ -571,15 +550,12 @@ std::string ObcParameters::getStateString( const char* title ) const {
@param distance the cutoff distance
@param distance the cutoff distance
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ObcParameters
::
setUseCutoff
(
RealOpenMM
distance
)
{
void
ObcParameters
::
setUseCutoff
(
RealOpenMM
distance
)
{
cutoff
=
true
;
cutoff
=
true
;
cutoffDistance
=
distance
;
cutoffDistance
=
distance
;
return
SimTKOpenMMCommon
::
DefaultReturn
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -610,11 +586,9 @@ RealOpenMM ObcParameters::getCutoffDistance() {
...
@@ -610,11 +586,9 @@ RealOpenMM ObcParameters::getCutoffDistance() {
@param boxSize the X, Y, and Z widths of the periodic box
@param boxSize the X, Y, and Z widths of the periodic box
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ObcParameters
::
setPeriodic
(
RealVec
&
boxSize
)
{
void
ObcParameters
::
setPeriodic
(
RealVec
&
boxSize
)
{
assert
(
cutoff
);
assert
(
cutoff
);
assert
(
boxSize
[
0
]
>=
2.0
*
cutoffDistance
);
assert
(
boxSize
[
0
]
>=
2.0
*
cutoffDistance
);
...
@@ -624,7 +598,6 @@ int ObcParameters::setPeriodic( RealVec& boxSize ) {
...
@@ -624,7 +598,6 @@ int ObcParameters::setPeriodic( RealVec& boxSize ) {
periodicBoxSize
[
0
]
=
boxSize
[
0
];
periodicBoxSize
[
0
]
=
boxSize
[
0
];
periodicBoxSize
[
1
]
=
boxSize
[
1
];
periodicBoxSize
[
1
]
=
boxSize
[
1
];
periodicBoxSize
[
2
]
=
boxSize
[
2
];
periodicBoxSize
[
2
]
=
boxSize
[
2
];
return
SimTKOpenMMCommon
::
DefaultReturn
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
...
platforms/reference/src/gbsa/ObcParameters.h
View file @
8086b201
...
@@ -68,12 +68,10 @@ class ObcParameters : public ImplicitSolventParameters {
...
@@ -68,12 +68,10 @@ class ObcParameters : public ImplicitSolventParameters {
Set solvent dielectric (Simbios)
Set solvent dielectric (Simbios)
@param dielectricOffset solvent dielectric
@param dielectricOffset solvent dielectric
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
setDielectricOffset
(
RealOpenMM
dielectricOffset
);
void
setDielectricOffset
(
RealOpenMM
dielectricOffset
);
public:
public:
...
@@ -119,11 +117,9 @@ class ObcParameters : public ImplicitSolventParameters {
...
@@ -119,11 +117,9 @@ class ObcParameters : public ImplicitSolventParameters {
@param obcType OBC type (ObcTypeI or ObcTypeII -- Eq. 7 or 8)
@param obcType OBC type (ObcTypeI or ObcTypeII -- Eq. 7 or 8)
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
setObcTypeParameters
(
ObcParameters
::
ObcType
obcType
);
void
setObcTypeParameters
(
ObcParameters
::
ObcType
obcType
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -183,8 +179,8 @@ class ObcParameters : public ImplicitSolventParameters {
...
@@ -183,8 +179,8 @@ class ObcParameters : public ImplicitSolventParameters {
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
setScaledRadiusFactors
(
RealOpenMM
*
scaledRadiusFactors
);
void
setScaledRadiusFactors
(
RealOpenMM
*
scaledRadiusFactors
);
int
setScaledRadiusFactors
(
const
RealOpenMMVector
&
scaledRadiusFactors
);
void
setScaledRadiusFactors
(
const
RealOpenMMVector
&
scaledRadiusFactors
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -192,12 +188,10 @@ class ObcParameters : public ImplicitSolventParameters {
...
@@ -192,12 +188,10 @@ class ObcParameters : public ImplicitSolventParameters {
@param ownScaledRadiusFactors flag indicating whether scale factors
@param ownScaledRadiusFactors flag indicating whether scale factors
array should be deleted
array should be deleted
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
setOwnScaleFactors
(
int
ownScaledRadiusFactors
);
void
setOwnScaleFactors
(
int
ownScaledRadiusFactors
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -215,11 +209,9 @@ class ObcParameters : public ImplicitSolventParameters {
...
@@ -215,11 +209,9 @@ class ObcParameters : public ImplicitSolventParameters {
@param radii array to store Macromodel radii for each atom
@param radii array to store Macromodel radii for each atom
@param log if set, then print error messages to log file
@param log if set, then print error messages to log file
@return SimTKOpenMMCommon::DefaultReturn always
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
getMacroModelAtomicRadii
(
int
numberOfAtoms
,
void
getMacroModelAtomicRadii
(
int
numberOfAtoms
,
char
***
atomNames
,
RealOpenMM
*
radii
,
FILE
*
log
);
char
***
atomNames
,
RealOpenMM
*
radii
,
FILE
*
log
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -238,11 +230,9 @@ class ObcParameters : public ImplicitSolventParameters {
...
@@ -238,11 +230,9 @@ class ObcParameters : public ImplicitSolventParameters {
@param atomicRadii array of atomic radii
@param atomicRadii array of atomic radii
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
setAtomicRadii
(
RealOpenMM
*
atomicRadii
);
void
setAtomicRadii
(
RealOpenMM
*
atomicRadii
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -250,11 +240,9 @@ class ObcParameters : public ImplicitSolventParameters {
...
@@ -250,11 +240,9 @@ class ObcParameters : public ImplicitSolventParameters {
@param atomicRadii vector of atomic radii
@param atomicRadii vector of atomic radii
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
setAtomicRadii
(
const
RealOpenMMVector
&
atomicRadii
);
void
setAtomicRadii
(
const
RealOpenMMVector
&
atomicRadii
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -287,11 +275,9 @@ class ObcParameters : public ImplicitSolventParameters {
...
@@ -287,11 +275,9 @@ class ObcParameters : public ImplicitSolventParameters {
@param distance the cutoff distance
@param distance the cutoff distance
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
setUseCutoff
(
RealOpenMM
distance
);
void
setUseCutoff
(
RealOpenMM
distance
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -317,11 +303,9 @@ class ObcParameters : public ImplicitSolventParameters {
...
@@ -317,11 +303,9 @@ class ObcParameters : public ImplicitSolventParameters {
@param boxSize the X, Y, and Z widths of the periodic box
@param boxSize the X, Y, and Z widths of the periodic box
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
setPeriodic
(
OpenMM
::
RealVec
&
boxSize
);
void
setPeriodic
(
OpenMM
::
RealVec
&
boxSize
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
...
platforms/reference/src/gbsa/ObcReadme.txt
deleted
100644 → 0
View file @
51475608
The OBC Generalized Born model is based on the following papers:
J. Phys. Chem. 1996 100, 19824-19839 (HCT paper)
Proteins: Structure, Function, and Bioinformatics 55:383-394 (2004) (OBC paper)
---------------------------------------------------------------------------------------
The two main interface methods perform the following tasks:
(1) set the GBSA parameters; this method is called once prior to execution of
the main simulation loop
(2) calculate the GBSA forces/energy given the atom coordinates and charges
for each simulation step
The two methods and helper methods are in the file cpuObcInterface.cpp
---------------------------------------------------------------------------------------
The setup call is
cpuSetObcParameters( int numberOfAtoms, RealOpenMM* atomicRadii, RealOpenMM* obcScaleFactors,
int includeAceApproximation,
RealOpenMM soluteDielectric, RealOpenMM solventDielectric, FILE* log );
The parameters include the following:
(1) number of atoms
(2) the OBC atomic radii (akin to VDW radii, but optimized for GBSA calculations)
(3) the OBC scale factors for each atom
(4) a flag indicating whether the nonpolar ACE approximation is to be included
in calculating the forces and energy: I do not have a reference for this term
(5-6) the solute and solvent dielectric (typically 1.0 & 78.3)
(7) a log file reference; the reference may be set to NULL,
if logging is unwanted. Note: if the reference is NULL, warnings, ... will be output to stderr
cpuSetObcParameters() creates a static CpuObc object which is then referenced when the
GBSA forces and energy are to be calculated
The default OBC model is the Type II model: Eq. 8 in the 2004 OBC paper;
for the Type I model, replace the call
ObcParameters* obcParameters = new ObcParameters( numberOfAtoms, ObcParameters::ObcTypeII );
with
ObcParameters* obcParameters = new ObcParameters( numberOfAtoms, ObcParameters::ObcTypeI );
---------------------------------------------------------------------------------------
The OBC scale factors may be obtained via calls to either of the following 'helper' methods
getObcScaleFactors( int numberOfAtoms, const int* atomicNumber, RealOpenMM* scaleFactors )
or
getObcScaleFactorsGivenAtomMasses( int numberOfAtoms, const RealOpenMM* masses, RealOpenMM* scaleFactors )
Documentation for the inputs to these routines is contained in the file, cpuObcInterface.cpp.
The scale factors are those used in Tinker5, and are based on the element type
of each atom (H, C, N, O, ...).
---------------------------------------------------------------------------------------
The OBC radii may be obtained via the helper method:
getGbsaRadii( int numberOfAtoms, const int* atomicNumber,
const int* numberOfCovalentPartners, const int* indexOfCovalentPartner,
RealOpenMM* gbsaRadii );
Documentation for the inputs to this routine is contained in the file, cpuObcInterface.cpp.
The radii are based on the atom type (methyl C, carbonyl C, ...). The value for a hydrogen
depends on its covalent heavy atom partner. As for the OBC scale factors, the values
hardwired into the method are the same as those used in Tinker5.
---------------------------------------------------------------------------------------
The energy/forces are calculated via the call
cpuCalculateImplicitSolventForces( RealOpenMM** atomCoordinates, const RealOpenMM* partialCharges,
RealOpenMM** forces, RealOpenMM* energy, int updateBornRadii );
The coordinate and force arrays should have the layout: atomCoordinates[atomIndex][3] &
forces[atomIndex][3]
If updateBornRadii = 0, then the Born radii from the previous iteration are used; this reduces the
number of O(N**2) loops from 3 to 2.
If updateBornRadii != 0, then the Born radii are calculated for the input configuration.
For MD runs, setting updateBornRadii = 0 is relatively safe since the radii change little
from one iteration to the next. However, for minimization techniques updateBornRadii
should probably be set to a nonzero value since the configuarations can change significantly
between adjacent calls.
---------------------------------------------------------------------------------------
Notes:
(1) The type (float or double) for floating-point numbers is set in the file SimTKOpenMMRealType.h.
If 'RealOpenMMType' is set to 1 in the file, the calculations are performed in
single-precision; otherwise they are performed in double-precision
(2) The units are Angstroms for the spatial dimensions, kcal/mol for energy, and kcal/mol.A for the forces
(3) The code in gromacsCpuObcInterface.cpp provides an example of the parameter setup, ... used for
interfacing w/ Gromacs; the details are somewhat different from the code in cpuObcInterface.cpp
(4) Output from Tinker for a singles ubiquitin configuration are in the directory 'Examples'.
The xyz file gives the coordinates and atom types (Amber99 -- note the charge for atom type 268
(line 2008 in the Tinker amber99.prm file) was changed from -0.2737 to -0.2774 to agree w/
the value used in the version of Gromacs we have access to.)
The key file specifies that OBC should be used for the implicit solvent.
The results are in the files 111UBQ.gbsaAce and 111UBQ.gbsaNoAce. The first file includes the
ACE approximation, while the second does not. On the first line of each file, the number of atoms
and GBSA energy are reported. The remaining lines (one for each atom) give the coordinates (3 entries),
Born radius, partial charge, GBSA radius (rsolv in Tinker), the OBC scaling factor, and the forces (3). The
last three fields give the atomic number, Tinker Amber99 atom name and type.
---------------------------------------------------------------------------------------
platforms/reference/src/gbsa/cpuObcInterface.cpp
View file @
8086b201
...
@@ -143,11 +143,9 @@ cpuSetObcParameters( int numberOfAtoms, RealOpenMM* atomicRadii, RealOpenMM* obc
...
@@ -143,11 +143,9 @@ cpuSetObcParameters( int numberOfAtoms, RealOpenMM* atomicRadii, RealOpenMM* obc
Function calls a static method in CpuImplicitSolvent class to calculate forces/energy
Function calls a static method in CpuImplicitSolvent class to calculate forces/energy
@return result from CpuImplicitSolvent::computeImplicitSolventForces
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
extern
"C"
int
extern
"C"
void
cpuCalculateImplicitSolventForces
(
vector
<
RealVec
>&
atomCoordinates
,
cpuCalculateImplicitSolventForces
(
vector
<
RealVec
>&
atomCoordinates
,
const
RealOpenMM
*
partialCharges
,
const
RealOpenMM
*
partialCharges
,
vector
<
RealVec
>&
forces
,
RealOpenMM
*
energy
,
vector
<
RealVec
>&
forces
,
RealOpenMM
*
energy
,
...
@@ -159,14 +157,11 @@ cpuCalculateImplicitSolventForces( vector<RealVec>& atomCoordinates,
...
@@ -159,14 +157,11 @@ cpuCalculateImplicitSolventForces( vector<RealVec>& atomCoordinates,
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
int
status
=
CpuImplicitSolvent
::
getCpuImplicitSolvent
()
->
computeImplicitSolventForces
(
atomCoordinates
,
partialCharges
,
CpuImplicitSolvent
::
getCpuImplicitSolvent
()
->
computeImplicitSolventForces
(
atomCoordinates
,
partialCharges
,
forces
,
updateBornRadii
);
forces
,
updateBornRadii
);
*
energy
=
CpuImplicitSolvent
::
getCpuImplicitSolvent
()
->
getEnergy
();
*
energy
=
CpuImplicitSolvent
::
getCpuImplicitSolvent
()
->
getEnergy
();
// printf( "\ncpuCalculateImplicitSolventForcesE=%.5e", *energy );
// printf( "\ncpuCalculateImplicitSolventForcesE=%.5e", *energy );
return
status
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -213,11 +208,9 @@ extern "C" int cpuDeleteObcParameters( void ){
...
@@ -213,11 +208,9 @@ extern "C" int cpuDeleteObcParameters( void ){
@param masses input masses
@param masses input masses
@param scaleFactors output atomic numbers
@param scaleFactors output atomic numbers
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
extern
"C"
int
getObcScaleFactorsGivenAtomMasses
(
int
numberOfAtoms
,
const
RealOpenMM
*
masses
,
extern
"C"
void
getObcScaleFactorsGivenAtomMasses
(
int
numberOfAtoms
,
const
RealOpenMM
*
masses
,
RealOpenMM
*
scaleFactors
){
RealOpenMM
*
scaleFactors
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -252,8 +245,6 @@ extern "C" int getObcScaleFactorsGivenAtomMasses( int numberOfAtoms, const RealO
...
@@ -252,8 +245,6 @@ extern "C" int getObcScaleFactorsGivenAtomMasses( int numberOfAtoms, const RealO
scaleFactors
[
atomI
]
=
(
RealOpenMM
)
scaleFactor
;
scaleFactors
[
atomI
]
=
(
RealOpenMM
)
scaleFactor
;
}
}
return
SimTKOpenMMCommon
::
DefaultReturn
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -264,11 +255,9 @@ extern "C" int getObcScaleFactorsGivenAtomMasses( int numberOfAtoms, const RealO
...
@@ -264,11 +255,9 @@ extern "C" int getObcScaleFactorsGivenAtomMasses( int numberOfAtoms, const RealO
@param atomicNumber input atomic number for each atom
@param atomicNumber input atomic number for each atom
@param scaleFactors output atomic numbers
@param scaleFactors output atomic numbers
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
extern
"C"
int
getObcScaleFactors
(
int
numberOfAtoms
,
const
int
*
atomicNumber
,
RealOpenMM
*
scaleFactors
){
extern
"C"
void
getObcScaleFactors
(
int
numberOfAtoms
,
const
int
*
atomicNumber
,
RealOpenMM
*
scaleFactors
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -324,8 +313,6 @@ extern "C" int getObcScaleFactors( int numberOfAtoms, const int* atomicNumber, R
...
@@ -324,8 +313,6 @@ extern "C" int getObcScaleFactors( int numberOfAtoms, const int* atomicNumber, R
scaleFactors
[
atomI
]
=
(
RealOpenMM
)
scaleFactor
;
scaleFactors
[
atomI
]
=
(
RealOpenMM
)
scaleFactor
;
}
}
return
SimTKOpenMMCommon
::
DefaultReturn
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -346,11 +333,9 @@ extern "C" int getObcScaleFactors( int numberOfAtoms, const int* atomicNumber, R
...
@@ -346,11 +333,9 @@ extern "C" int getObcScaleFactors( int numberOfAtoms, const int* atomicNumber, R
@param gbsaRadii output GBSA radii
@param gbsaRadii output GBSA radii
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
extern
"C"
int
getGbsaRadii
(
int
numberOfAtoms
,
const
int
*
atomicNumber
,
extern
"C"
void
getGbsaRadii
(
int
numberOfAtoms
,
const
int
*
atomicNumber
,
const
int
*
numberOfCovalentPartners
,
const
int
*
numberOfCovalentPartners
,
const
int
*
indexOfCovalentPartner
,
const
int
*
indexOfCovalentPartner
,
RealOpenMM
*
gbsaRadii
){
RealOpenMM
*
gbsaRadii
){
...
@@ -488,6 +473,4 @@ extern "C" int getGbsaRadii( int numberOfAtoms, const int* atomicNumber,
...
@@ -488,6 +473,4 @@ extern "C" int getGbsaRadii( int numberOfAtoms, const int* atomicNumber,
gbsaRadii
[
atomI
]
=
(
RealOpenMM
)
radius
;
gbsaRadii
[
atomI
]
=
(
RealOpenMM
)
radius
;
}
}
return
SimTKOpenMMCommon
::
DefaultReturn
;
}
}
platforms/reference/src/gbsa/cpuObcInterface.h
View file @
8086b201
...
@@ -104,11 +104,9 @@ int cpuSetObcParameters( int numberOfAtoms, RealOpenMM* atomicRadii, RealOpenMM*
...
@@ -104,11 +104,9 @@ int cpuSetObcParameters( int numberOfAtoms, RealOpenMM* atomicRadii, RealOpenMM*
Function calls a static method in CpuImplicitSolvent class to calculate forces/energy
Function calls a static method in CpuImplicitSolvent class to calculate forces/energy
@return result from CpuImplicitSolvent::computeImplicitSolventForces
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
externC
int
cpuCalculateImplicitSolventForces
(
std
::
vector
<
OpenMM
::
RealVec
>&
atomCoordinates
,
externC
void
cpuCalculateImplicitSolventForces
(
std
::
vector
<
OpenMM
::
RealVec
>&
atomCoordinates
,
const
RealOpenMM
*
partialChargesIn
,
const
RealOpenMM
*
partialChargesIn
,
std
::
vector
<
OpenMM
::
RealVec
>&
forces
,
RealOpenMM
*
energy
,
std
::
vector
<
OpenMM
::
RealVec
>&
forces
,
RealOpenMM
*
energy
,
int
updateBornRadii
);
int
updateBornRadii
);
...
@@ -121,11 +119,9 @@ externC int cpuCalculateImplicitSolventForces( std::vector<OpenMM::RealVec>& ato
...
@@ -121,11 +119,9 @@ externC int cpuCalculateImplicitSolventForces( std::vector<OpenMM::RealVec>& ato
@param masses input masses
@param masses input masses
@param scaleFactors output atomic numbers
@param scaleFactors output atomic numbers
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
externC
int
getObcScaleFactorsGivenAtomMasses
(
int
numberOfAtoms
,
const
RealOpenMM
*
masses
,
externC
void
getObcScaleFactorsGivenAtomMasses
(
int
numberOfAtoms
,
const
RealOpenMM
*
masses
,
RealOpenMM
*
scaleFactors
);
RealOpenMM
*
scaleFactors
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -136,11 +132,9 @@ externC int getObcScaleFactorsGivenAtomMasses( int numberOfAtoms, const RealOpen
...
@@ -136,11 +132,9 @@ externC int getObcScaleFactorsGivenAtomMasses( int numberOfAtoms, const RealOpen
@param atomicNumber input atomic number for each atom
@param atomicNumber input atomic number for each atom
@param scaleFactors output atomic numbers
@param scaleFactors output atomic numbers
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
externC
int
getObcScaleFactors
(
int
numberOfAtoms
,
const
int
*
atomicNumber
,
externC
void
getObcScaleFactors
(
int
numberOfAtoms
,
const
int
*
atomicNumber
,
RealOpenMM
*
scaleFactors
);
RealOpenMM
*
scaleFactors
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -156,11 +150,9 @@ externC int getObcScaleFactors( int numberOfAtoms, const int* atomicNumber,
...
@@ -156,11 +150,9 @@ externC int getObcScaleFactors( int numberOfAtoms, const int* atomicNumber,
then indexOfCovalentPartner[22] = 24
then indexOfCovalentPartner[22] = 24
@param gbsaRadii output GBSA radii
@param gbsaRadii output GBSA radii
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
externC
int
getGbsaRadii
(
int
numberOfAtoms
,
const
int
*
atomicNumber
,
externC
void
getGbsaRadii
(
int
numberOfAtoms
,
const
int
*
atomicNumber
,
const
int
*
numberOfCovalentPartners
,
const
int
*
numberOfCovalentPartners
,
const
int
*
indexOfCovalentPartner
,
RealOpenMM
*
gbsaRadii
);
const
int
*
indexOfCovalentPartner
,
RealOpenMM
*
gbsaRadii
);
...
...
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceTorsionTorsionForce.cpp
View file @
8086b201
...
@@ -43,8 +43,6 @@ using OpenMM::RealVec;
...
@@ -43,8 +43,6 @@ using OpenMM::RealVec;
@param fValues2 on return contains the values of the derivative of the function wrt second dimension
@param fValues2 on return contains the values of the derivative of the function wrt second dimension
@param fValues12 on return contains the values of the derivative of the function wrt first & second dimension
@param fValues12 on return contains the values of the derivative of the function wrt first & second dimension
@return AmoebaCommon::DefaultReturn
On first call a check is performed to see if the grid is valid
On first call a check is performed to see if the grid is valid
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
...
...
plugins/amoeba/platforms/reference/src/SimTKReference/AmoebaReferenceTorsionTorsionForce.h
View file @
8086b201
...
@@ -160,8 +160,6 @@ private:
...
@@ -160,8 +160,6 @@ private:
@param functionValue1 d(energy)/dx1
@param functionValue1 d(energy)/dx1
@param functionValue2 d(energy)/dx2
@param functionValue2 d(energy)/dx2
@return AmoebaCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
void
getBicubicValues
(
void
getBicubicValues
(
...
...
plugins/freeEnergy/platforms/reference/src/SimTKReference/ReferenceFreeEnergyLJCoulomb14Softcore.cpp
View file @
8086b201
...
@@ -73,18 +73,14 @@ ReferenceFreeEnergyLJCoulomb14Softcore::~ReferenceFreeEnergyLJCoulomb14Softcore(
...
@@ -73,18 +73,14 @@ ReferenceFreeEnergyLJCoulomb14Softcore::~ReferenceFreeEnergyLJCoulomb14Softcore(
@param distance the cutoff distance
@param distance the cutoff distance
@param solventDielectric the dielectric constant of the bulk solvent
@param solventDielectric the dielectric constant of the bulk solvent
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ReferenceFreeEnergyLJCoulomb14Softcore
::
setUseCutoff
(
RealOpenMM
distance
,
RealOpenMM
solventDielectric
)
{
void
ReferenceFreeEnergyLJCoulomb14Softcore
::
setUseCutoff
(
RealOpenMM
distance
,
RealOpenMM
solventDielectric
)
{
cutoff
=
true
;
cutoff
=
true
;
cutoffDistance
=
distance
;
cutoffDistance
=
distance
;
krf
=
pow
(
cutoffDistance
,
(
RealOpenMM
)
-
3.0
)
*
(
solventDielectric
-
1.0
f
)
/
(
2.0
f
*
solventDielectric
+
1.0
f
);
krf
=
pow
(
cutoffDistance
,
(
RealOpenMM
)
-
3.0
)
*
(
solventDielectric
-
1.0
f
)
/
(
2.0
f
*
solventDielectric
+
1.0
f
);
crf
=
(
1.0
f
/
cutoffDistance
)
*
(
3.0
f
*
solventDielectric
)
/
(
2.0
f
*
solventDielectric
+
1.0
f
);
crf
=
(
1.0
f
/
cutoffDistance
)
*
(
3.0
f
*
solventDielectric
)
/
(
2.0
f
*
solventDielectric
+
1.0
f
);
return
ReferenceForce
::
DefaultReturn
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -101,11 +97,9 @@ ReferenceFreeEnergyLJCoulomb14Softcore::~ReferenceFreeEnergyLJCoulomb14Softcore(
...
@@ -101,11 +97,9 @@ ReferenceFreeEnergyLJCoulomb14Softcore::~ReferenceFreeEnergyLJCoulomb14Softcore(
parameter[1]= (c12/c6)**1/6
parameter[1]= (c12/c6)**1/6
parameter[2]= epsfactor*q1*q2
parameter[2]= epsfactor*q1*q2
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ReferenceFreeEnergyLJCoulomb14Softcore
::
getDerivedParameters
(
RealOpenMM
c6
,
RealOpenMM
c12
,
RealOpenMM
q1
,
void
ReferenceFreeEnergyLJCoulomb14Softcore
::
getDerivedParameters
(
RealOpenMM
c6
,
RealOpenMM
c12
,
RealOpenMM
q1
,
RealOpenMM
q2
,
RealOpenMM
epsfac
,
RealOpenMM
q2
,
RealOpenMM
epsfac
,
RealOpenMM
*
parameters
)
const
{
RealOpenMM
*
parameters
)
const
{
...
@@ -128,8 +122,6 @@ int ReferenceFreeEnergyLJCoulomb14Softcore::getDerivedParameters( RealOpenMM c6,
...
@@ -128,8 +122,6 @@ int ReferenceFreeEnergyLJCoulomb14Softcore::getDerivedParameters( RealOpenMM c6,
parameters
[
1
]
=
POW
(
(
c12
/
c6
),
oneSixth
);
parameters
[
1
]
=
POW
(
(
c12
/
c6
),
oneSixth
);
}
}
parameters
[
2
]
=
epsfac
*
q1
*
q2
;
parameters
[
2
]
=
epsfac
*
q1
*
q2
;
return
ReferenceForce
::
DefaultReturn
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -236,11 +228,9 @@ void ReferenceFreeEnergyLJCoulomb14Softcore::calculateBondIxn( int* atomIndices,
...
@@ -236,11 +228,9 @@ void ReferenceFreeEnergyLJCoulomb14Softcore::calculateBondIxn( int* atomIndices,
@param dEdR output force factor
@param dEdR output force factor
@param energy LJ energy
@param energy LJ energy
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ReferenceFreeEnergyLJCoulomb14Softcore
::
calculateOneLJ14Ixn
(
RealOpenMM
inverseR
,
RealOpenMM
sig
,
RealOpenMM
eps
,
void
ReferenceFreeEnergyLJCoulomb14Softcore
::
calculateOneLJ14Ixn
(
RealOpenMM
inverseR
,
RealOpenMM
sig
,
RealOpenMM
eps
,
RealOpenMM
*
dEdR
,
RealOpenMM
*
energy
)
const
{
RealOpenMM
*
dEdR
,
RealOpenMM
*
energy
)
const
{
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -262,8 +252,6 @@ int ReferenceFreeEnergyLJCoulomb14Softcore::calculateOneLJ14Ixn( RealOpenMM inve
...
@@ -262,8 +252,6 @@ int ReferenceFreeEnergyLJCoulomb14Softcore::calculateOneLJ14Ixn( RealOpenMM inve
*
dEdR
=
eps
*
(
twelve
*
sig6
-
six
)
*
sig6
;
*
dEdR
=
eps
*
(
twelve
*
sig6
-
six
)
*
sig6
;
*
energy
+=
eps
*
(
sig6
-
one
)
*
sig6
;
*
energy
+=
eps
*
(
sig6
-
one
)
*
sig6
;
return
ReferenceForce
::
DefaultReturn
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -277,11 +265,9 @@ int ReferenceFreeEnergyLJCoulomb14Softcore::calculateOneLJ14Ixn( RealOpenMM inve
...
@@ -277,11 +265,9 @@ int ReferenceFreeEnergyLJCoulomb14Softcore::calculateOneLJ14Ixn( RealOpenMM inve
@param dEdR output force factor
@param dEdR output force factor
@param energy LJ energy
@param energy LJ energy
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ReferenceFreeEnergyLJCoulomb14Softcore
::
calculateOneSoftCoreLJ14Ixn
(
RealOpenMM
r
,
RealOpenMM
sig
,
RealOpenMM
eps
,
void
ReferenceFreeEnergyLJCoulomb14Softcore
::
calculateOneSoftCoreLJ14Ixn
(
RealOpenMM
r
,
RealOpenMM
sig
,
RealOpenMM
eps
,
RealOpenMM
lambda
,
RealOpenMM
lambda
,
RealOpenMM
*
dEdR
,
RealOpenMM
*
energy
)
const
{
RealOpenMM
*
dEdR
,
RealOpenMM
*
energy
)
const
{
...
@@ -328,5 +314,4 @@ if( maxPrint++ < 5 ){
...
@@ -328,5 +314,4 @@ if( maxPrint++ < 5 ){
r, sig, eps/lambda, lambda, dEdROrig, *dEdR, E_Orig, *energy, softcoreLJInv, sig6 );
r, sig, eps/lambda, lambda, dEdROrig, *dEdR, E_Orig, *energy, softcoreLJInv, sig6 );
}
}
#endif
#endif
return
ReferenceForce
::
DefaultReturn
;
}
}
plugins/freeEnergy/platforms/reference/src/SimTKReference/ReferenceFreeEnergyLJCoulomb14Softcore.h
View file @
8086b201
...
@@ -62,11 +62,9 @@ class ReferenceFreeEnergyLJCoulomb14Softcore : public ReferenceBondIxn {
...
@@ -62,11 +62,9 @@ class ReferenceFreeEnergyLJCoulomb14Softcore : public ReferenceBondIxn {
@param distance the cutoff distance
@param distance the cutoff distance
@param solventDielectric the dielectric constant of the bulk solvent
@param solventDielectric the dielectric constant of the bulk solvent
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
setUseCutoff
(
RealOpenMM
distance
,
RealOpenMM
solventDielectric
);
void
setUseCutoff
(
RealOpenMM
distance
,
RealOpenMM
solventDielectric
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -82,11 +80,9 @@ class ReferenceFreeEnergyLJCoulomb14Softcore : public ReferenceBondIxn {
...
@@ -82,11 +80,9 @@ class ReferenceFreeEnergyLJCoulomb14Softcore : public ReferenceBondIxn {
parameter[1]= (c12/c6)**1/6
parameter[1]= (c12/c6)**1/6
parameter[2]= epsfactor*q1*q2
parameter[2]= epsfactor*q1*q2
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
getDerivedParameters
(
RealOpenMM
c6
,
RealOpenMM
c12
,
RealOpenMM
q1
,
void
getDerivedParameters
(
RealOpenMM
c6
,
RealOpenMM
c12
,
RealOpenMM
q1
,
RealOpenMM
q2
,
RealOpenMM
epsfac
,
RealOpenMM
q2
,
RealOpenMM
epsfac
,
RealOpenMM
*
parameters
)
const
;
RealOpenMM
*
parameters
)
const
;
...
@@ -116,11 +112,9 @@ class ReferenceFreeEnergyLJCoulomb14Softcore : public ReferenceBondIxn {
...
@@ -116,11 +112,9 @@ class ReferenceFreeEnergyLJCoulomb14Softcore : public ReferenceBondIxn {
@param dEdR output force factor
@param dEdR output force factor
@param energy LJ energy
@param energy LJ energy
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
calculateOneLJ14Ixn
(
RealOpenMM
inverseR
,
RealOpenMM
sig
,
RealOpenMM
eps
,
void
calculateOneLJ14Ixn
(
RealOpenMM
inverseR
,
RealOpenMM
sig
,
RealOpenMM
eps
,
RealOpenMM
*
dEdR
,
RealOpenMM
*
energy
)
const
;
RealOpenMM
*
dEdR
,
RealOpenMM
*
energy
)
const
;
...
@@ -135,11 +129,9 @@ class ReferenceFreeEnergyLJCoulomb14Softcore : public ReferenceBondIxn {
...
@@ -135,11 +129,9 @@ class ReferenceFreeEnergyLJCoulomb14Softcore : public ReferenceBondIxn {
@param dEdR output force factor
@param dEdR output force factor
@param energy LJ energy
@param energy LJ energy
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
calculateOneSoftCoreLJ14Ixn
(
RealOpenMM
r
,
RealOpenMM
sig
,
RealOpenMM
eps
,
void
calculateOneSoftCoreLJ14Ixn
(
RealOpenMM
r
,
RealOpenMM
sig
,
RealOpenMM
eps
,
RealOpenMM
lambda
,
RealOpenMM
*
dEdR
,
RealOpenMM
*
energy
)
const
;
RealOpenMM
lambda
,
RealOpenMM
*
dEdR
,
RealOpenMM
*
energy
)
const
;
};
};
...
...
plugins/freeEnergy/platforms/reference/src/SimTKReference/ReferenceFreeEnergyLJCoulombSoftcoreIxn.cpp
View file @
8086b201
...
@@ -81,19 +81,15 @@ ReferenceFreeEnergyLJCoulombSoftcoreIxn::~ReferenceFreeEnergyLJCoulombSoftcoreIx
...
@@ -81,19 +81,15 @@ ReferenceFreeEnergyLJCoulombSoftcoreIxn::~ReferenceFreeEnergyLJCoulombSoftcoreIx
@param neighbors the neighbor list to use
@param neighbors the neighbor list to use
@param solventDielectric the dielectric constant of the bulk solvent
@param solventDielectric the dielectric constant of the bulk solvent
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ReferenceFreeEnergyLJCoulombSoftcoreIxn
::
setUseCutoff
(
RealOpenMM
distance
,
const
OpenMM
::
NeighborList
&
neighbors
,
RealOpenMM
solventDielectric
)
{
void
ReferenceFreeEnergyLJCoulombSoftcoreIxn
::
setUseCutoff
(
RealOpenMM
distance
,
const
OpenMM
::
NeighborList
&
neighbors
,
RealOpenMM
solventDielectric
)
{
cutoff
=
true
;
cutoff
=
true
;
cutoffDistance
=
distance
;
cutoffDistance
=
distance
;
neighborList
=
&
neighbors
;
neighborList
=
&
neighbors
;
krf
=
pow
(
cutoffDistance
,
(
RealOpenMM
)
-
3.0
)
*
(
solventDielectric
-
1.0
f
)
/
(
2.0
f
*
solventDielectric
+
1.0
f
);
krf
=
pow
(
cutoffDistance
,
(
RealOpenMM
)
-
3.0
)
*
(
solventDielectric
-
1.0
f
)
/
(
2.0
f
*
solventDielectric
+
1.0
f
);
crf
=
(
1.0
f
/
cutoffDistance
)
*
(
3.0
f
*
solventDielectric
)
/
(
2.0
f
*
solventDielectric
+
1.0
f
);
crf
=
(
1.0
f
/
cutoffDistance
)
*
(
3.0
f
*
solventDielectric
)
/
(
2.0
f
*
solventDielectric
+
1.0
f
);
return
ReferenceForce
::
DefaultReturn
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -104,11 +100,9 @@ ReferenceFreeEnergyLJCoulombSoftcoreIxn::~ReferenceFreeEnergyLJCoulombSoftcoreIx
...
@@ -104,11 +100,9 @@ ReferenceFreeEnergyLJCoulombSoftcoreIxn::~ReferenceFreeEnergyLJCoulombSoftcoreIx
@param boxSize the X, Y, and Z widths of the periodic box
@param boxSize the X, Y, and Z widths of the periodic box
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ReferenceFreeEnergyLJCoulombSoftcoreIxn
::
setPeriodic
(
RealVec
&
boxSize
)
{
void
ReferenceFreeEnergyLJCoulombSoftcoreIxn
::
setPeriodic
(
RealVec
&
boxSize
)
{
assert
(
cutoff
);
assert
(
cutoff
);
assert
(
boxSize
[
0
]
>=
2.0
*
cutoffDistance
);
assert
(
boxSize
[
0
]
>=
2.0
*
cutoffDistance
);
...
@@ -118,8 +112,6 @@ ReferenceFreeEnergyLJCoulombSoftcoreIxn::~ReferenceFreeEnergyLJCoulombSoftcoreIx
...
@@ -118,8 +112,6 @@ ReferenceFreeEnergyLJCoulombSoftcoreIxn::~ReferenceFreeEnergyLJCoulombSoftcoreIx
periodicBoxSize
[
0
]
=
boxSize
[
0
];
periodicBoxSize
[
0
]
=
boxSize
[
0
];
periodicBoxSize
[
1
]
=
boxSize
[
1
];
periodicBoxSize
[
1
]
=
boxSize
[
1
];
periodicBoxSize
[
2
]
=
boxSize
[
2
];
periodicBoxSize
[
2
]
=
boxSize
[
2
];
return
ReferenceForce
::
DefaultReturn
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -180,11 +172,9 @@ ReferenceFreeEnergyLJCoulombSoftcoreIxn::~ReferenceFreeEnergyLJCoulombSoftcoreIx
...
@@ -180,11 +172,9 @@ ReferenceFreeEnergyLJCoulombSoftcoreIxn::~ReferenceFreeEnergyLJCoulombSoftcoreIx
parameter[EpsIndex] = sqrt(c6*c6/c12) (2*sqrt(epsilon))
parameter[EpsIndex] = sqrt(c6*c6/c12) (2*sqrt(epsilon))
parameter[QIndex] = epsfactorSqrt*q1
parameter[QIndex] = epsfactorSqrt*q1
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ReferenceFreeEnergyLJCoulombSoftcoreIxn
::
getDerivedParameters
(
RealOpenMM
c6
,
RealOpenMM
c12
,
RealOpenMM
q1
,
void
ReferenceFreeEnergyLJCoulombSoftcoreIxn
::
getDerivedParameters
(
RealOpenMM
c6
,
RealOpenMM
c12
,
RealOpenMM
q1
,
RealOpenMM
epsfacSqrt
,
RealOpenMM
epsfacSqrt
,
RealOpenMM
*
parameters
)
const
{
RealOpenMM
*
parameters
)
const
{
...
@@ -215,8 +205,6 @@ int ReferenceFreeEnergyLJCoulombSoftcoreIxn::getDerivedParameters( RealOpenMM c6
...
@@ -215,8 +205,6 @@ int ReferenceFreeEnergyLJCoulombSoftcoreIxn::getDerivedParameters( RealOpenMM c6
}
}
parameters
[
QIndex
]
=
epsfacSqrt
*
q1
;
parameters
[
QIndex
]
=
epsfacSqrt
*
q1
;
return
ReferenceForce
::
DefaultReturn
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -235,11 +223,9 @@ int ReferenceFreeEnergyLJCoulombSoftcoreIxn::getDerivedParameters( RealOpenMM c6
...
@@ -235,11 +223,9 @@ int ReferenceFreeEnergyLJCoulombSoftcoreIxn::getDerivedParameters( RealOpenMM c6
@param energyByAtom atom energy
@param energyByAtom atom energy
@param totalEnergy total energy
@param totalEnergy total energy
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ReferenceFreeEnergyLJCoulombSoftcoreIxn
::
calculateEwaldIxn
(
int
numberOfAtoms
,
vector
<
RealVec
>&
atomCoordinates
,
void
ReferenceFreeEnergyLJCoulombSoftcoreIxn
::
calculateEwaldIxn
(
int
numberOfAtoms
,
vector
<
RealVec
>&
atomCoordinates
,
RealOpenMM
**
atomParameters
,
int
**
exclusions
,
RealOpenMM
**
atomParameters
,
int
**
exclusions
,
RealOpenMM
*
fixedParameters
,
vector
<
RealVec
>&
forces
,
RealOpenMM
*
fixedParameters
,
vector
<
RealVec
>&
forces
,
RealOpenMM
*
energyByAtom
,
RealOpenMM
*
totalEnergy
)
const
{
RealOpenMM
*
energyByAtom
,
RealOpenMM
*
totalEnergy
)
const
{
...
@@ -524,7 +510,6 @@ int ReferenceFreeEnergyLJCoulombSoftcoreIxn::calculateEwaldIxn( int numberOfAtom
...
@@ -524,7 +510,6 @@ int ReferenceFreeEnergyLJCoulombSoftcoreIxn::calculateEwaldIxn( int numberOfAtom
// ***********************************************************************
// ***********************************************************************
#endif
#endif
return
ReferenceForce
::
DefaultReturn
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -542,12 +527,10 @@ int ReferenceFreeEnergyLJCoulombSoftcoreIxn::calculateEwaldIxn( int numberOfAtom
...
@@ -542,12 +527,10 @@ int ReferenceFreeEnergyLJCoulombSoftcoreIxn::calculateEwaldIxn( int numberOfAtom
@param forces force array (forces added)
@param forces force array (forces added)
@param energyByAtom atom energy
@param energyByAtom atom energy
@param totalEnergy total energy
@param totalEnergy total energy
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ReferenceFreeEnergyLJCoulombSoftcoreIxn
::
calculatePMEIxn
(
int
numberOfAtoms
,
vector
<
RealVec
>&
atomCoordinates
,
void
ReferenceFreeEnergyLJCoulombSoftcoreIxn
::
calculatePMEIxn
(
int
numberOfAtoms
,
vector
<
RealVec
>&
atomCoordinates
,
RealOpenMM
**
atomParameters
,
int
**
exclusions
,
RealOpenMM
**
atomParameters
,
int
**
exclusions
,
RealOpenMM
*
fixedParameters
,
vector
<
RealVec
>&
forces
,
RealOpenMM
*
fixedParameters
,
vector
<
RealVec
>&
forces
,
RealOpenMM
*
energyByAtom
,
RealOpenMM
*
totalEnergy
)
const
{
RealOpenMM
*
energyByAtom
,
RealOpenMM
*
totalEnergy
)
const
{
...
@@ -655,7 +638,6 @@ int ReferenceFreeEnergyLJCoulombSoftcoreIxn::calculatePMEIxn( int numberOfAtoms,
...
@@ -655,7 +638,6 @@ int ReferenceFreeEnergyLJCoulombSoftcoreIxn::calculatePMEIxn( int numberOfAtoms,
// ***********************************************************************
// ***********************************************************************
#endif
#endif
return
ReferenceForce
::
DefaultReturn
;
}
}
...
@@ -675,11 +657,9 @@ int ReferenceFreeEnergyLJCoulombSoftcoreIxn::calculatePMEIxn( int numberOfAtoms,
...
@@ -675,11 +657,9 @@ int ReferenceFreeEnergyLJCoulombSoftcoreIxn::calculatePMEIxn( int numberOfAtoms,
@param energyByAtom atom energy
@param energyByAtom atom energy
@param totalEnergy total energy
@param totalEnergy total energy
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ReferenceFreeEnergyLJCoulombSoftcoreIxn
::
calculatePairIxn
(
int
numberOfAtoms
,
vector
<
RealVec
>&
atomCoordinates
,
void
ReferenceFreeEnergyLJCoulombSoftcoreIxn
::
calculatePairIxn
(
int
numberOfAtoms
,
vector
<
RealVec
>&
atomCoordinates
,
RealOpenMM
**
atomParameters
,
int
**
exclusions
,
RealOpenMM
**
atomParameters
,
int
**
exclusions
,
RealOpenMM
*
fixedParameters
,
vector
<
RealVec
>&
forces
,
RealOpenMM
*
fixedParameters
,
vector
<
RealVec
>&
forces
,
RealOpenMM
*
energyByAtom
,
RealOpenMM
*
totalEnergy
)
const
{
RealOpenMM
*
energyByAtom
,
RealOpenMM
*
totalEnergy
)
const
{
...
@@ -720,8 +700,6 @@ int ReferenceFreeEnergyLJCoulombSoftcoreIxn::calculatePairIxn( int numberOfAtoms
...
@@ -720,8 +700,6 @@ int ReferenceFreeEnergyLJCoulombSoftcoreIxn::calculatePairIxn( int numberOfAtoms
delete
[]
exclusionIndices
;
delete
[]
exclusionIndices
;
}
}
return
ReferenceForce
::
DefaultReturn
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -736,11 +714,9 @@ int ReferenceFreeEnergyLJCoulombSoftcoreIxn::calculatePairIxn( int numberOfAtoms
...
@@ -736,11 +714,9 @@ int ReferenceFreeEnergyLJCoulombSoftcoreIxn::calculatePairIxn( int numberOfAtoms
@param energyByAtom atom energy
@param energyByAtom atom energy
@param totalEnergy total energy
@param totalEnergy total energy
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ReferenceFreeEnergyLJCoulombSoftcoreIxn
::
calculateOneIxn
(
int
ii
,
int
jj
,
vector
<
RealVec
>&
atomCoordinates
,
void
ReferenceFreeEnergyLJCoulombSoftcoreIxn
::
calculateOneIxn
(
int
ii
,
int
jj
,
vector
<
RealVec
>&
atomCoordinates
,
RealOpenMM
**
atomParameters
,
vector
<
RealVec
>&
forces
,
RealOpenMM
**
atomParameters
,
vector
<
RealVec
>&
forces
,
RealOpenMM
*
energyByAtom
,
RealOpenMM
*
totalEnergy
)
const
{
RealOpenMM
*
energyByAtom
,
RealOpenMM
*
totalEnergy
)
const
{
...
@@ -827,7 +803,6 @@ int ReferenceFreeEnergyLJCoulombSoftcoreIxn::calculateOneIxn( int ii, int jj, ve
...
@@ -827,7 +803,6 @@ int ReferenceFreeEnergyLJCoulombSoftcoreIxn::calculateOneIxn( int ii, int jj, ve
energyByAtom
[
jj
]
+=
energy
;
energyByAtom
[
jj
]
+=
energy
;
}
}
}
}
return
ReferenceForce
::
DefaultReturn
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -840,11 +815,9 @@ int ReferenceFreeEnergyLJCoulombSoftcoreIxn::calculateOneIxn( int ii, int jj, ve
...
@@ -840,11 +815,9 @@ int ReferenceFreeEnergyLJCoulombSoftcoreIxn::calculateOneIxn( int ii, int jj, ve
@param dEdR output force factor
@param dEdR output force factor
@param energy LJ energy
@param energy LJ energy
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ReferenceFreeEnergyLJCoulombSoftcoreIxn
::
calculateOneLJIxn
(
RealOpenMM
inverseR
,
RealOpenMM
sig
,
RealOpenMM
eps
,
void
ReferenceFreeEnergyLJCoulombSoftcoreIxn
::
calculateOneLJIxn
(
RealOpenMM
inverseR
,
RealOpenMM
sig
,
RealOpenMM
eps
,
RealOpenMM
*
dEdR
,
RealOpenMM
*
energy
)
const
{
RealOpenMM
*
dEdR
,
RealOpenMM
*
energy
)
const
{
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -866,8 +839,6 @@ int ReferenceFreeEnergyLJCoulombSoftcoreIxn::calculateOneLJIxn( RealOpenMM inver
...
@@ -866,8 +839,6 @@ int ReferenceFreeEnergyLJCoulombSoftcoreIxn::calculateOneLJIxn( RealOpenMM inver
*
dEdR
=
eps
*
(
twelve
*
sig6
-
six
)
*
sig6
;
*
dEdR
=
eps
*
(
twelve
*
sig6
-
six
)
*
sig6
;
*
energy
+=
eps
*
(
sig6
-
one
)
*
sig6
;
*
energy
+=
eps
*
(
sig6
-
one
)
*
sig6
;
return
ReferenceForce
::
DefaultReturn
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -881,11 +852,9 @@ int ReferenceFreeEnergyLJCoulombSoftcoreIxn::calculateOneLJIxn( RealOpenMM inver
...
@@ -881,11 +852,9 @@ int ReferenceFreeEnergyLJCoulombSoftcoreIxn::calculateOneLJIxn( RealOpenMM inver
@param dEdR output force factor
@param dEdR output force factor
@param energy LJ energy
@param energy LJ energy
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ReferenceFreeEnergyLJCoulombSoftcoreIxn
::
calculateOneSoftCoreLJIxn
(
RealOpenMM
r
,
RealOpenMM
sig
,
RealOpenMM
eps
,
void
ReferenceFreeEnergyLJCoulombSoftcoreIxn
::
calculateOneSoftCoreLJIxn
(
RealOpenMM
r
,
RealOpenMM
sig
,
RealOpenMM
eps
,
RealOpenMM
lambda
,
RealOpenMM
lambda
,
RealOpenMM
*
dEdR
,
RealOpenMM
*
energy
)
const
{
RealOpenMM
*
dEdR
,
RealOpenMM
*
energy
)
const
{
...
@@ -932,5 +901,4 @@ if( maxPrint++ < 5 ){
...
@@ -932,5 +901,4 @@ if( maxPrint++ < 5 ){
r, sig, eps/lambda, lambda, dEdROrig, *dEdR, E_Orig, *energy, softcoreLJInv, sig6 );
r, sig, eps/lambda, lambda, dEdROrig, *dEdR, E_Orig, *energy, softcoreLJInv, sig6 );
}
}
#endif
#endif
return
ReferenceForce
::
DefaultReturn
;
}
}
plugins/freeEnergy/platforms/reference/src/SimTKReference/ReferenceFreeEnergyLJCoulombSoftcoreIxn.h
View file @
8086b201
...
@@ -65,11 +65,9 @@ class ReferenceFreeEnergyLJCoulombSoftcoreIxn : public ReferencePairIxn {
...
@@ -65,11 +65,9 @@ class ReferenceFreeEnergyLJCoulombSoftcoreIxn : public ReferencePairIxn {
@param energyByAtom atom energy
@param energyByAtom atom energy
@param totalEnergy total energy
@param totalEnergy total energy
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
calculateOneIxn
(
int
atom1
,
int
atom2
,
std
::
vector
<
OpenMM
::
RealVec
>&
atomCoordinates
,
void
calculateOneIxn
(
int
atom1
,
int
atom2
,
std
::
vector
<
OpenMM
::
RealVec
>&
atomCoordinates
,
RealOpenMM
**
atomParameters
,
std
::
vector
<
OpenMM
::
RealVec
>&
forces
,
RealOpenMM
**
atomParameters
,
std
::
vector
<
OpenMM
::
RealVec
>&
forces
,
RealOpenMM
*
energyByAtom
,
RealOpenMM
*
totalEnergy
)
const
;
RealOpenMM
*
energyByAtom
,
RealOpenMM
*
totalEnergy
)
const
;
...
@@ -100,11 +98,9 @@ class ReferenceFreeEnergyLJCoulombSoftcoreIxn : public ReferencePairIxn {
...
@@ -100,11 +98,9 @@ class ReferenceFreeEnergyLJCoulombSoftcoreIxn : public ReferencePairIxn {
@param neighbors the neighbor list to use
@param neighbors the neighbor list to use
@param solventDielectric the dielectric constant of the bulk solvent
@param solventDielectric the dielectric constant of the bulk solvent
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
setUseCutoff
(
RealOpenMM
distance
,
const
OpenMM
::
NeighborList
&
neighbors
,
RealOpenMM
solventDielectric
);
void
setUseCutoff
(
RealOpenMM
distance
,
const
OpenMM
::
NeighborList
&
neighbors
,
RealOpenMM
solventDielectric
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -114,11 +110,9 @@ class ReferenceFreeEnergyLJCoulombSoftcoreIxn : public ReferencePairIxn {
...
@@ -114,11 +110,9 @@ class ReferenceFreeEnergyLJCoulombSoftcoreIxn : public ReferencePairIxn {
@param boxSize the X, Y, and Z widths of the periodic box
@param boxSize the X, Y, and Z widths of the periodic box
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
setPeriodic
(
OpenMM
::
RealVec
&
boxSize
);
void
setPeriodic
(
OpenMM
::
RealVec
&
boxSize
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -167,11 +161,9 @@ class ReferenceFreeEnergyLJCoulombSoftcoreIxn : public ReferencePairIxn {
...
@@ -167,11 +161,9 @@ class ReferenceFreeEnergyLJCoulombSoftcoreIxn : public ReferencePairIxn {
parameter[EpsIndex] = 0.5*( (c12/c6)**1/6 )
parameter[EpsIndex] = 0.5*( (c12/c6)**1/6 )
parameter[QIndex] = epsfactorSqrt*q1
parameter[QIndex] = epsfactorSqrt*q1
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
getDerivedParameters
(
RealOpenMM
c6
,
RealOpenMM
c12
,
RealOpenMM
q1
,
void
getDerivedParameters
(
RealOpenMM
c6
,
RealOpenMM
c12
,
RealOpenMM
q1
,
RealOpenMM
epsfacSqrt
,
RealOpenMM
epsfacSqrt
,
RealOpenMM
*
parameters
)
const
;
RealOpenMM
*
parameters
)
const
;
...
@@ -191,11 +183,9 @@ class ReferenceFreeEnergyLJCoulombSoftcoreIxn : public ReferencePairIxn {
...
@@ -191,11 +183,9 @@ class ReferenceFreeEnergyLJCoulombSoftcoreIxn : public ReferencePairIxn {
@param energyByAtom atom energy
@param energyByAtom atom energy
@param totalEnergy total energy
@param totalEnergy total energy
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
calculatePairIxn
(
int
numberOfAtoms
,
std
::
vector
<
OpenMM
::
RealVec
>&
atomCoordinates
,
void
calculatePairIxn
(
int
numberOfAtoms
,
std
::
vector
<
OpenMM
::
RealVec
>&
atomCoordinates
,
RealOpenMM
**
atomParameters
,
int
**
exclusions
,
RealOpenMM
**
atomParameters
,
int
**
exclusions
,
RealOpenMM
*
fixedParameters
,
std
::
vector
<
OpenMM
::
RealVec
>&
forces
,
RealOpenMM
*
fixedParameters
,
std
::
vector
<
OpenMM
::
RealVec
>&
forces
,
RealOpenMM
*
energyByAtom
,
RealOpenMM
*
totalEnergy
)
const
;
RealOpenMM
*
energyByAtom
,
RealOpenMM
*
totalEnergy
)
const
;
...
@@ -217,11 +207,9 @@ private:
...
@@ -217,11 +207,9 @@ private:
@param energyByAtom atom energy
@param energyByAtom atom energy
@param totalEnergy total energy
@param totalEnergy total energy
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
calculateEwaldIxn
(
int
numberOfAtoms
,
std
::
vector
<
OpenMM
::
RealVec
>&
atomCoordinates
,
void
calculateEwaldIxn
(
int
numberOfAtoms
,
std
::
vector
<
OpenMM
::
RealVec
>&
atomCoordinates
,
RealOpenMM
**
atomParameters
,
int
**
exclusions
,
RealOpenMM
**
atomParameters
,
int
**
exclusions
,
RealOpenMM
*
fixedParameters
,
std
::
vector
<
OpenMM
::
RealVec
>&
forces
,
RealOpenMM
*
fixedParameters
,
std
::
vector
<
OpenMM
::
RealVec
>&
forces
,
RealOpenMM
*
energyByAtom
,
RealOpenMM
*
totalEnergy
)
const
;
RealOpenMM
*
energyByAtom
,
RealOpenMM
*
totalEnergy
)
const
;
...
@@ -241,12 +229,10 @@ private:
...
@@ -241,12 +229,10 @@ private:
@param forces force array (forces added)
@param forces force array (forces added)
@param energyByAtom atom energy
@param energyByAtom atom energy
@param totalEnergy total energy
@param totalEnergy total energy
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
calculatePMEIxn
(
int
numberOfAtoms
,
std
::
vector
<
OpenMM
::
RealVec
>&
atomCoordinates
,
void
calculatePMEIxn
(
int
numberOfAtoms
,
std
::
vector
<
OpenMM
::
RealVec
>&
atomCoordinates
,
RealOpenMM
**
atomParameters
,
int
**
exclusions
,
RealOpenMM
**
atomParameters
,
int
**
exclusions
,
RealOpenMM
*
fixedParameters
,
std
::
vector
<
OpenMM
::
RealVec
>&
forces
,
RealOpenMM
*
fixedParameters
,
std
::
vector
<
OpenMM
::
RealVec
>&
forces
,
RealOpenMM
*
energyByAtom
,
RealOpenMM
*
totalEnergy
)
const
;
RealOpenMM
*
energyByAtom
,
RealOpenMM
*
totalEnergy
)
const
;
...
@@ -261,11 +247,9 @@ private:
...
@@ -261,11 +247,9 @@ private:
@param dEdR output force factor
@param dEdR output force factor
@param energy LJ energy
@param energy LJ energy
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
calculateOneLJIxn
(
RealOpenMM
inverseR
,
RealOpenMM
sig
,
RealOpenMM
eps
,
void
calculateOneLJIxn
(
RealOpenMM
inverseR
,
RealOpenMM
sig
,
RealOpenMM
eps
,
RealOpenMM
*
dEdR
,
RealOpenMM
*
energy
)
const
;
RealOpenMM
*
dEdR
,
RealOpenMM
*
energy
)
const
;
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -279,11 +263,9 @@ private:
...
@@ -279,11 +263,9 @@ private:
@param dEdR output force factor
@param dEdR output force factor
@param energy LJ energy
@param energy LJ energy
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
calculateOneSoftCoreLJIxn
(
RealOpenMM
r
,
RealOpenMM
sig
,
RealOpenMM
eps
,
void
calculateOneSoftCoreLJIxn
(
RealOpenMM
r
,
RealOpenMM
sig
,
RealOpenMM
eps
,
RealOpenMM
lambda
,
RealOpenMM
*
dEdR
,
RealOpenMM
*
energy
)
const
;
RealOpenMM
lambda
,
RealOpenMM
*
dEdR
,
RealOpenMM
*
energy
)
const
;
...
...
plugins/freeEnergy/platforms/reference/src/gbsa/CpuGBVISoftcore.cpp
View file @
8086b201
...
@@ -122,11 +122,9 @@ GBVISoftcoreParameters* CpuGBVISoftcore::getGBVISoftcoreParameters( void ) const
...
@@ -122,11 +122,9 @@ GBVISoftcoreParameters* CpuGBVISoftcore::getGBVISoftcoreParameters( void ) const
@param GBVISoftcoreParameters reference
@param GBVISoftcoreParameters reference
@return 0;
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
CpuGBVISoftcore
::
setGBVISoftcoreParameters
(
GBVISoftcoreParameters
*
gbviParameters
){
void
CpuGBVISoftcore
::
setGBVISoftcoreParameters
(
GBVISoftcoreParameters
*
gbviParameters
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -135,7 +133,6 @@ int CpuGBVISoftcore::setGBVISoftcoreParameters( GBVISoftcoreParameters* gbviPara
...
@@ -135,7 +133,6 @@ int CpuGBVISoftcore::setGBVISoftcoreParameters( GBVISoftcoreParameters* gbviPara
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
_gbviParameters
=
gbviParameters
;
_gbviParameters
=
gbviParameters
;
return
0
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -190,13 +187,11 @@ RealOpenMM* CpuGBVISoftcore::getSwitchDeriviativeConst( void ) const {
...
@@ -190,13 +187,11 @@ RealOpenMM* CpuGBVISoftcore::getSwitchDeriviativeConst( void ) const {
@param outValue value of spline at x
@param outValue value of spline at x
@param outDerivative value of derivative of spline at x
@param outDerivative value of derivative of spline at x
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
#define GBVISoftcoreDebug 0
#define GBVISoftcoreDebug 0
int
CpuGBVISoftcore
::
quinticSpline
(
RealOpenMM
x
,
RealOpenMM
rl
,
RealOpenMM
ru
,
void
CpuGBVISoftcore
::
quinticSpline
(
RealOpenMM
x
,
RealOpenMM
rl
,
RealOpenMM
ru
,
RealOpenMM
*
outValue
,
RealOpenMM
*
outDerivative
){
RealOpenMM
*
outValue
,
RealOpenMM
*
outDerivative
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -220,8 +215,6 @@ int CpuGBVISoftcore::quinticSpline( RealOpenMM x, RealOpenMM rl, RealOpenMM ru,
...
@@ -220,8 +215,6 @@ int CpuGBVISoftcore::quinticSpline( RealOpenMM x, RealOpenMM rl, RealOpenMM ru,
*
outValue
=
one
+
ratio3
*
(
minusTen
+
fifteen
*
ratio
+
minusSix
*
ratio2
);
*
outValue
=
one
+
ratio3
*
(
minusTen
+
fifteen
*
ratio
+
minusSix
*
ratio2
);
*
outDerivative
=
ratio2
*
(
minusThirty
+
sixty
*
ratio
+
minusThirty
*
ratio2
)
/
denominator
;
*
outDerivative
=
ratio2
*
(
minusThirty
+
sixty
*
ratio
+
minusThirty
*
ratio2
)
/
denominator
;
return
0
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -236,13 +229,11 @@ int CpuGBVISoftcore::quinticSpline( RealOpenMM x, RealOpenMM rl, RealOpenMM ru,
...
@@ -236,13 +229,11 @@ int CpuGBVISoftcore::quinticSpline( RealOpenMM x, RealOpenMM rl, RealOpenMM ru,
@param bornRadius output Born radius
@param bornRadius output Born radius
@param switchDeriviative output switching function deriviative
@param switchDeriviative output switching function deriviative
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
#define GBVISoftcoreDebug 0
#define GBVISoftcoreDebug 0
int
CpuGBVISoftcore
::
computeBornRadiiUsingQuinticSpline
(
RealOpenMM
atomicRadius3
,
RealOpenMM
bornSum
,
void
CpuGBVISoftcore
::
computeBornRadiiUsingQuinticSpline
(
RealOpenMM
atomicRadius3
,
RealOpenMM
bornSum
,
GBVISoftcoreParameters
*
gbviParameters
,
GBVISoftcoreParameters
*
gbviParameters
,
RealOpenMM
&
bornRadius
,
RealOpenMM
*
switchDeriviative
){
RealOpenMM
&
bornRadius
,
RealOpenMM
*
switchDeriviative
){
...
@@ -303,8 +294,6 @@ int CpuGBVISoftcore::computeBornRadiiUsingQuinticSpline( RealOpenMM atomicRadius
...
@@ -303,8 +294,6 @@ int CpuGBVISoftcore::computeBornRadiiUsingQuinticSpline( RealOpenMM atomicRadius
*
switchDeriviative
=
one
;
*
switchDeriviative
=
one
;
}
}
bornRadius
=
POW
(
sum
,
minusOneThird
);
bornRadius
=
POW
(
sum
,
minusOneThird
);
return
0
;
}
}
#undef GBVISoftcoreDebug
#undef GBVISoftcoreDebug
...
@@ -317,13 +306,11 @@ int CpuGBVISoftcore::computeBornRadiiUsingQuinticSpline( RealOpenMM atomicRadius
...
@@ -317,13 +306,11 @@ int CpuGBVISoftcore::computeBornRadiiUsingQuinticSpline( RealOpenMM atomicRadius
@param bornRadii output array of Born radii
@param bornRadii output array of Born radii
@param chain not used here
@param chain not used here
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
#define GBVISoftcoreDebug 0
#define GBVISoftcoreDebug 0
int
CpuGBVISoftcore
::
computeBornRadii
(
vector
<
RealVec
>&
atomCoordinates
,
vector
<
RealOpenMM
>&
bornRadii
,
RealOpenMM
*
switchDeriviative
){
void
CpuGBVISoftcore
::
computeBornRadii
(
vector
<
RealVec
>&
atomCoordinates
,
vector
<
RealOpenMM
>&
bornRadii
,
RealOpenMM
*
switchDeriviative
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -412,8 +399,6 @@ if( atomI == 0 || atomI == 1 ){
...
@@ -412,8 +399,6 @@ if( atomI == 0 || atomI == 1 ){
}
}
return
0
;
}
}
#undef GBVISoftcoreDebug
#undef GBVISoftcoreDebug
...
@@ -715,12 +700,10 @@ RealOpenMM e3 = -partialChargeI2*partialCharges[atomJ]*Sgb( t )/deltaR[Reference
...
@@ -715,12 +700,10 @@ RealOpenMM e3 = -partialChargeI2*partialCharges[atomJ]*Sgb( t )/deltaR[Reference
@param partialCharges partial charges
@param partialCharges partial charges
@param forces forces
@param forces forces
@return 0;
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
CpuGBVISoftcore
::
computeBornForces
(
const
vector
<
RealOpenMM
>&
bornRadii
,
vector
<
RealVec
>&
atomCoordinates
,
void
CpuGBVISoftcore
::
computeBornForces
(
const
vector
<
RealOpenMM
>&
bornRadii
,
vector
<
RealVec
>&
atomCoordinates
,
const
RealOpenMM
*
partialCharges
,
vector
<
RealVec
>&
inputForces
){
const
RealOpenMM
*
partialCharges
,
vector
<
RealVec
>&
inputForces
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -1103,9 +1086,6 @@ if( atomI == 0 ){
...
@@ -1103,9 +1086,6 @@ if( atomI == 0 ){
delete
[]
forces
;
delete
[]
forces
;
delete
[]
block
;
delete
[]
block
;
return
0
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
...
plugins/freeEnergy/platforms/reference/src/gbsa/CpuGBVISoftcore.h
View file @
8086b201
...
@@ -85,11 +85,9 @@ class CpuGBVISoftcore : public CpuImplicitSolvent {
...
@@ -85,11 +85,9 @@ class CpuGBVISoftcore : public CpuImplicitSolvent {
@param ImplicitSolventParameters
@param ImplicitSolventParameters
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
setGBVISoftcoreParameters
(
GBVISoftcoreParameters
*
gbviParameters
);
void
setGBVISoftcoreParameters
(
GBVISoftcoreParameters
*
gbviParameters
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -111,11 +109,9 @@ class CpuGBVISoftcore : public CpuImplicitSolvent {
...
@@ -111,11 +109,9 @@ class CpuGBVISoftcore : public CpuImplicitSolvent {
@param bornRadii output array of Born radii
@param bornRadii output array of Born radii
@param switchDeriviative derivative of switch function
@param switchDeriviative derivative of switch function
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
computeBornRadii
(
std
::
vector
<
OpenMM
::
RealVec
>&
atomCoordinates
,
std
::
vector
<
RealOpenMM
>&
bornRadii
,
void
computeBornRadii
(
std
::
vector
<
OpenMM
::
RealVec
>&
atomCoordinates
,
std
::
vector
<
RealOpenMM
>&
bornRadii
,
RealOpenMM
*
switchDeriviative
=
NULL
);
RealOpenMM
*
switchDeriviative
=
NULL
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -222,11 +218,9 @@ class CpuGBVISoftcore : public CpuImplicitSolvent {
...
@@ -222,11 +218,9 @@ class CpuGBVISoftcore : public CpuImplicitSolvent {
@param partialCharges partial charges
@param partialCharges partial charges
@param forces output forces
@param forces output forces
@return SimTKOpenMMCommon::DefaultReturn;
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
computeBornForces
(
const
std
::
vector
<
RealOpenMM
>&
bornRadii
,
std
::
vector
<
OpenMM
::
RealVec
>&
atomCoordinates
,
void
computeBornForces
(
const
std
::
vector
<
RealOpenMM
>&
bornRadii
,
std
::
vector
<
OpenMM
::
RealVec
>&
atomCoordinates
,
const
RealOpenMM
*
partialCharges
,
std
::
vector
<
OpenMM
::
RealVec
>&
inputForces
);
const
RealOpenMM
*
partialCharges
,
std
::
vector
<
OpenMM
::
RealVec
>&
inputForces
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -295,11 +289,9 @@ class CpuGBVISoftcore : public CpuImplicitSolvent {
...
@@ -295,11 +289,9 @@ class CpuGBVISoftcore : public CpuImplicitSolvent {
@param outValue value of spline at x
@param outValue value of spline at x
@param outDerivative value of derivative of spline at x
@param outDerivative value of derivative of spline at x
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
quinticSpline
(
RealOpenMM
x
,
RealOpenMM
rl
,
RealOpenMM
ru
,
RealOpenMM
*
outValue
,
RealOpenMM
*
outDerivative
);
void
quinticSpline
(
RealOpenMM
x
,
RealOpenMM
rl
,
RealOpenMM
ru
,
RealOpenMM
*
outValue
,
RealOpenMM
*
outDerivative
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -313,11 +305,9 @@ class CpuGBVISoftcore : public CpuImplicitSolvent {
...
@@ -313,11 +305,9 @@ class CpuGBVISoftcore : public CpuImplicitSolvent {
@param bornRadius output Born radius
@param bornRadius output Born radius
@param switchDeriviative output switching function deriviative
@param switchDeriviative output switching function deriviative
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
computeBornRadiiUsingQuinticSpline
(
RealOpenMM
atomicRadius3
,
RealOpenMM
bornSum
,
void
computeBornRadiiUsingQuinticSpline
(
RealOpenMM
atomicRadius3
,
RealOpenMM
bornSum
,
GBVISoftcoreParameters
*
gbviParameters
,
GBVISoftcoreParameters
*
gbviParameters
,
RealOpenMM
&
bornRadius
,
RealOpenMM
*
switchDeriviative
);
RealOpenMM
&
bornRadius
,
RealOpenMM
*
switchDeriviative
);
...
...
plugins/freeEnergy/platforms/reference/src/gbsa/CpuObcSoftcore.cpp
View file @
8086b201
...
@@ -116,11 +116,9 @@ ObcSoftcoreParameters* CpuObcSoftcore::getObcSoftcoreParameters( void ) const {
...
@@ -116,11 +116,9 @@ ObcSoftcoreParameters* CpuObcSoftcore::getObcSoftcoreParameters( void ) const {
@param ObcSoftcoreParameters reference
@param ObcSoftcoreParameters reference
@return SimTKOpenMMCommon::DefaultReturn;
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
CpuObcSoftcore
::
setObcSoftcoreParameters
(
ObcSoftcoreParameters
*
obcSoftcoreParameters
){
void
CpuObcSoftcore
::
setObcSoftcoreParameters
(
ObcSoftcoreParameters
*
obcSoftcoreParameters
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -129,7 +127,6 @@ int CpuObcSoftcore::setObcSoftcoreParameters( ObcSoftcoreParameters* obcSoftcor
...
@@ -129,7 +127,6 @@ int CpuObcSoftcore::setObcSoftcoreParameters( ObcSoftcoreParameters* obcSoftcor
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
_obcSoftcoreParameters
=
obcSoftcoreParameters
;
_obcSoftcoreParameters
=
obcSoftcoreParameters
;
return
0
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -207,11 +204,9 @@ vector<RealOpenMM>& CpuObcSoftcore::getObcChainTemp( void ){
...
@@ -207,11 +204,9 @@ vector<RealOpenMM>& CpuObcSoftcore::getObcChainTemp( void ){
@param atomCoordinates atomic coordinates
@param atomCoordinates atomic coordinates
@param bornRadii output array of Born radii
@param bornRadii output array of Born radii
@return array of Born radii
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
CpuObcSoftcore
::
computeBornRadii
(
vector
<
RealVec
>&
atomCoordinates
,
RealOpenMM
*
bornRadii
){
void
CpuObcSoftcore
::
computeBornRadii
(
vector
<
RealVec
>&
atomCoordinates
,
RealOpenMM
*
bornRadii
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -333,9 +328,6 @@ if( logFile ){
...
@@ -333,9 +328,6 @@ if( logFile ){
(void) fclose( logFile );
(void) fclose( logFile );
}
}
#endif
#endif
return
0
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -348,11 +340,9 @@ if( logFile ){
...
@@ -348,11 +340,9 @@ if( logFile ){
@param energy energy (output): value is incremented from input value
@param energy energy (output): value is incremented from input value
@param forces forces: values are incremented from input values
@param forces forces: values are incremented from input values
@return 0
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
CpuObcSoftcore
::
computeAceNonPolarForce
(
const
ObcSoftcoreParameters
*
obcSoftcoreParameters
,
void
CpuObcSoftcore
::
computeAceNonPolarForce
(
const
ObcSoftcoreParameters
*
obcSoftcoreParameters
,
const
vector
<
RealOpenMM
>&
bornRadii
,
RealOpenMM
*
energy
,
const
vector
<
RealOpenMM
>&
bornRadii
,
RealOpenMM
*
energy
,
vector
<
RealOpenMM
>&
forces
)
const
{
vector
<
RealOpenMM
>&
forces
)
const
{
...
@@ -398,9 +388,6 @@ int CpuObcSoftcore::computeAceNonPolarForce( const ObcSoftcoreParameters* obcSof
...
@@ -398,9 +388,6 @@ int CpuObcSoftcore::computeAceNonPolarForce( const ObcSoftcoreParameters* obcSof
forces
[
atomI
]
+=
minusSix
*
saTerm
/
bornRadii
[
atomI
];
forces
[
atomI
]
+=
minusSix
*
saTerm
/
bornRadii
[
atomI
];
}
}
}
}
return
0
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -413,13 +400,11 @@ int CpuObcSoftcore::computeAceNonPolarForce( const ObcSoftcoreParameters* obcSof
...
@@ -413,13 +400,11 @@ int CpuObcSoftcore::computeAceNonPolarForce( const ObcSoftcoreParameters* obcSof
@param partialCharges partial charges
@param partialCharges partial charges
@param forces forces
@param forces forces
@return 0
The array bornRadii is also updated and the obcEnergy
The array bornRadii is also updated and the obcEnergy
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
CpuObcSoftcore
::
computeBornEnergyForces
(
vector
<
RealOpenMM
>&
bornRadii
,
vector
<
RealVec
>&
atomCoordinates
,
void
CpuObcSoftcore
::
computeBornEnergyForces
(
vector
<
RealOpenMM
>&
bornRadii
,
vector
<
RealVec
>&
atomCoordinates
,
const
RealOpenMM
*
partialCharges
,
vector
<
RealVec
>&
inputForces
){
const
RealOpenMM
*
partialCharges
,
vector
<
RealVec
>&
inputForces
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -720,9 +705,6 @@ int CpuObcSoftcore::computeBornEnergyForces( vector<RealOpenMM>& bornRadii, vect
...
@@ -720,9 +705,6 @@ int CpuObcSoftcore::computeBornEnergyForces( vector<RealOpenMM>& bornRadii, vect
bornRadii
=
bornRadiiTemp
;
bornRadii
=
bornRadiiTemp
;
obcChain
=
obcChainTemp
;
obcChain
=
obcChainTemp
;
free
(
(
char
*
)
block
);
free
(
(
char
*
)
block
);
free
(
(
char
*
)
forces
);
free
(
(
char
*
)
forces
);
return
0
;
}
}
plugins/freeEnergy/platforms/reference/src/gbsa/CpuObcSoftcore.h
View file @
8086b201
...
@@ -86,11 +86,9 @@ class CpuObcSoftcore : public CpuImplicitSolvent {
...
@@ -86,11 +86,9 @@ class CpuObcSoftcore : public CpuImplicitSolvent {
@param ImplicitSolventParameters
@param ImplicitSolventParameters
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
setObcSoftcoreParameters
(
ObcSoftcoreParameters
*
obcSoftcoreParameters
);
void
setObcSoftcoreParameters
(
ObcSoftcoreParameters
*
obcSoftcoreParameters
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -124,11 +122,9 @@ class CpuObcSoftcore : public CpuImplicitSolvent {
...
@@ -124,11 +122,9 @@ class CpuObcSoftcore : public CpuImplicitSolvent {
@param obcChain output array of OBC chain derivative factors; if NULL,
@param obcChain output array of OBC chain derivative factors; if NULL,
then ignored
then ignored
@return array of Born radii
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
computeBornRadii
(
std
::
vector
<
OpenMM
::
RealVec
>&
atomCoordinates
,
RealOpenMM
*
bornRadii
);
void
computeBornRadii
(
std
::
vector
<
OpenMM
::
RealVec
>&
atomCoordinates
,
RealOpenMM
*
bornRadii
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -140,11 +136,9 @@ class CpuObcSoftcore : public CpuImplicitSolvent {
...
@@ -140,11 +136,9 @@ class CpuObcSoftcore : public CpuImplicitSolvent {
@param energy energy (output): value is incremented from input value
@param energy energy (output): value is incremented from input value
@param forces forces: values are incremented from input values
@param forces forces: values are incremented from input values
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
computeAceNonPolarForce
(
const
ObcSoftcoreParameters
*
obcSoftcoreParameters
,
void
computeAceNonPolarForce
(
const
ObcSoftcoreParameters
*
obcSoftcoreParameters
,
const
std
::
vector
<
RealOpenMM
>&
bornRadii
,
RealOpenMM
*
energy
,
const
std
::
vector
<
RealOpenMM
>&
bornRadii
,
RealOpenMM
*
energy
,
std
::
vector
<
RealOpenMM
>&
forces
)
const
;
std
::
vector
<
RealOpenMM
>&
forces
)
const
;
...
@@ -157,11 +151,9 @@ class CpuObcSoftcore : public CpuImplicitSolvent {
...
@@ -157,11 +151,9 @@ class CpuObcSoftcore : public CpuImplicitSolvent {
@param partialCharges partial charges
@param partialCharges partial charges
@param forces forces
@param forces forces
@return force array
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
computeBornEnergyForces
(
std
::
vector
<
RealOpenMM
>&
bornRadii
,
std
::
vector
<
OpenMM
::
RealVec
>&
atomCoordinates
,
void
computeBornEnergyForces
(
std
::
vector
<
RealOpenMM
>&
bornRadii
,
std
::
vector
<
OpenMM
::
RealVec
>&
atomCoordinates
,
const
RealOpenMM
*
partialCharges
,
std
::
vector
<
OpenMM
::
RealVec
>&
forces
);
const
RealOpenMM
*
partialCharges
,
std
::
vector
<
OpenMM
::
RealVec
>&
forces
);
};
};
...
...
plugins/freeEnergy/platforms/reference/src/gbsa/GBVISoftcoreParameters.cpp
View file @
8086b201
...
@@ -187,11 +187,10 @@ RealOpenMM GBVISoftcoreParameters::getQuinticLowerLimitFactor( void ) const {
...
@@ -187,11 +187,10 @@ RealOpenMM GBVISoftcoreParameters::getQuinticLowerLimitFactor( void ) const {
Set the quintic spline lower limit factor
Set the quintic spline lower limit factor
@param quintic spline lower limit factor
@param quintic spline lower limit factor
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
GBVISoftcoreParameters
::
setQuinticLowerLimitFactor
(
RealOpenMM
quinticLowerLimitFactor
){
void
GBVISoftcoreParameters
::
setQuinticLowerLimitFactor
(
RealOpenMM
quinticLowerLimitFactor
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -200,7 +199,6 @@ int GBVISoftcoreParameters::setQuinticLowerLimitFactor( RealOpenMM quinticLowerL
...
@@ -200,7 +199,6 @@ int GBVISoftcoreParameters::setQuinticLowerLimitFactor( RealOpenMM quinticLowerL
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
_quinticLowerLimitFactor
=
quinticLowerLimitFactor
;
_quinticLowerLimitFactor
=
quinticLowerLimitFactor
;
return
0
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -228,11 +226,9 @@ RealOpenMM GBVISoftcoreParameters::getQuinticUpperBornRadiusLimit( void ) const
...
@@ -228,11 +226,9 @@ RealOpenMM GBVISoftcoreParameters::getQuinticUpperBornRadiusLimit( void ) const
@param quintic spline upper limit
@param quintic spline upper limit
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
GBVISoftcoreParameters
::
setQuinticUpperBornRadiusLimit
(
RealOpenMM
quinticUpperBornRadiusLimit
){
void
GBVISoftcoreParameters
::
setQuinticUpperBornRadiusLimit
(
RealOpenMM
quinticUpperBornRadiusLimit
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -242,7 +238,6 @@ int GBVISoftcoreParameters::setQuinticUpperBornRadiusLimit( RealOpenMM quinticUp
...
@@ -242,7 +238,6 @@ int GBVISoftcoreParameters::setQuinticUpperBornRadiusLimit( RealOpenMM quinticUp
_quinticUpperBornRadiusLimit
=
quinticUpperBornRadiusLimit
;
_quinticUpperBornRadiusLimit
=
quinticUpperBornRadiusLimit
;
_quinticUpperSplineLimit
=
POW
(
_quinticUpperBornRadiusLimit
,
static_cast
<
RealOpenMM
>
(
-
3.0
)
);
_quinticUpperSplineLimit
=
POW
(
_quinticUpperBornRadiusLimit
,
static_cast
<
RealOpenMM
>
(
-
3.0
)
);
return
0
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -291,11 +286,9 @@ RealOpenMM* GBVISoftcoreParameters::getAtomicRadii( void ) const {
...
@@ -291,11 +286,9 @@ RealOpenMM* GBVISoftcoreParameters::getAtomicRadii( void ) const {
@param atomicRadii array of atomic radii
@param atomicRadii array of atomic radii
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
GBVISoftcoreParameters
::
setAtomicRadii
(
RealOpenMM
*
atomicRadii
){
void
GBVISoftcoreParameters
::
setAtomicRadii
(
RealOpenMM
*
atomicRadii
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -303,7 +296,7 @@ int GBVISoftcoreParameters::setAtomicRadii( RealOpenMM* atomicRadii ){
...
@@ -303,7 +296,7 @@ int GBVISoftcoreParameters::setAtomicRadii( RealOpenMM* atomicRadii ){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
return
ImplicitSolventParameters
::
setAtomicRadii
(
atomicRadii
);
ImplicitSolventParameters
::
setAtomicRadii
(
atomicRadii
);
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -312,11 +305,9 @@ int GBVISoftcoreParameters::setAtomicRadii( RealOpenMM* atomicRadii ){
...
@@ -312,11 +305,9 @@ int GBVISoftcoreParameters::setAtomicRadii( RealOpenMM* atomicRadii ){
@param atomicRadii vector of atomic radii
@param atomicRadii vector of atomic radii
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
GBVISoftcoreParameters
::
setAtomicRadii
(
const
RealOpenMMVector
&
atomicRadii
){
void
GBVISoftcoreParameters
::
setAtomicRadii
(
const
RealOpenMMVector
&
atomicRadii
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -324,7 +315,7 @@ int GBVISoftcoreParameters::setAtomicRadii( const RealOpenMMVector& atomicRadii
...
@@ -324,7 +315,7 @@ int GBVISoftcoreParameters::setAtomicRadii( const RealOpenMMVector& atomicRadii
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
return
ImplicitSolventParameters
::
setAtomicRadii
(
atomicRadii
);
ImplicitSolventParameters
::
setAtomicRadii
(
atomicRadii
);
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -360,11 +351,9 @@ const RealOpenMM* GBVISoftcoreParameters::getScaledRadii( void ) const {
...
@@ -360,11 +351,9 @@ const RealOpenMM* GBVISoftcoreParameters::getScaledRadii( void ) const {
@param ownScaledRadii flag indicating whether scale factors
@param ownScaledRadii flag indicating whether scale factors
array should be deleted
array should be deleted
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
GBVISoftcoreParameters
::
setOwnScaledRadii
(
int
ownScaledRadii
){
void
GBVISoftcoreParameters
::
setOwnScaledRadii
(
int
ownScaledRadii
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -373,8 +362,6 @@ int GBVISoftcoreParameters::setOwnScaledRadii( int ownScaledRadii ){
...
@@ -373,8 +362,6 @@ int GBVISoftcoreParameters::setOwnScaledRadii( int ownScaledRadii ){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
_ownScaledRadii
=
ownScaledRadii
;
_ownScaledRadii
=
ownScaledRadii
;
return
0
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -383,11 +370,9 @@ int GBVISoftcoreParameters::setOwnScaledRadii( int ownScaledRadii ){
...
@@ -383,11 +370,9 @@ int GBVISoftcoreParameters::setOwnScaledRadii( int ownScaledRadii ){
@param scaledRadii scaledRadii
@param scaledRadii scaledRadii
@return SimTKOpenMMCommon::DefaultReturn always
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
GBVISoftcoreParameters
::
setScaledRadii
(
RealOpenMM
*
scaledRadii
){
void
GBVISoftcoreParameters
::
setScaledRadii
(
RealOpenMM
*
scaledRadii
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -401,9 +386,6 @@ int GBVISoftcoreParameters::setScaledRadii( RealOpenMM* scaledRadii ){
...
@@ -401,9 +386,6 @@ int GBVISoftcoreParameters::setScaledRadii( RealOpenMM* scaledRadii ){
}
}
_scaledRadii
=
scaledRadii
;
_scaledRadii
=
scaledRadii
;
return
0
;
}
}
#if RealOpenMMType == 0
#if RealOpenMMType == 0
...
@@ -414,11 +396,9 @@ int GBVISoftcoreParameters::setScaledRadii( RealOpenMM* scaledRadii ){
...
@@ -414,11 +396,9 @@ int GBVISoftcoreParameters::setScaledRadii( RealOpenMM* scaledRadii ){
@param scaledRadii scaledRadii
@param scaledRadii scaledRadii
@return SimTKOpenMMCommon::DefaultReturn always
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
GBVISoftcoreParameters
::
setScaledRadii
(
float
*
scaledRadii
){
void
GBVISoftcoreParameters
::
setScaledRadii
(
float
*
scaledRadii
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -433,9 +413,6 @@ int GBVISoftcoreParameters::setScaledRadii( float* scaledRadii ){
...
@@ -433,9 +413,6 @@ int GBVISoftcoreParameters::setScaledRadii( float* scaledRadii ){
for
(
int
ii
=
0
;
ii
<
getNumberOfAtoms
();
ii
++
){
for
(
int
ii
=
0
;
ii
<
getNumberOfAtoms
();
ii
++
){
_scaledRadii
[
ii
]
=
(
RealOpenMM
)
scaledRadii
[
ii
];
_scaledRadii
[
ii
]
=
(
RealOpenMM
)
scaledRadii
[
ii
];
}
}
return
0
;
}
}
#endif
#endif
...
@@ -446,11 +423,9 @@ int GBVISoftcoreParameters::setScaledRadii( float* scaledRadii ){
...
@@ -446,11 +423,9 @@ int GBVISoftcoreParameters::setScaledRadii( float* scaledRadii ){
@param scaledRadii scaledRadii
@param scaledRadii scaledRadii
@return SimTKOpenMMCommon::DefaultReturn always
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
GBVISoftcoreParameters
::
setScaledRadii
(
const
RealOpenMMVector
&
scaledRadii
){
void
GBVISoftcoreParameters
::
setScaledRadii
(
const
RealOpenMMVector
&
scaledRadii
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -466,8 +441,6 @@ int GBVISoftcoreParameters::setScaledRadii( const RealOpenMMVector& scaledRadii
...
@@ -466,8 +441,6 @@ int GBVISoftcoreParameters::setScaledRadii( const RealOpenMMVector& scaledRadii
for
(
int
ii
=
0
;
ii
<
(
int
)
scaledRadii
.
size
();
ii
++
){
for
(
int
ii
=
0
;
ii
<
(
int
)
scaledRadii
.
size
();
ii
++
){
_scaledRadii
[
ii
]
=
scaledRadii
[
ii
];
_scaledRadii
[
ii
]
=
scaledRadii
[
ii
];
}
}
return
0
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -503,11 +476,9 @@ RealOpenMM* GBVISoftcoreParameters::getGammaParameters( void ) const {
...
@@ -503,11 +476,9 @@ RealOpenMM* GBVISoftcoreParameters::getGammaParameters( void ) const {
@param ownGammaParameters flag indicating whether gamma parameter
@param ownGammaParameters flag indicating whether gamma parameter
array should be deleted
array should be deleted
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
GBVISoftcoreParameters
::
setOwnGammaParameters
(
int
ownGammaParameters
){
void
GBVISoftcoreParameters
::
setOwnGammaParameters
(
int
ownGammaParameters
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -516,8 +487,6 @@ int GBVISoftcoreParameters::setOwnGammaParameters( int ownGammaParameters ){
...
@@ -516,8 +487,6 @@ int GBVISoftcoreParameters::setOwnGammaParameters( int ownGammaParameters ){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
_ownGammaParameters
=
ownGammaParameters
;
_ownGammaParameters
=
ownGammaParameters
;
return
0
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -526,11 +495,9 @@ int GBVISoftcoreParameters::setOwnGammaParameters( int ownGammaParameters ){
...
@@ -526,11 +495,9 @@ int GBVISoftcoreParameters::setOwnGammaParameters( int ownGammaParameters ){
@param gammas gamma parameters
@param gammas gamma parameters
@return SimTKOpenMMCommon::DefaultReturn always
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
GBVISoftcoreParameters
::
setGammaParameters
(
RealOpenMM
*
gammas
){
void
GBVISoftcoreParameters
::
setGammaParameters
(
RealOpenMM
*
gammas
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -544,9 +511,6 @@ int GBVISoftcoreParameters::setGammaParameters( RealOpenMM* gammas ){
...
@@ -544,9 +511,6 @@ int GBVISoftcoreParameters::setGammaParameters( RealOpenMM* gammas ){
}
}
_gammaParameters
=
gammas
;
_gammaParameters
=
gammas
;
return
0
;
}
}
#if RealOpenMMType == 0
#if RealOpenMMType == 0
...
@@ -557,11 +521,9 @@ int GBVISoftcoreParameters::setGammaParameters( RealOpenMM* gammas ){
...
@@ -557,11 +521,9 @@ int GBVISoftcoreParameters::setGammaParameters( RealOpenMM* gammas ){
@param gammas gammas
@param gammas gammas
@return SimTKOpenMMCommon::DefaultReturn always
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
GBVISoftcoreParameters
::
setGammaParameters
(
float
*
gammas
){
void
GBVISoftcoreParameters
::
setGammaParameters
(
float
*
gammas
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -576,9 +538,6 @@ int GBVISoftcoreParameters::setGammaParameters( float* gammas ){
...
@@ -576,9 +538,6 @@ int GBVISoftcoreParameters::setGammaParameters( float* gammas ){
for
(
int
ii
=
0
;
ii
<
getNumberOfAtoms
();
ii
++
){
for
(
int
ii
=
0
;
ii
<
getNumberOfAtoms
();
ii
++
){
_gammaParameters
[
ii
]
=
(
RealOpenMM
)
gammas
[
ii
];
_gammaParameters
[
ii
]
=
(
RealOpenMM
)
gammas
[
ii
];
}
}
return
0
;
}
}
#endif
#endif
...
@@ -589,11 +548,9 @@ int GBVISoftcoreParameters::setGammaParameters( float* gammas ){
...
@@ -589,11 +548,9 @@ int GBVISoftcoreParameters::setGammaParameters( float* gammas ){
@param gammas gammas
@param gammas gammas
@return SimTKOpenMMCommon::DefaultReturn always
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
GBVISoftcoreParameters
::
setGammaParameters
(
const
RealOpenMMVector
&
gammas
){
void
GBVISoftcoreParameters
::
setGammaParameters
(
const
RealOpenMMVector
&
gammas
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -610,8 +567,6 @@ int GBVISoftcoreParameters::setGammaParameters( const RealOpenMMVector& gammas )
...
@@ -610,8 +567,6 @@ int GBVISoftcoreParameters::setGammaParameters( const RealOpenMMVector& gammas )
for
(
int
ii
=
0
;
ii
<
(
int
)
gammas
.
size
();
ii
++
){
for
(
int
ii
=
0
;
ii
<
(
int
)
gammas
.
size
();
ii
++
){
_gammaParameters
[
ii
]
=
gammas
[
ii
];
_gammaParameters
[
ii
]
=
gammas
[
ii
];
}
}
return
0
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -647,11 +602,9 @@ RealOpenMM* GBVISoftcoreParameters::getBornRadiusScaleFactors( void ) const {
...
@@ -647,11 +602,9 @@ RealOpenMM* GBVISoftcoreParameters::getBornRadiusScaleFactors( void ) const {
@param ownBornRadiusScaleFactors flag indicating whether Born radius scale factors
@param ownBornRadiusScaleFactors flag indicating whether Born radius scale factors
array should be deleted
array should be deleted
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
GBVISoftcoreParameters
::
setOwnBornRadiusScaleFactors
(
int
ownBornRadiusScaleFactorsParameters
){
void
GBVISoftcoreParameters
::
setOwnBornRadiusScaleFactors
(
int
ownBornRadiusScaleFactorsParameters
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -660,8 +613,6 @@ int GBVISoftcoreParameters::setOwnBornRadiusScaleFactors( int ownBornRadiusScale
...
@@ -660,8 +613,6 @@ int GBVISoftcoreParameters::setOwnBornRadiusScaleFactors( int ownBornRadiusScale
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
_ownBornRadiusScaleFactors
=
ownBornRadiusScaleFactorsParameters
;
_ownBornRadiusScaleFactors
=
ownBornRadiusScaleFactorsParameters
;
return
0
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -670,11 +621,9 @@ int GBVISoftcoreParameters::setOwnBornRadiusScaleFactors( int ownBornRadiusScale
...
@@ -670,11 +621,9 @@ int GBVISoftcoreParameters::setOwnBornRadiusScaleFactors( int ownBornRadiusScale
@param bornRadiusScaleFactors Born radius scale factors
@param bornRadiusScaleFactors Born radius scale factors
@return SimTKOpenMMCommon::DefaultReturn always
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
GBVISoftcoreParameters
::
setBornRadiusScaleFactors
(
RealOpenMM
*
bornRadiusScaleFactors
){
void
GBVISoftcoreParameters
::
setBornRadiusScaleFactors
(
RealOpenMM
*
bornRadiusScaleFactors
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -688,9 +637,6 @@ int GBVISoftcoreParameters::setBornRadiusScaleFactors( RealOpenMM* bornRadiusSca
...
@@ -688,9 +637,6 @@ int GBVISoftcoreParameters::setBornRadiusScaleFactors( RealOpenMM* bornRadiusSca
}
}
_bornRadiusScaleFactors
=
bornRadiusScaleFactors
;
_bornRadiusScaleFactors
=
bornRadiusScaleFactors
;
return
0
;
}
}
#if RealOpenMMType == 0
#if RealOpenMMType == 0
...
@@ -701,11 +647,9 @@ int GBVISoftcoreParameters::setBornRadiusScaleFactors( RealOpenMM* bornRadiusSca
...
@@ -701,11 +647,9 @@ int GBVISoftcoreParameters::setBornRadiusScaleFactors( RealOpenMM* bornRadiusSca
@param bornRadiusScaleFactorss bornRadiusScaleFactorss
@param bornRadiusScaleFactorss bornRadiusScaleFactorss
@return SimTKOpenMMCommon::DefaultReturn always
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
GBVISoftcoreParameters
::
setBornRadiusScaleFactors
(
float
*
bornRadiusScaleFactorss
){
void
GBVISoftcoreParameters
::
setBornRadiusScaleFactors
(
float
*
bornRadiusScaleFactorss
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -733,11 +677,9 @@ int GBVISoftcoreParameters::setBornRadiusScaleFactors( float* bornRadiusScaleFac
...
@@ -733,11 +677,9 @@ int GBVISoftcoreParameters::setBornRadiusScaleFactors( float* bornRadiusScaleFac
@param bornRadiusScaleFactors bornRadiusScaleFactors
@param bornRadiusScaleFactors bornRadiusScaleFactors
@return SimTKOpenMMCommon::DefaultReturn always
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
GBVISoftcoreParameters
::
setBornRadiusScaleFactors
(
const
RealOpenMMVector
&
bornRadiusScaleFactors
){
void
GBVISoftcoreParameters
::
setBornRadiusScaleFactors
(
const
RealOpenMMVector
&
bornRadiusScaleFactors
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -754,8 +696,6 @@ int GBVISoftcoreParameters::setBornRadiusScaleFactors( const RealOpenMMVector& b
...
@@ -754,8 +696,6 @@ int GBVISoftcoreParameters::setBornRadiusScaleFactors( const RealOpenMMVector& b
for
(
int
ii
=
0
;
ii
<
(
int
)
bornRadiusScaleFactors
.
size
();
ii
++
){
for
(
int
ii
=
0
;
ii
<
(
int
)
bornRadiusScaleFactors
.
size
();
ii
++
){
_bornRadiusScaleFactors
[
ii
]
=
bornRadiusScaleFactors
[
ii
];
_bornRadiusScaleFactors
[
ii
]
=
bornRadiusScaleFactors
[
ii
];
}
}
return
0
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -791,15 +731,12 @@ std::string GBVISoftcoreParameters::getStateString( const char* title ) const {
...
@@ -791,15 +731,12 @@ std::string GBVISoftcoreParameters::getStateString( const char* title ) const {
@param distance the cutoff distance
@param distance the cutoff distance
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
GBVISoftcoreParameters
::
setUseCutoff
(
RealOpenMM
distance
)
{
void
GBVISoftcoreParameters
::
setUseCutoff
(
RealOpenMM
distance
)
{
cutoff
=
true
;
cutoff
=
true
;
cutoffDistance
=
distance
;
cutoffDistance
=
distance
;
return
0
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -830,11 +767,9 @@ RealOpenMM GBVISoftcoreParameters::getCutoffDistance() {
...
@@ -830,11 +767,9 @@ RealOpenMM GBVISoftcoreParameters::getCutoffDistance() {
@param boxSize the X, Y, and Z widths of the periodic box
@param boxSize the X, Y, and Z widths of the periodic box
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
GBVISoftcoreParameters
::
setPeriodic
(
RealOpenMM
*
boxSize
)
{
void
GBVISoftcoreParameters
::
setPeriodic
(
RealOpenMM
*
boxSize
)
{
assert
(
cutoff
);
assert
(
cutoff
);
assert
(
boxSize
[
0
]
>=
2.0
*
cutoffDistance
);
assert
(
boxSize
[
0
]
>=
2.0
*
cutoffDistance
);
...
@@ -844,7 +779,6 @@ int GBVISoftcoreParameters::setPeriodic( RealOpenMM* boxSize ) {
...
@@ -844,7 +779,6 @@ int GBVISoftcoreParameters::setPeriodic( RealOpenMM* boxSize ) {
periodicBoxSize
[
0
]
=
boxSize
[
0
];
periodicBoxSize
[
0
]
=
boxSize
[
0
];
periodicBoxSize
[
1
]
=
boxSize
[
1
];
periodicBoxSize
[
1
]
=
boxSize
[
1
];
periodicBoxSize
[
2
]
=
boxSize
[
2
];
periodicBoxSize
[
2
]
=
boxSize
[
2
];
return
0
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
...
plugins/freeEnergy/platforms/reference/src/gbsa/GBVISoftcoreParameters.h
View file @
8086b201
...
@@ -119,11 +119,11 @@ class GBVISoftcoreParameters : public ImplicitSolventParameters {
...
@@ -119,11 +119,11 @@ class GBVISoftcoreParameters : public ImplicitSolventParameters {
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
setScaledRadii
(
RealOpenMM
*
scaledRadii
);
void
setScaledRadii
(
RealOpenMM
*
scaledRadii
);
#if RealOpenMMType == 0
#if RealOpenMMType == 0
int
setScaledRadii
(
float
*
scaledRadii
);
void
setScaledRadii
(
float
*
scaledRadii
);
#endif
#endif
int
setScaledRadii
(
const
RealOpenMMVector
&
scaledRadii
);
void
setScaledRadii
(
const
RealOpenMMVector
&
scaledRadii
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -131,12 +131,10 @@ class GBVISoftcoreParameters : public ImplicitSolventParameters {
...
@@ -131,12 +131,10 @@ class GBVISoftcoreParameters : public ImplicitSolventParameters {
@param ownScaledRadiusFactors flag indicating whether scaled radii
@param ownScaledRadiusFactors flag indicating whether scaled radii
array should be deleted
array should be deleted
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
setOwnScaledRadii
(
int
ownScaledRadii
);
void
setOwnScaledRadii
(
int
ownScaledRadii
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -154,11 +152,9 @@ class GBVISoftcoreParameters : public ImplicitSolventParameters {
...
@@ -154,11 +152,9 @@ class GBVISoftcoreParameters : public ImplicitSolventParameters {
@param atomicRadii array of atomic radii
@param atomicRadii array of atomic radii
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
setAtomicRadii
(
RealOpenMM
*
atomicRadii
);
void
setAtomicRadii
(
RealOpenMM
*
atomicRadii
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -166,11 +162,9 @@ class GBVISoftcoreParameters : public ImplicitSolventParameters {
...
@@ -166,11 +162,9 @@ class GBVISoftcoreParameters : public ImplicitSolventParameters {
@param atomicRadii vector of atomic radii
@param atomicRadii vector of atomic radii
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
setAtomicRadii
(
const
RealOpenMMVector
&
atomicRadii
);
void
setAtomicRadii
(
const
RealOpenMMVector
&
atomicRadii
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -178,12 +172,10 @@ class GBVISoftcoreParameters : public ImplicitSolventParameters {
...
@@ -178,12 +172,10 @@ class GBVISoftcoreParameters : public ImplicitSolventParameters {
@param ownGammaParameters flag indicating whether gamma parameter
@param ownGammaParameters flag indicating whether gamma parameter
array should be deleted
array should be deleted
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
setOwnGammaParameters
(
int
ownGammaParameters
);
void
setOwnGammaParameters
(
int
ownGammaParameters
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -201,11 +193,9 @@ class GBVISoftcoreParameters : public ImplicitSolventParameters {
...
@@ -201,11 +193,9 @@ class GBVISoftcoreParameters : public ImplicitSolventParameters {
@param gammaParameters array of gamma parameters
@param gammaParameters array of gamma parameters
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
setGammaParameters
(
RealOpenMM
*
gammaParameters
);
void
setGammaParameters
(
RealOpenMM
*
gammaParameters
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -213,11 +203,9 @@ class GBVISoftcoreParameters : public ImplicitSolventParameters {
...
@@ -213,11 +203,9 @@ class GBVISoftcoreParameters : public ImplicitSolventParameters {
@param gammaParameters array of gamma parameters
@param gammaParameters array of gamma parameters
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
setGammaParameters
(
const
RealOpenMMVector
&
gammaParameters
);
void
setGammaParameters
(
const
RealOpenMMVector
&
gammaParameters
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -225,12 +213,10 @@ class GBVISoftcoreParameters : public ImplicitSolventParameters {
...
@@ -225,12 +213,10 @@ class GBVISoftcoreParameters : public ImplicitSolventParameters {
@param ownBornRadiusScaleFactors flag indicating whether bornRadiusScaleFactor parameter
@param ownBornRadiusScaleFactors flag indicating whether bornRadiusScaleFactor parameter
array should be deleted
array should be deleted
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
setOwnBornRadiusScaleFactors
(
int
ownBornRadiusScaleFactors
);
void
setOwnBornRadiusScaleFactors
(
int
ownBornRadiusScaleFactors
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -248,11 +234,9 @@ class GBVISoftcoreParameters : public ImplicitSolventParameters {
...
@@ -248,11 +234,9 @@ class GBVISoftcoreParameters : public ImplicitSolventParameters {
@param bornRadiusScaleFactors array of bornRadiusScaleFactor parameters
@param bornRadiusScaleFactors array of bornRadiusScaleFactor parameters
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
setBornRadiusScaleFactors
(
RealOpenMM
*
bornRadiusScaleFactors
);
void
setBornRadiusScaleFactors
(
RealOpenMM
*
bornRadiusScaleFactors
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -260,11 +244,9 @@ class GBVISoftcoreParameters : public ImplicitSolventParameters {
...
@@ -260,11 +244,9 @@ class GBVISoftcoreParameters : public ImplicitSolventParameters {
@param bornRadiusScaleFactors array of bornRadiusScaleFactor parameters
@param bornRadiusScaleFactors array of bornRadiusScaleFactor parameters
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
setBornRadiusScaleFactors
(
const
RealOpenMMVector
&
bornRadiusScaleFactors
);
void
setBornRadiusScaleFactors
(
const
RealOpenMMVector
&
bornRadiusScaleFactors
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -284,11 +266,9 @@ class GBVISoftcoreParameters : public ImplicitSolventParameters {
...
@@ -284,11 +266,9 @@ class GBVISoftcoreParameters : public ImplicitSolventParameters {
@param distance the cutoff distance
@param distance the cutoff distance
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
setUseCutoff
(
RealOpenMM
distance
);
void
setUseCutoff
(
RealOpenMM
distance
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -314,11 +294,9 @@ class GBVISoftcoreParameters : public ImplicitSolventParameters {
...
@@ -314,11 +294,9 @@ class GBVISoftcoreParameters : public ImplicitSolventParameters {
@param boxSize the X, Y, and Z widths of the periodic box
@param boxSize the X, Y, and Z widths of the periodic box
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
setPeriodic
(
RealOpenMM
*
boxSize
);
void
setPeriodic
(
RealOpenMM
*
boxSize
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -350,7 +328,7 @@ class GBVISoftcoreParameters : public ImplicitSolventParameters {
...
@@ -350,7 +328,7 @@ class GBVISoftcoreParameters : public ImplicitSolventParameters {
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
setQuinticLowerLimitFactor
(
RealOpenMM
quinticLowerLimitFactor
);
void
setQuinticLowerLimitFactor
(
RealOpenMM
quinticLowerLimitFactor
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -367,7 +345,7 @@ class GBVISoftcoreParameters : public ImplicitSolventParameters {
...
@@ -367,7 +345,7 @@ class GBVISoftcoreParameters : public ImplicitSolventParameters {
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
setQuinticUpperBornRadiusLimit
(
RealOpenMM
quinticUpperBornRadiusLimit
);
void
setQuinticUpperBornRadiusLimit
(
RealOpenMM
quinticUpperBornRadiusLimit
);
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
...
plugins/freeEnergy/platforms/reference/src/gbsa/ObcSoftcoreParameters.cpp
View file @
8086b201
...
@@ -196,11 +196,9 @@ ObcSoftcoreParameters::ObcType ObcSoftcoreParameters::getObcType( void ) const {
...
@@ -196,11 +196,9 @@ ObcSoftcoreParameters::ObcType ObcSoftcoreParameters::getObcType( void ) const {
@param obcType OBC type (ObcTypeI or ObcTypeII -- Eq. 7 or 8)
@param obcType OBC type (ObcTypeI or ObcTypeII -- Eq. 7 or 8)
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ObcSoftcoreParameters
::
setObcTypeParameters
(
ObcSoftcoreParameters
::
ObcType
obcType
){
void
ObcSoftcoreParameters
::
setObcTypeParameters
(
ObcSoftcoreParameters
::
ObcType
obcType
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -218,8 +216,6 @@ int ObcSoftcoreParameters::setObcTypeParameters( ObcSoftcoreParameters::ObcType
...
@@ -218,8 +216,6 @@ int ObcSoftcoreParameters::setObcTypeParameters( ObcSoftcoreParameters::ObcType
_gammaObc
=
4.85
f
;
_gammaObc
=
4.85
f
;
}
}
_obcType
=
obcType
;
_obcType
=
obcType
;
return
0
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -327,11 +323,9 @@ RealOpenMM* ObcSoftcoreParameters::getAtomicRadii( void ) const {
...
@@ -327,11 +323,9 @@ RealOpenMM* ObcSoftcoreParameters::getAtomicRadii( void ) const {
@param atomicRadii array of atomic radii
@param atomicRadii array of atomic radii
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ObcSoftcoreParameters
::
setAtomicRadii
(
RealOpenMM
*
atomicRadii
){
void
ObcSoftcoreParameters
::
setAtomicRadii
(
RealOpenMM
*
atomicRadii
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -339,7 +333,7 @@ int ObcSoftcoreParameters::setAtomicRadii( RealOpenMM* atomicRadii ){
...
@@ -339,7 +333,7 @@ int ObcSoftcoreParameters::setAtomicRadii( RealOpenMM* atomicRadii ){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
return
ImplicitSolventParameters
::
setAtomicRadii
(
atomicRadii
);
ImplicitSolventParameters
::
setAtomicRadii
(
atomicRadii
);
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -348,11 +342,9 @@ int ObcSoftcoreParameters::setAtomicRadii( RealOpenMM* atomicRadii ){
...
@@ -348,11 +342,9 @@ int ObcSoftcoreParameters::setAtomicRadii( RealOpenMM* atomicRadii ){
@param atomicRadii vector of atomic radii
@param atomicRadii vector of atomic radii
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ObcSoftcoreParameters
::
setAtomicRadii
(
const
RealOpenMMVector
&
atomicRadii
){
void
ObcSoftcoreParameters
::
setAtomicRadii
(
const
RealOpenMMVector
&
atomicRadii
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -360,7 +352,7 @@ int ObcSoftcoreParameters::setAtomicRadii( const RealOpenMMVector& atomicRadii )
...
@@ -360,7 +352,7 @@ int ObcSoftcoreParameters::setAtomicRadii( const RealOpenMMVector& atomicRadii )
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
return
ImplicitSolventParameters
::
setAtomicRadii
(
atomicRadii
);
ImplicitSolventParameters
::
setAtomicRadii
(
atomicRadii
);
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -396,11 +388,9 @@ const RealOpenMM* ObcSoftcoreParameters::getScaledRadiusFactors( void ) const {
...
@@ -396,11 +388,9 @@ const RealOpenMM* ObcSoftcoreParameters::getScaledRadiusFactors( void ) const {
@param ownScaledRadiusFactors flag indicating whether scale factors
@param ownScaledRadiusFactors flag indicating whether scale factors
array should be deleted
array should be deleted
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ObcSoftcoreParameters
::
setOwnScaleFactors
(
int
ownScaledRadiusFactors
){
void
ObcSoftcoreParameters
::
setOwnScaleFactors
(
int
ownScaledRadiusFactors
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -409,8 +399,6 @@ int ObcSoftcoreParameters::setOwnScaleFactors( int ownScaledRadiusFactors ){
...
@@ -409,8 +399,6 @@ int ObcSoftcoreParameters::setOwnScaleFactors( int ownScaledRadiusFactors ){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
_ownScaledRadiusFactors
=
ownScaledRadiusFactors
;
_ownScaledRadiusFactors
=
ownScaledRadiusFactors
;
return
0
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -419,11 +407,9 @@ int ObcSoftcoreParameters::setOwnScaleFactors( int ownScaledRadiusFactors ){
...
@@ -419,11 +407,9 @@ int ObcSoftcoreParameters::setOwnScaleFactors( int ownScaledRadiusFactors ){
@param scaledRadiusFactors scaledRadiusFactors
@param scaledRadiusFactors scaledRadiusFactors
@return SimTKOpenMMCommon::DefaultReturn always
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ObcSoftcoreParameters
::
setScaledRadiusFactors
(
RealOpenMM
*
scaledRadiusFactors
){
void
ObcSoftcoreParameters
::
setScaledRadiusFactors
(
RealOpenMM
*
scaledRadiusFactors
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -437,9 +423,6 @@ int ObcSoftcoreParameters::setScaledRadiusFactors( RealOpenMM* scaledRadiusFacto
...
@@ -437,9 +423,6 @@ int ObcSoftcoreParameters::setScaledRadiusFactors( RealOpenMM* scaledRadiusFacto
}
}
_scaledRadiusFactors
=
scaledRadiusFactors
;
_scaledRadiusFactors
=
scaledRadiusFactors
;
return
0
;
}
}
#if RealOpenMMType == 0
#if RealOpenMMType == 0
...
@@ -450,11 +433,9 @@ int ObcSoftcoreParameters::setScaledRadiusFactors( RealOpenMM* scaledRadiusFacto
...
@@ -450,11 +433,9 @@ int ObcSoftcoreParameters::setScaledRadiusFactors( RealOpenMM* scaledRadiusFacto
@param scaledRadiusFactors scaledRadiusFactors
@param scaledRadiusFactors scaledRadiusFactors
@return SimTKOpenMMCommon::DefaultReturn always
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ObcSoftcoreParameters
::
setScaledRadiusFactors
(
float
*
scaledRadiusFactors
){
void
ObcSoftcoreParameters
::
setScaledRadiusFactors
(
float
*
scaledRadiusFactors
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -469,9 +450,6 @@ int ObcSoftcoreParameters::setScaledRadiusFactors( float* scaledRadiusFactors ){
...
@@ -469,9 +450,6 @@ int ObcSoftcoreParameters::setScaledRadiusFactors( float* scaledRadiusFactors ){
for
(
int
ii
=
0
;
ii
<
getNumberOfAtoms
();
ii
++
){
for
(
int
ii
=
0
;
ii
<
getNumberOfAtoms
();
ii
++
){
_scaledRadiusFactors
[
ii
]
=
(
RealOpenMM
)
scaledRadiusFactors
[
ii
];
_scaledRadiusFactors
[
ii
]
=
(
RealOpenMM
)
scaledRadiusFactors
[
ii
];
}
}
return
0
;
}
}
#endif
#endif
...
@@ -482,11 +460,9 @@ int ObcSoftcoreParameters::setScaledRadiusFactors( float* scaledRadiusFactors ){
...
@@ -482,11 +460,9 @@ int ObcSoftcoreParameters::setScaledRadiusFactors( float* scaledRadiusFactors ){
@param scaledRadiusFactors scaledRadiusFactors
@param scaledRadiusFactors scaledRadiusFactors
@return SimTKOpenMMCommon::DefaultReturn always
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ObcSoftcoreParameters
::
setScaledRadiusFactors
(
const
RealOpenMMVector
&
scaledRadiusFactors
){
void
ObcSoftcoreParameters
::
setScaledRadiusFactors
(
const
RealOpenMMVector
&
scaledRadiusFactors
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -502,8 +478,6 @@ int ObcSoftcoreParameters::setScaledRadiusFactors( const RealOpenMMVector& scale
...
@@ -502,8 +478,6 @@ int ObcSoftcoreParameters::setScaledRadiusFactors( const RealOpenMMVector& scale
for
(
int
ii
=
0
;
ii
<
(
int
)
scaledRadiusFactors
.
size
();
ii
++
){
for
(
int
ii
=
0
;
ii
<
(
int
)
scaledRadiusFactors
.
size
();
ii
++
){
_scaledRadiusFactors
[
ii
]
=
scaledRadiusFactors
[
ii
];
_scaledRadiusFactors
[
ii
]
=
scaledRadiusFactors
[
ii
];
}
}
return
0
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -621,15 +595,12 @@ std::string ObcSoftcoreParameters::getStateString( const char* title ) const {
...
@@ -621,15 +595,12 @@ std::string ObcSoftcoreParameters::getStateString( const char* title ) const {
@param distance the cutoff distance
@param distance the cutoff distance
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ObcSoftcoreParameters
::
setUseCutoff
(
RealOpenMM
distance
)
{
void
ObcSoftcoreParameters
::
setUseCutoff
(
RealOpenMM
distance
)
{
cutoff
=
true
;
cutoff
=
true
;
cutoffDistance
=
distance
;
cutoffDistance
=
distance
;
return
0
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -660,11 +631,9 @@ RealOpenMM ObcSoftcoreParameters::getCutoffDistance() {
...
@@ -660,11 +631,9 @@ RealOpenMM ObcSoftcoreParameters::getCutoffDistance() {
@param boxSize the X, Y, and Z widths of the periodic box
@param boxSize the X, Y, and Z widths of the periodic box
@return ReferenceForce::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ObcSoftcoreParameters
::
setPeriodic
(
RealOpenMM
*
boxSize
)
{
void
ObcSoftcoreParameters
::
setPeriodic
(
RealOpenMM
*
boxSize
)
{
assert
(
cutoff
);
assert
(
cutoff
);
assert
(
boxSize
[
0
]
>=
2.0
*
cutoffDistance
);
assert
(
boxSize
[
0
]
>=
2.0
*
cutoffDistance
);
...
@@ -674,7 +643,6 @@ int ObcSoftcoreParameters::setPeriodic( RealOpenMM* boxSize ) {
...
@@ -674,7 +643,6 @@ int ObcSoftcoreParameters::setPeriodic( RealOpenMM* boxSize ) {
periodicBoxSize
[
0
]
=
boxSize
[
0
];
periodicBoxSize
[
0
]
=
boxSize
[
0
];
periodicBoxSize
[
1
]
=
boxSize
[
1
];
periodicBoxSize
[
1
]
=
boxSize
[
1
];
periodicBoxSize
[
2
]
=
boxSize
[
2
];
periodicBoxSize
[
2
]
=
boxSize
[
2
];
return
0
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -730,11 +698,9 @@ const RealOpenMM* ObcSoftcoreParameters::getNonPolarScaleFactors( void ) const {
...
@@ -730,11 +698,9 @@ const RealOpenMM* ObcSoftcoreParameters::getNonPolarScaleFactors( void ) const {
@param ownNonPolarScaleFactors flag indicating whether scale factors
@param ownNonPolarScaleFactors flag indicating whether scale factors
array should be deleted
array should be deleted
@return SimTKOpenMMCommon::DefaultReturn
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ObcSoftcoreParameters
::
setOwnNonPolarScaleFactors
(
int
ownNonPolarScaleFactors
){
void
ObcSoftcoreParameters
::
setOwnNonPolarScaleFactors
(
int
ownNonPolarScaleFactors
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -743,8 +709,6 @@ int ObcSoftcoreParameters::setOwnNonPolarScaleFactors( int ownNonPolarScaleFacto
...
@@ -743,8 +709,6 @@ int ObcSoftcoreParameters::setOwnNonPolarScaleFactors( int ownNonPolarScaleFacto
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
_ownNonPolarScaleFactors
=
ownNonPolarScaleFactors
;
_ownNonPolarScaleFactors
=
ownNonPolarScaleFactors
;
return
0
;
}
}
/**---------------------------------------------------------------------------------------
/**---------------------------------------------------------------------------------------
...
@@ -753,11 +717,9 @@ int ObcSoftcoreParameters::setOwnNonPolarScaleFactors( int ownNonPolarScaleFacto
...
@@ -753,11 +717,9 @@ int ObcSoftcoreParameters::setOwnNonPolarScaleFactors( int ownNonPolarScaleFacto
@param nonPolarScaleFactors nonPolarScaleFactors
@param nonPolarScaleFactors nonPolarScaleFactors
@return SimTKOpenMMCommon::DefaultReturn always
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ObcSoftcoreParameters
::
setNonPolarScaleFactors
(
const
RealOpenMMVector
&
nonPolarScaleFactors
){
void
ObcSoftcoreParameters
::
setNonPolarScaleFactors
(
const
RealOpenMMVector
&
nonPolarScaleFactors
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -774,9 +736,6 @@ int ObcSoftcoreParameters::setNonPolarScaleFactors( const RealOpenMMVector& nonP
...
@@ -774,9 +736,6 @@ int ObcSoftcoreParameters::setNonPolarScaleFactors( const RealOpenMMVector& nonP
for
(
int
ii
=
0
;
ii
<
getNumberOfAtoms
();
ii
++
){
for
(
int
ii
=
0
;
ii
<
getNumberOfAtoms
();
ii
++
){
_nonPolarScaleFactors
[
ii
]
=
nonPolarScaleFactors
[
ii
];
_nonPolarScaleFactors
[
ii
]
=
nonPolarScaleFactors
[
ii
];
}
}
return
0
;
}
}
#if RealOpenMMType == 0
#if RealOpenMMType == 0
...
@@ -787,11 +746,9 @@ int ObcSoftcoreParameters::setNonPolarScaleFactors( const RealOpenMMVector& nonP
...
@@ -787,11 +746,9 @@ int ObcSoftcoreParameters::setNonPolarScaleFactors( const RealOpenMMVector& nonP
@param nonPolarScaleFactors nonPolarScaleFactors
@param nonPolarScaleFactors nonPolarScaleFactors
@return SimTKOpenMMCommon::DefaultReturn always
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ObcSoftcoreParameters
::
setNonPolarScaleFactors
(
float
*
nonPolarScaleFactors
){
void
ObcSoftcoreParameters
::
setNonPolarScaleFactors
(
float
*
nonPolarScaleFactors
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -806,9 +763,6 @@ int ObcSoftcoreParameters::setNonPolarScaleFactors( float* nonPolarScaleFactors
...
@@ -806,9 +763,6 @@ int ObcSoftcoreParameters::setNonPolarScaleFactors( float* nonPolarScaleFactors
for
(
int
ii
=
0
;
ii
<
getNumberOfAtoms
();
ii
++
){
for
(
int
ii
=
0
;
ii
<
getNumberOfAtoms
();
ii
++
){
_nonPolarScaleFactors
[
ii
]
=
(
RealOpenMM
)
nonPolarScaleFactors
[
ii
];
_nonPolarScaleFactors
[
ii
]
=
(
RealOpenMM
)
nonPolarScaleFactors
[
ii
];
}
}
return
0
;
}
}
#endif
#endif
...
@@ -819,11 +773,9 @@ int ObcSoftcoreParameters::setNonPolarScaleFactors( float* nonPolarScaleFactors
...
@@ -819,11 +773,9 @@ int ObcSoftcoreParameters::setNonPolarScaleFactors( float* nonPolarScaleFactors
@param nonPolarScaleFactors nonPolarScaleFactors
@param nonPolarScaleFactors nonPolarScaleFactors
@return SimTKOpenMMCommon::DefaultReturn always
--------------------------------------------------------------------------------------- */
--------------------------------------------------------------------------------------- */
int
ObcSoftcoreParameters
::
setNonPolarPrefactor
(
RealOpenMM
nonPolarPreFactor
){
void
ObcSoftcoreParameters
::
setNonPolarPrefactor
(
RealOpenMM
nonPolarPreFactor
){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
...
@@ -832,6 +784,5 @@ int ObcSoftcoreParameters::setNonPolarPrefactor( RealOpenMM nonPolarPreFactor ){
...
@@ -832,6 +784,5 @@ int ObcSoftcoreParameters::setNonPolarPrefactor( RealOpenMM nonPolarPreFactor ){
// ---------------------------------------------------------------------------------------
// ---------------------------------------------------------------------------------------
_nonPolarPreFactor
=
nonPolarPreFactor
;
_nonPolarPreFactor
=
nonPolarPreFactor
;
return
0
;
}
}
Prev
1
2
3
4
Next
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment