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Commit b5858a8e authored by Peter Eastman's avatar Peter Eastman
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Deleted lots of obsolete debugging code from the reference platform

parent c87cee06
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platforms/reference/src/SimTKReference/ReferenceVariableStochasticDynamics.h
View file @ b5858a8e
...@@ -89,18 +89,6 @@ class ReferenceVariableStochasticDynamics : public ReferenceDynamics { ...@@ -89,18 +89,6 @@ class ReferenceVariableStochasticDynamics : public ReferenceDynamics {
void setAccuracy( RealOpenMM accuracy ); void setAccuracy( RealOpenMM accuracy );
/**---------------------------------------------------------------------------------------
Print parameters
@param message message
@return ReferenceDynamics::DefaultReturn
--------------------------------------------------------------------------------------- */
int printParameters( std::stringstream& message ) const;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Update Update
......
platforms/reference/src/SimTKReference/ReferenceVariableVerletDynamics.cpp
View file @ b5858a8e
...@@ -95,32 +95,6 @@ void ReferenceVariableVerletDynamics::setAccuracy( RealOpenMM accuracy ) { ...@@ -95,32 +95,6 @@ void ReferenceVariableVerletDynamics::setAccuracy( RealOpenMM accuracy ) {
_accuracy = accuracy; _accuracy = accuracy;
} }
/**---------------------------------------------------------------------------------------
Print parameters
@param message message
@return ReferenceDynamics::DefaultReturn
--------------------------------------------------------------------------------------- */
int ReferenceVariableVerletDynamics::printParameters( std::stringstream& message ) const {
// ---------------------------------------------------------------------------------------
static const char* methodName = "\nReferenceVariableVerletDynamics::printParameters";
// ---------------------------------------------------------------------------------------
// print parameters
ReferenceDynamics::printParameters( message );
return ReferenceDynamics::DefaultReturn;
}
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Update -- driver routine for performing Verlet dynamics update of coordinates Update -- driver routine for performing Verlet dynamics update of coordinates
...@@ -148,8 +122,6 @@ int ReferenceVariableVerletDynamics::update( int numberOfAtoms, RealOpenMM** ato ...@@ -148,8 +122,6 @@ int ReferenceVariableVerletDynamics::update( int numberOfAtoms, RealOpenMM** ato
static const RealOpenMM zero = 0.0; static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0; static const RealOpenMM one = 1.0;
static int debug = 0;
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
// get work arrays // get work arrays
......
platforms/reference/src/SimTKReference/ReferenceVariableVerletDynamics.h
View file @ b5858a8e
...@@ -76,18 +76,6 @@ class ReferenceVariableVerletDynamics : public ReferenceDynamics { ...@@ -76,18 +76,6 @@ class ReferenceVariableVerletDynamics : public ReferenceDynamics {
void setAccuracy( RealOpenMM accuracy ); void setAccuracy( RealOpenMM accuracy );
/**---------------------------------------------------------------------------------------
Print parameters
@param message message
@return ReferenceDynamics::DefaultReturn
--------------------------------------------------------------------------------------- */
int printParameters( std::stringstream& message ) const;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Update Update
......
platforms/reference/src/SimTKReference/ReferenceVerletDynamics.cpp
View file @ b5858a8e
...@@ -77,32 +77,6 @@ ReferenceVerletDynamics::~ReferenceVerletDynamics( ){ ...@@ -77,32 +77,6 @@ ReferenceVerletDynamics::~ReferenceVerletDynamics( ){
} }
/**---------------------------------------------------------------------------------------
Print parameters
@param message message
@return ReferenceDynamics::DefaultReturn
--------------------------------------------------------------------------------------- */
int ReferenceVerletDynamics::printParameters( std::stringstream& message ) const {
// ---------------------------------------------------------------------------------------
static const char* methodName = "\nReferenceVerletDynamics::printParameters";
// ---------------------------------------------------------------------------------------
// print parameters
ReferenceDynamics::printParameters( message );
return ReferenceDynamics::DefaultReturn;
}
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Update -- driver routine for performing Verlet dynamics update of coordinates Update -- driver routine for performing Verlet dynamics update of coordinates
...@@ -129,8 +103,6 @@ int ReferenceVerletDynamics::update( int numberOfAtoms, RealOpenMM** atomCoordin ...@@ -129,8 +103,6 @@ int ReferenceVerletDynamics::update( int numberOfAtoms, RealOpenMM** atomCoordin
static const RealOpenMM zero = 0.0; static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0; static const RealOpenMM one = 1.0;
static int debug = 0;
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
// get work arrays // get work arrays
...@@ -191,132 +163,3 @@ int ReferenceVerletDynamics::update( int numberOfAtoms, RealOpenMM** atomCoordin ...@@ -191,132 +163,3 @@ int ReferenceVerletDynamics::update( int numberOfAtoms, RealOpenMM** atomCoordin
return ReferenceDynamics::DefaultReturn; return ReferenceDynamics::DefaultReturn;
} }
/**---------------------------------------------------------------------------------------
Write state
@param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates
@param velocities velocities
@param forces forces
@param masses atom masses
@param state 0 if initial state; otherwise nonzero
@param baseFileName base file name
@return ReferenceDynamics::DefaultReturn
--------------------------------------------------------------------------------------- */
int ReferenceVerletDynamics::writeState( int numberOfAtoms, RealOpenMM** atomCoordinates,
RealOpenMM** velocities,
RealOpenMM** forces, RealOpenMM* masses,
int state, const std::string& baseFileName ) const {
// ---------------------------------------------------------------------------------------
static const char* methodName = "\nReferenceVerletDynamics::writeState";
static const RealOpenMM zero = 0.0;
static const RealOpenMM one = 1.0;
static const int threeI = 3;
// ---------------------------------------------------------------------------------------
std::stringstream stateFileName;
stateFileName << baseFileName;
stateFileName << "_Step" << getTimeStep();
// stateFileName << "_State" << state;
stateFileName << ".txt";
// ---------------------------------------------------------------------------------------
// open file -- return if unsuccessful
FILE* stateFile = NULL;
#ifdef _MSC_VER
fopen_s( &stateFile, stateFileName.str().c_str(), "w" );
#else
stateFile = fopen( stateFileName.str().c_str(), "w" );
#endif
// ---------------------------------------------------------------------------------------
// diagnostics
if( stateFile != NULL ){
std::stringstream message;
message << methodName;
message << " Opened file=<" << stateFileName.str() << ">.\n";
SimTKOpenMMLog::printMessage( message );
} else {
std::stringstream message;
message << methodName;
message << " could not open file=<" << stateFileName.str() << "> -- abort output.\n";
SimTKOpenMMLog::printMessage( message );
return ReferenceDynamics::ErrorReturn;
}
// ---------------------------------------------------------------------------------------
StringVector scalarNameI;
IntVector scalarI;
StringVector scalarNameR;
RealOpenMMVector scalarR;
StringVector scalarNameR1;
RealOpenMMPtrVector scalarR1;
StringVector scalarNameR2;
RealOpenMMPtrPtrVector scalarR2;
scalarI.push_back( getNumberOfAtoms() );
scalarNameI.push_back( "Atoms" );
scalarI.push_back( getTimeStep() );
scalarNameI.push_back( "Timestep" );
if( state == 0 || state == -1 ){
scalarR.push_back( getDeltaT() );
scalarNameR.push_back( "delta_t" );
scalarR1.push_back( masses );
scalarNameR1.push_back( "mass" );
scalarR2.push_back( atomCoordinates );
scalarNameR2.push_back( "coord" );
scalarR2.push_back( velocities );
scalarNameR2.push_back( "velocities" );
scalarR2.push_back( forces );
scalarNameR2.push_back( "forces" );
if( state == -1 ){
RealOpenMM** xPrime = get2DArrayAtIndex( xPrime2D );
scalarR2.push_back( xPrime );
scalarNameR2.push_back( "xPrime" );
}
} else {
scalarR2.push_back( atomCoordinates );
scalarNameR2.push_back( "coord" );
scalarR2.push_back( velocities );
scalarNameR2.push_back( "velocities" );
}
writeStateToFile( stateFile, scalarNameI, scalarI, scalarNameR, scalarR, getNumberOfAtoms(), scalarNameR1, scalarR1, threeI, scalarNameR2, scalarR2 );
(void) fclose( stateFile );
return ReferenceDynamics::DefaultReturn;
}
platforms/reference/src/SimTKReference/ReferenceVerletDynamics.h
View file @ b5858a8e
...@@ -59,19 +59,6 @@ class ReferenceVerletDynamics : public ReferenceDynamics { ...@@ -59,19 +59,6 @@ class ReferenceVerletDynamics : public ReferenceDynamics {
~ReferenceVerletDynamics( ); ~ReferenceVerletDynamics( );
/**---------------------------------------------------------------------------------------
Print parameters
@param message message
@return ReferenceDynamics::DefaultReturn
--------------------------------------------------------------------------------------- */
int printParameters( std::stringstream& message ) const;
/**--------------------------------------------------------------------------------------- /**---------------------------------------------------------------------------------------
Update Update
...@@ -89,26 +76,6 @@ class ReferenceVerletDynamics : public ReferenceDynamics { ...@@ -89,26 +76,6 @@ class ReferenceVerletDynamics : public ReferenceDynamics {
int update( int numberOfAtoms, RealOpenMM** atomCoordinates, int update( int numberOfAtoms, RealOpenMM** atomCoordinates,
RealOpenMM** velocities, RealOpenMM** forces, RealOpenMM* masses ); RealOpenMM** velocities, RealOpenMM** forces, RealOpenMM* masses );
/**---------------------------------------------------------------------------------------
Write state
@param numberOfAtoms number of atoms
@param atomCoordinates atom coordinates
@param velocities velocities
@param forces forces
@param masses atom masses
@param state 0 if initial state; otherwise nonzero
@param baseFileName base file name
@return ReferenceDynamics::DefaultReturn
--------------------------------------------------------------------------------------- */
int writeState( int numberOfAtoms, RealOpenMM** atomCoordinates,
RealOpenMM** velocities, RealOpenMM** forces, RealOpenMM* masses,
int state, const std::string& baseFileName ) const;
}; };
// --------------------------------------------------------------------------------------- // ---------------------------------------------------------------------------------------
......
platforms/reference/src/SimTKReference/SimTKReference-old-2005.vcproj deleted 100644 → 0
View file @ c87cee06
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platforms/reference/src/SimTKReference/SimTKReference.sln deleted 100755 → 0
View file @ c87cee06

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platforms/reference/src/SimTKReference/SimTKReference.vcproj deleted 100755 → 0
View file @ c87cee06
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platforms/reference/src/SimTKReference/gromacsReferenceInterface.h deleted 100644 → 0
View file @ c87cee06
/* Portions copyright (c) 2006 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
* a copy of this software and associated documentation files (the
* "Software"), to deal in the Software without restriction, including
* without limitation the rights to use, copy, modify, merge, publish,
* distribute, sublicense, and/or sell copies of the Software, and to
* permit persons to whom the Software is furnished to do so, subject
* to the following conditions:
*
* The above copyright notice and this permission notice shall be included
* in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
* OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
* MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
* IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
* LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
* OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#ifndef __GromacsReferenceInterface_H__
#define __GromacsReferenceInterface_H__
#ifdef __cplusplus
#define externC extern "C"
#else
#define externC extern
#endif
#include "../SimTKUtilities/SimTKOpenMMCommon.h"
/**---------------------------------------------------------------------------------------
Calculate forces for given configuration and topology
@param top Gromacs t_topology data struct
@param gromacAtomCoordinates atom configuration
@param partialChargesIn array of partial charges
@param fr Gromac's force_record?????
@param log log reference (stdlog in md.c)
@return 0
--------------------------------------------------------------------------------------- */
externC
int gromacsReferenceForce( const t_topology* top, const rvec* gromacAtomCoordinates,
const t_mdatoms *md, t_forcerec* fr,
char* baseFileName, FILE* log );
externC
int gromacsReferenceSdUpdate( int numberOfAtoms, const t_topology* top, const rvec* gromacAtomCoordinates,
const t_mdatoms *md, t_forcerec* fr,
const rvec* gromacsVelocities, const rvec* gromacsForces,
real* masses, real deltaT, real tau, real temperature,
char* baseFileName, FILE* log );
/**---------------------------------------------------------------------------------------
Calculate forces for given configuration and topology
Used in self-test; parameter arrays, ... only allocated once (static); freed
if debug is -1
@param top Gromacs t_topology data struct
@param gromacAtomCoordinates atom configuration
@param md Gromacs t_mdatoms data struct
@param fr Gromacs t_forcerec data struct
@param includeNonBonded include nonbonded ixn
@param baseFileName Base file name
@param debug debug flag (== -1, free arrays and return)
@param log log reference (stdlog in md.c)
@return 0
--------------------------------------------------------------------------------------- */
externC
int gromacsReferenceForceSelfTest(
const t_topology* top, const rvec* gromacAtomCoordinates,
const t_mdatoms *md, t_forcerec* fr,
rvec* forces, int includeNonBonded, char* baseFileName,
int debug, FILE* log );
/**---------------------------------------------------------------------------------------
Remove linear momentum from velocities
@param numberOfAtoms number of atoms
@param gromacsMasses masses
@param gromacsVelocities velocities
@param baseFileName base file name
@param log log reference (stdlog in md.c)
@return 0
--------------------------------------------------------------------------------------- */
externC
int gromacsReferenceRemoveLinearMomentum( int numberOfAtoms, const real* gromacsMasses,
rvec* gromacsVelocities, char* baseFileName, FILE* log );
#endif
platforms/reference/src/SimTKReference/gromacsReferenceInterfaceCpp.h deleted 100644 → 0
View file @ c87cee06
/* Portions copyright (c) 2006 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
* a copy of this software and associated documentation files (the
* "Software"), to deal in the Software without restriction, including
* without limitation the rights to use, copy, modify, merge, publish,
* distribute, sublicense, and/or sell copies of the Software, and to
* permit persons to whom the Software is furnished to do so, subject
* to the following conditions:
*
* The above copyright notice and this permission notice shall be included
* in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
* OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
* MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
* IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
* LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
* OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#ifndef __GromacsReferenceInterfaceCpp_H__
#define __GromacsReferenceInterfaceCpp_H__
#ifdef __cplusplus
#define externC extern "C"
#else
#define externC extern
#endif
/**---------------------------------------------------------------------------------------
Allocate memory for atom indices participating in bonds and the bond parameters
@param numberOfBonds number of bonds
@param numberOfAtomIndices (number of atoms)/bond
@param outputBondIndices allocated memory for atom indices outputBondIndices[bondIndex][atomIndex]
@param numberParameters number of parameters/bond
@param outputBondParameters allocated memory for parameters outputBondParameters[bondIndex][parameterIndex]
@return 0
--------------------------------------------------------------------------------------- */
externC
int gromacsAllocateBondIxnArrays( int numberOfBonds, int numberOfAtomIndices,
int*** outputBondIndices, int numberParameters,
RealOpenMM*** outputBondParameters );
/**---------------------------------------------------------------------------------------
Get bond atom indices and parameters for harmonic bonds
@param top Gromacs t_topology data struct
@param atomIndices array of atomIndices[bondIndex][atomIndex]
@param bondParameters array of bond parameters[bondIndex][parameterIndex]
The arrays atomIndices & bondParameters are allocated off the heap;
The memory for the second index is one block of size (number of bonds)*(number of atoms in bond)
The memory should be freed by the callee via calls:
free( atomIndices[0] ); free( atomIndices );
@return number of bonds
--------------------------------------------------------------------------------------- */
externC
int gromacsGetHarmonicBondParameters( const t_topology* top, int*** atomIndices,
RealOpenMM*** bondParameters );
/**---------------------------------------------------------------------------------------
Calculate harmonic bond forces/energies for given configuration and topology
@param top Gromacs t_topology data struct
@param atomCoordinates atom configuration
@param harmonicBondForces output array of forces: harmonicBondForces[atomIndex][3]
@param harmonicBondEnergies output array of bond energies[atomIndex]
@param totalEnergy output total energy
@return 0
--------------------------------------------------------------------------------------- */
externC
int gromacsHarmonicBondReferenceForce( const t_topology* top, RealOpenMM** atomCoordinates,
RealOpenMM** harmonicBondForces,
RealOpenMM* harmonicBondAtomEnergies,
RealOpenMM* totalEnergy );
/**---------------------------------------------------------------------------------------
Get bond atom indices and parameters for angle bonds
@param top Gromacs t_topology data struct
@param atomIndices array of atomIndices[bondIndex][atomIndex]
@param bondParameters array of bond parameters[bondIndex][parameterIndex]
The arrays atomIndices & bondParameters are allocated off the heap;
The memory for the second index is one block of size (number of bonds)*(number of atoms in bond)
The memory should be freed by the callee via calls:
free( atomIndices[0] ); free( atomIndices );
@return number of bonds
--------------------------------------------------------------------------------------- */
externC
int gromacsGetAngleBondParameters( const t_topology* top, int*** atomIndices,
RealOpenMM*** bondParameters );
/**---------------------------------------------------------------------------------------
Calculate angle bond forces/energies for given configuration and topology
@param top Gromacs t_topology data struct
@param atomCoordinates atom configuration
@param angleBondForces output array of forces: angleBondForces[atomIndex][3]
@param angleBondEnergies output array of bond energies[atomIndex]
@param totalEnergy output total energy
@return 0
--------------------------------------------------------------------------------------- */
externC
int gromacsAngleBondReferenceForce( const t_topology* top, RealOpenMM** atomCoordinates,
RealOpenMM** angleBondForces,
RealOpenMM* angleBondAtomEnergies,
RealOpenMM* totalEnergy );
/**---------------------------------------------------------------------------------------
Get bond atom indices and parameters for properDihedral bonds
@param top Gromacs t_topology data struct
@param atomIndices array of atomIndices[bondIndex][atomIndex]
@param bondParameters array of bond parameters[bondIndex][parameterIndex]
The arrays atomIndices & bondParameters are allocated off the heap;
The memory for the second index is one block of size (number of bonds)*(number of atoms in bond)
The memory should be freed by the callee via calls:
free( atomIndices[0] ); free( atomIndices );
@return number of bonds
--------------------------------------------------------------------------------------- */
externC
int gromacsGetProperDihedralBondParameters( const t_topology* top, int*** atomIndices,
RealOpenMM*** bondParameters );
/**---------------------------------------------------------------------------------------
Calculate properDihedral bond forces/energies for given configuration and topology
@param top Gromacs t_topology data struct
@param atomCoordinates atom configuration
@param properDihedralBondForces output array of forces: angleBondForces[atomIndex][3]
@param properDihedralBondEnergies output array of bond energies[atomIndex]
@param totalEnergy output total energy
@return 0
--------------------------------------------------------------------------------------- */
externC
int gromacsProperDihedralBondReferenceForce( const t_topology* top, RealOpenMM** atomCoordinates,
RealOpenMM** properDihedralBondForces,
RealOpenMM* properDihedralBondAtomEnergies,
RealOpenMM* totalEnergy );
/**---------------------------------------------------------------------------------------
Get bond atom indices and parameters for RB Dihedral bonds
@param top Gromacs t_topology data struct
@param atomIndices array of atomIndices[bondIndex][atomIndex]
@param bondParameters array of bond parameters[bondIndex][parameterIndex]
The arrays atomIndices & bondParameters are allocated off the heap;
The memory for the second index is one block of size (number of bonds)*(number of atoms in bond)
The memory should be freed by the callee via calls:
free( atomIndices[0] ); free( atomIndices );
@return number of bonds
--------------------------------------------------------------------------------------- */
externC
int gromacsGetRbDihedralBondParameters( const t_topology* top, int*** atomIndices,
RealOpenMM*** bondParameters );
/**---------------------------------------------------------------------------------------
Calculate RB dihedral bond forces/energies for given configuration and topology
@param top Gromacs t_topology data struct
@param atomCoordinates atom configuration
@param rbDihedralBondForces output array of forces: angleBondForces[atomIndex][3]
@param rbDihedralBondEnergies output array of bond energies[atomIndex]
@param totalEnergy output total energy
@return 0
--------------------------------------------------------------------------------------- */
externC
int gromacsRbDihedralBondReferenceForce( const t_topology* top, RealOpenMM** atomCoordinates,
RealOpenMM** rbDihedralBondForces,
RealOpenMM* rbDihedralBondAtomEnergies,
RealOpenMM* totalEnergy );
/**---------------------------------------------------------------------------------------
Get bond atom indices and parameters for LJ 14 bonds
@param top Gromacs t_topology data struct
@param atomIndices array of atomIndices[bondIndex][atomIndex]
@param bondParameters array of bond parameters[bondIndex][parameterIndex]
The arrays atomIndices & bondParameters are allocated off the heap;
The memory for the second index is one block of size (number of bonds)*(number of atoms in bond)
The memory should be freed by the callee via calls:
free( atomIndices[0] ); free( atomIndices );
@return number of bonds
--------------------------------------------------------------------------------------- */
externC
int gromacsGetLJ14Parameters( const t_topology* top, int*** atomIndices,
RealOpenMM*** bondParameters );
/**---------------------------------------------------------------------------------------
Calculate LJ 14 forces/energies for given configuration and topology
@param top Gromacs t_topology data struct
@param atomCoordinates atom configuration
@param fr Gromacs t_forcerec struct
@param lj14Forces output array of forces: lj14Forces[atomIndex][3]
@param lj14AtomEnergies output array of LJ 14 energies[atomIndex]
@param totalEnergy output total energy
@return 0
--------------------------------------------------------------------------------------- */
externC
int gromacsLJ14ReferenceForce( const t_topology* top, RealOpenMM** atomCoordinates,
t_forcerec *fr, const RealOpenMM* charges, RealOpenMM** lj14Forces,
RealOpenMM* lj14AtomEnergies,
RealOpenMM* totalEnergy );
#endif
platforms/reference/src/SimTKReference/gromacsReferenceParameterPrint.h deleted 100644 → 0
View file @ c87cee06
/* Portions copyright (c) 2006 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
* a copy of this software and associated documentation files (the
* "Software"), to deal in the Software without restriction, including
* without limitation the rights to use, copy, modify, merge, publish,
* distribute, sublicense, and/or sell copies of the Software, and to
* permit persons to whom the Software is furnished to do so, subject
* to the following conditions:
*
* The above copyright notice and this permission notice shall be included
* in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
* OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
* MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
* IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
* LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
* OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#ifndef __GromacsReferenceParameterPrint_H__
#define __GromacsReferenceParameterPrint_H__
#ifdef __cplusplus
#define externC extern "C"
#else
#define externC extern
#endif
/**---------------------------------------------------------------------------------------
Print bond parameters
@param idef Gromacs parameter data struct
@param fr force record?
@param charges atom charges
@param file FILE* reference
@return 0
--------------------------------------------------------------------------------------- */
externC int printBondParameters( t_topology *top, t_forcerec *fr, t_mdatoms *md, FILE* bondFile );
/**---------------------------------------------------------------------------------------
Print angle parameters
@param idef Gromacs parameter data struct
@param fr force record?
@param charges atom charges
@param file FILE* reference
@return 0
--------------------------------------------------------------------------------------- */
externC int printAngleParameters( t_topology *top, t_forcerec *fr, t_mdatoms *md, FILE* angleFile );
/**---------------------------------------------------------------------------------------
Print rbDihedral parameters
@param idef Gromacs parameter data struct
@param fr force record?
@param charges atom charges
@param file FILE* reference
@return 0
--------------------------------------------------------------------------------------- */
externC int printRbDihedralParameters( t_topology *top, t_forcerec *fr, t_mdatoms *md, FILE* rbDihedralFile );
/**---------------------------------------------------------------------------------------
Print properDihedral parameters
@param idef Gromacs parameter data struct
@param fr force record?
@param charges atom charges
@param file FILE* reference
@return 0
--------------------------------------------------------------------------------------- */
externC int printProperDihedralParameters( t_topology *top, t_forcerec *fr, t_mdatoms *md, FILE* properDihedralFile );
/**---------------------------------------------------------------------------------------
Print LJ 14 parameters
@param idef Gromacs parameter data struct
@param fr force record?
@param charges atom charges
@param file FILE* reference
@return 0
--------------------------------------------------------------------------------------- */
externC int printLJ14Parameters( t_topology *top, t_forcerec *fr, t_mdatoms *md, FILE* lj14File );
/**---------------------------------------------------------------------------------------
Print LJ Coulomb parameters
@param idef Gromacs parameter data struct
@param fr force record?
@param charges atom charges
@param file FILE* reference
@return 0
--------------------------------------------------------------------------------------- */
externC int printLJCoulombParameters( t_topology *top, t_forcerec *fr, t_mdatoms *md, FILE* ljCoulombFile );
/**---------------------------------------------------------------------------------------
Print Shake parameters
@param idef Gromacs parameter data struct
@param fr force record?
@param charges atom charges
@param file FILE* reference
@return 0
--------------------------------------------------------------------------------------- */
externC int printShakeParameters( t_topology *top, t_forcerec *fr, t_mdatoms *md, FILE* shakeFile );
/**---------------------------------------------------------------------------------------
Print Gromacs parameters
@param baseFileName base file name
@param top Gromacs parameter data struct
@param fr Gromacs parameter data struct
@param md Gromacs parameter data struct
@param file FILE* reference
@return 0
--------------------------------------------------------------------------------------- */
externC void printReferenceParameters( char* baseFileName, t_topology *top, t_forcerec *fr,
t_mdatoms *md, FILE *log );
/**---------------------------------------------------------------------------------------
Print forces/energies
@param numberOfAtoms number of atoms
@param x atom coordinates
@param f atom forces
@param energies energies by atom
@param totalEnergy total energy
@param fileName file name
@return 0
--------------------------------------------------------------------------------------- */
externC void writeGromacsForceFile( int numberOfAtoms, rvec x[], rvec f[], real* energies,
real totalEnergy, char* fileName );
/**---------------------------------------------------------------------------------------
Print 'state' mass/coordinates/velocities/forces
@param numberOfAtoms number of atoms
@param x atom coordinates
@param v atom velocities
@param f atom forces
@param timestep time step
@param deltaT delta t
@param temperature temperature
@param tau tau
@param fileName file name
@return 0
--------------------------------------------------------------------------------------- */
externC void writeGromacsStateFile( int numberOfAtoms, real mass[], rvec x[], rvec v[],
rvec f[], int timestep, real deltaT,
real temperature, real tau, char* fileName );
#endif
platforms/reference/src/SimTKUtilities/Makefile deleted 100644 → 0
View file @ c87cee06
# ---------------------------------------------------------------------------------------
include ../makeConfig/Top.mk
# ---------------------------------------------------------------------------------------
# target is gmxGbsa library
# ld reference is in ../gromacs/vc7.mk
# include file reference is in ../gromacs/gmxgpu.h
STATIC_LIBRARY := gmxUtilities
# ---------------------------------------------------------------------------------------
BaseFiles := $(SimTkBaseFiles)
IncludeDirectories := $(SimTkDirectory) $(GromacsIncludeDirectory)
# ---------------------------------------------------------------------------------------
include $(MakeDirectory)/BaseMake.mk
# ---------------------------------------------------------------------------------------
platforms/reference/src/SimTKUtilities/NewOverrideSimTk.cpp2 deleted 100644 → 0
View file @ c87cee06
/* Portions copyright (c) 2006 Stanford University and Simbios.
* Contributors: Pande Group
*
* Permission is hereby granted, free of charge, to any person obtaining
* a copy of this software and associated documentation files (the
* "Software"), to deal in the Software without restriction, including
* without limitation the rights to use, copy, modify, merge, publish,
* distribute, sublicense, and/or sell copies of the Software, and to
* permit persons to whom the Software is furnished to do so, subject
* to the following conditions:
*
* The above copyright notice and this permission notice shall be included
* in all copies or substantial portions of the Software.
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
* OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
* MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
* IN NO EVENT SHALL THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE
* LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
* OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
* WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
*/
#include <new>
#include <stdio.h>
// Replacement new/delete w/ Gromac's smalloc() and sfree()
extern "C" {
#include "smalloc.h"
}
/* ---------------------------------------------------------------------------------------
Override C++ new w/ Gromac's smalloc/sfree (Simbios)
@param size bytes to allocate
@return ptr to allocated memory
--------------------------------------------------------------------------------------- */
void* operator new( size_t size ){
void *ptr;
smalloc(ptr, (int) size);
// (void) fprintf( stdout, "\nGlobal override new called -- size=%u", size );
// (void) fflush( stdout );
return ptr;
}
/* ---------------------------------------------------------------------------------------
Override C++ delete w/ Gromac's sfree (Simbios)
@param ptr ptr to block to free
--------------------------------------------------------------------------------------- */
void operator delete( void *ptr ){
// (void) fprintf( stdout, "\nGlobal override delete called." );
// (void) fflush( stdout );
sfree( ptr );
}
platforms/reference/src/SimTKUtilities/SimTk-old-2005.sln deleted 100755 → 0
View file @ c87cee06
Microsoft Visual Studio Solution File, Format Version 9.00
# Visual Studio 2005
Project("{8BC9CEB8-8B4A-11D0-8D11-00A0C91BC942}") = "SimTk", "SimTk-old-2005.vcproj", "{82165226-E7AC-4C35-8914-80C31C7B4754}"
EndProject
Global
GlobalSection(SolutionConfigurationPlatforms) = preSolution
Debug|Win32 = Debug|Win32
Release|Win32 = Release|Win32
EndGlobalSection
GlobalSection(ProjectConfigurationPlatforms) = postSolution
{82165226-E7AC-4C35-8914-80C31C7B4754}.Debug|Win32.ActiveCfg = Debug|Win32
{82165226-E7AC-4C35-8914-80C31C7B4754}.Debug|Win32.Build.0 = Debug|Win32
{82165226-E7AC-4C35-8914-80C31C7B4754}.Release|Win32.ActiveCfg = Release|Win32
{82165226-E7AC-4C35-8914-80C31C7B4754}.Release|Win32.Build.0 = Release|Win32
EndGlobalSection
GlobalSection(SolutionProperties) = preSolution
HideSolutionNode = FALSE
EndGlobalSection
EndGlobal
platforms/reference/src/SimTKUtilities/SimTk-old-2005.vcproj deleted 100755 → 0
View file @ c87cee06
<?xml version="1.0" encoding="UTF-8"?>
<VisualStudioProject
ProjectType="Visual C++"
Version="8.00"
Name="SimTk"
ProjectGUID="{82165226-E7AC-4C35-8914-80C31C7B4754}"
RootNamespace="SimTk"
Keyword="Win32Proj"
>
<Platforms>
<Platform
Name="Win32"
/>
</Platforms>
<ToolFiles>
</ToolFiles>
<Configurations>
<Configuration
Name="Debug|Win32"
OutputDirectory="Debug"
IntermediateDirectory="Debug"
ConfigurationType="4"
>
<Tool
Name="VCPreBuildEventTool"
/>
<Tool
Name="VCCustomBuildTool"
/>
<Tool
Name="VCXMLDataGeneratorTool"
/>
<Tool
Name="VCWebServiceProxyGeneratorTool"
/>
<Tool
Name="VCMIDLTool"
/>
<Tool
Name="VCCLCompilerTool"
Optimization="0"
AdditionalIncludeDirectories="..\gromacs\include"
PreprocessorDefinitions="WIN32;_DEBUG;_LIB;"
MinimalRebuild="true"
BasicRuntimeChecks="3"
RuntimeLibrary="1"
UsePrecompiledHeader="0"
WarningLevel="3"
Detect64BitPortabilityProblems="true"
DebugInformationFormat="4"
/>
<Tool
Name="VCManagedResourceCompilerTool"
/>
<Tool
Name="VCResourceCompilerTool"
/>
<Tool
Name="VCPreLinkEventTool"
/>
<Tool
Name="VCLibrarianTool"
OutputFile="$(OutDir)\simtkUtilities.lib"
/>
<Tool
Name="VCALinkTool"
/>
<Tool
Name="VCXDCMakeTool"
/>
<Tool
Name="VCBscMakeTool"
/>
<Tool
Name="VCFxCopTool"
/>
<Tool
Name="VCPostBuildEventTool"
/>
</Configuration>
<Configuration
Name="Release|Win32"
OutputDirectory="Release"
IntermediateDirectory="Release"
ConfigurationType="4"
>
<Tool
Name="VCPreBuildEventTool"
/>
<Tool
Name="VCCustomBuildTool"
/>
<Tool
Name="VCXMLDataGeneratorTool"
/>
<Tool
Name="VCWebServiceProxyGeneratorTool"
/>
<Tool
Name="VCMIDLTool"
/>
<Tool
Name="VCCLCompilerTool"
AdditionalIncludeDirectories="..\gromacs\include"
PreprocessorDefinitions="WIN32;NDEBUG;_LIB;"
RuntimeLibrary="0"
UsePrecompiledHeader="0"
WarningLevel="3"
Detect64BitPortabilityProblems="true"
DebugInformationFormat="3"
/>
<Tool
Name="VCManagedResourceCompilerTool"
/>
<Tool
Name="VCResourceCompilerTool"
/>
<Tool
Name="VCPreLinkEventTool"
/>
<Tool
Name="VCLibrarianTool"
OutputFile="$(OutDir)\simtkUtilities.lib"
/>
<Tool
Name="VCALinkTool"
/>
<Tool
Name="VCXDCMakeTool"
/>
<Tool
Name="VCBscMakeTool"
/>
<Tool
Name="VCFxCopTool"
/>
<Tool
Name="VCPostBuildEventTool"
/>
</Configuration>
<Configuration
Name="Debug_FAHCORE|Win32"
OutputDirectory="$(ConfigurationName)"
IntermediateDirectory="$(ConfigurationName)"
ConfigurationType="4"
>
<Tool
Name="VCPreBuildEventTool"
/>
<Tool
Name="VCCustomBuildTool"
/>
<Tool
Name="VCXMLDataGeneratorTool"
/>
<Tool
Name="VCWebServiceProxyGeneratorTool"
/>
<Tool
Name="VCMIDLTool"
/>
<Tool
Name="VCCLCompilerTool"
Optimization="0"
AdditionalIncludeDirectories="..\gromacs\include"
PreprocessorDefinitions="WIN32;_DEBUG;_LIB;"
MinimalRebuild="true"
BasicRuntimeChecks="3"
RuntimeLibrary="3"
UsePrecompiledHeader="0"
WarningLevel="3"
Detect64BitPortabilityProblems="true"
DebugInformationFormat="4"
/>
<Tool
Name="VCManagedResourceCompilerTool"
/>
<Tool
Name="VCResourceCompilerTool"
/>
<Tool
Name="VCPreLinkEventTool"
/>
<Tool
Name="VCLibrarianTool"
OutputFile="$(OutDir)/simtkUtilities.lib"
/>
<Tool
Name="VCALinkTool"
/>
<Tool
Name="VCXDCMakeTool"
/>
<Tool
Name="VCBscMakeTool"
/>
<Tool
Name="VCFxCopTool"
/>
<Tool
Name="VCPostBuildEventTool"
/>
</Configuration>
<Configuration
Name="Release_FAHCORE|Win32"
OutputDirectory="$(ConfigurationName)"
IntermediateDirectory="$(ConfigurationName)"
ConfigurationType="4"
>
<Tool
Name="VCPreBuildEventTool"
/>
<Tool
Name="VCCustomBuildTool"
/>
<Tool
Name="VCXMLDataGeneratorTool"
/>
<Tool
Name="VCWebServiceProxyGeneratorTool"
/>
<Tool
Name="VCMIDLTool"
/>
<Tool
Name="VCCLCompilerTool"
Optimization="0"
AdditionalIncludeDirectories="..\gromacs\include;../../corewrap"
PreprocessorDefinitions="WIN32;_LIB;FULLINDIRECT"
MinimalRebuild="true"
BasicRuntimeChecks="3"
RuntimeLibrary="0"
UsePrecompiledHeader="0"
WarningLevel="3"
Detect64BitPortabilityProblems="true"
DebugInformationFormat="4"
ForcedIncludeFiles="swindirect.h"
/>
<Tool
Name="VCManagedResourceCompilerTool"
/>
<Tool
Name="VCResourceCompilerTool"
/>
<Tool
Name="VCPreLinkEventTool"
/>
<Tool
Name="VCLibrarianTool"
OutputFile="$(OutDir)/simtkUtilities.lib"
/>
<Tool
Name="VCALinkTool"
/>
<Tool
Name="VCXDCMakeTool"
/>
<Tool
Name="VCBscMakeTool"
/>
<Tool
Name="VCFxCopTool"
/>
<Tool
Name="VCPostBuildEventTool"
/>
</Configuration>
<Configuration
Name="DebugNoGPU_FAH|Win32"
OutputDirectory="$(ConfigurationName)"
IntermediateDirectory="$(ConfigurationName)"
ConfigurationType="4"
>
<Tool
Name="VCPreBuildEventTool"
/>
<Tool
Name="VCCustomBuildTool"
/>
<Tool
Name="VCXMLDataGeneratorTool"
/>
<Tool
Name="VCWebServiceProxyGeneratorTool"
/>
<Tool
Name="VCMIDLTool"
/>
<Tool
Name="VCCLCompilerTool"
Optimization="0"
AdditionalIncludeDirectories="..\gromacs\include"
PreprocessorDefinitions="WIN32;_DEBUG;_LIB;NoGPU"
MinimalRebuild="true"
BasicRuntimeChecks="3"
RuntimeLibrary="3"
UsePrecompiledHeader="0"
WarningLevel="3"
Detect64BitPortabilityProblems="true"
DebugInformationFormat="4"
/>
<Tool
Name="VCManagedResourceCompilerTool"
/>
<Tool
Name="VCResourceCompilerTool"
/>
<Tool
Name="VCPreLinkEventTool"
/>
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platforms/reference/src/SimTKUtilities/SimTk.vcproj deleted 100644 → 0
View file @ c87cee06
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