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Commit 7fb10336 authored by peastman's avatar peastman
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Cleaned up lots of formatting to be more consistent with the rest of OpenMM

parent 1d3ffd7b
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Showing with 605 additions and 606 deletions
platforms/reference/src/SimTKReference/ReferenceStochasticDynamics.cpp
View file @ 7fb10336
......@@ -47,10 +47,10 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */
ReferenceStochasticDynamics::ReferenceStochasticDynamics( int numberOfAtoms,
RealOpenMM deltaT, RealOpenMM tau,
RealOpenMM temperature ) :
ReferenceDynamics( numberOfAtoms, deltaT, temperature ), _tau( tau ) {
ReferenceStochasticDynamics::ReferenceStochasticDynamics(int numberOfAtoms,
RealOpenMM deltaT, RealOpenMM tau,
RealOpenMM temperature) :
ReferenceDynamics(numberOfAtoms, deltaT, temperature), _tau(tau) {
if (tau <= 0) {
std::stringstream message;
message << "illegal tau value: " << tau;
......@@ -66,7 +66,7 @@ ReferenceStochasticDynamics::ReferenceStochasticDynamics( int numberOfAtoms,
--------------------------------------------------------------------------------------- */
ReferenceStochasticDynamics::~ReferenceStochasticDynamics( ){
ReferenceStochasticDynamics::~ReferenceStochasticDynamics() {
// ---------------------------------------------------------------------------------------
......@@ -84,7 +84,7 @@ ReferenceStochasticDynamics::~ReferenceStochasticDynamics( ){
--------------------------------------------------------------------------------------- */
RealOpenMM ReferenceStochasticDynamics::getTau( void ) const {
RealOpenMM ReferenceStochasticDynamics::getTau() const {
// ---------------------------------------------------------------------------------------
......@@ -108,10 +108,10 @@ RealOpenMM ReferenceStochasticDynamics::getTau( void ) const {
--------------------------------------------------------------------------------------- */
void ReferenceStochasticDynamics::updatePart1( int numberOfAtoms, vector<RealVec>& atomCoordinates,
void ReferenceStochasticDynamics::updatePart1(int numberOfAtoms, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities,
vector<RealVec>& forces, vector<RealOpenMM>& inverseMasses,
vector<RealVec>& xPrime ){
vector<RealVec>& xPrime) {
// ---------------------------------------------------------------------------------------
......@@ -149,10 +149,10 @@ void ReferenceStochasticDynamics::updatePart1( int numberOfAtoms, vector<RealVec
--------------------------------------------------------------------------------------- */
void ReferenceStochasticDynamics::updatePart2( int numberOfAtoms, vector<RealVec>& atomCoordinates,
void ReferenceStochasticDynamics::updatePart2(int numberOfAtoms, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities,
vector<RealVec>& forces, vector<RealOpenMM>& inverseMasses,
vector<RealVec>& xPrime ){
vector<RealVec>& xPrime) {
// ---------------------------------------------------------------------------------------
......@@ -197,10 +197,10 @@ void ReferenceStochasticDynamics::update(const OpenMM::System& system, vector<Re
// first-time-through initialization
int numberOfAtoms = system.getNumParticles();
if( getTimeStep() == 0 ){
if (getTimeStep() == 0) {
// invert masses
for( int ii = 0; ii < numberOfAtoms; ii++ ){
for (int ii = 0; ii < numberOfAtoms; ii++) {
if (masses[ii] == zero)
inverseMasses[ii] = zero;
else
......@@ -210,11 +210,11 @@ void ReferenceStochasticDynamics::update(const OpenMM::System& system, vector<Re
// 1st update
updatePart1( numberOfAtoms, atomCoordinates, velocities, forces, inverseMasses, xPrime );
updatePart1(numberOfAtoms, atomCoordinates, velocities, forces, inverseMasses, xPrime);
// 2nd update
updatePart2( numberOfAtoms, atomCoordinates, velocities, forces, inverseMasses, xPrime );
updatePart2(numberOfAtoms, atomCoordinates, velocities, forces, inverseMasses, xPrime);
ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
if (referenceConstraintAlgorithm)
......
platforms/reference/src/SimTKReference/ReferenceVariableStochasticDynamics.cpp
View file @ 7fb10336
......@@ -49,9 +49,9 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */
ReferenceVariableStochasticDynamics::ReferenceVariableStochasticDynamics( int numberOfAtoms,
ReferenceVariableStochasticDynamics::ReferenceVariableStochasticDynamics(int numberOfAtoms,
RealOpenMM tau, RealOpenMM temperature,
RealOpenMM accuracy ) :
RealOpenMM accuracy) :
ReferenceDynamics(numberOfAtoms, 0.0f, temperature), _tau(tau), _accuracy(accuracy) {
if (tau <= 0) {
std::stringstream message;
......@@ -68,7 +68,7 @@ ReferenceVariableStochasticDynamics::ReferenceVariableStochasticDynamics( int nu
--------------------------------------------------------------------------------------- */
ReferenceVariableStochasticDynamics::~ReferenceVariableStochasticDynamics( ){
ReferenceVariableStochasticDynamics::~ReferenceVariableStochasticDynamics() {
// ---------------------------------------------------------------------------------------
......@@ -86,7 +86,7 @@ ReferenceVariableStochasticDynamics::~ReferenceVariableStochasticDynamics( ){
--------------------------------------------------------------------------------------- */
RealOpenMM ReferenceVariableStochasticDynamics::getAccuracy( void ) const {
RealOpenMM ReferenceVariableStochasticDynamics::getAccuracy() const {
return _accuracy;
}
......@@ -96,7 +96,7 @@ RealOpenMM ReferenceVariableStochasticDynamics::getAccuracy( void ) const {
--------------------------------------------------------------------------------------- */
void ReferenceVariableStochasticDynamics::setAccuracy( RealOpenMM accuracy ) {
void ReferenceVariableStochasticDynamics::setAccuracy(RealOpenMM accuracy) {
_accuracy = accuracy;
}
......@@ -108,7 +108,7 @@ void ReferenceVariableStochasticDynamics::setAccuracy( RealOpenMM accuracy ) {
--------------------------------------------------------------------------------------- */
RealOpenMM ReferenceVariableStochasticDynamics::getTau( void ) const {
RealOpenMM ReferenceVariableStochasticDynamics::getTau() const {
// ---------------------------------------------------------------------------------------
......@@ -134,10 +134,10 @@ RealOpenMM ReferenceVariableStochasticDynamics::getTau( void ) const {
--------------------------------------------------------------------------------------- */
void ReferenceVariableStochasticDynamics::updatePart1( int numberOfAtoms, vector<RealVec>& atomCoordinates,
void ReferenceVariableStochasticDynamics::updatePart1(int numberOfAtoms, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities,
vector<RealVec>& forces, vector<RealOpenMM>& masses, vector<RealOpenMM>& inverseMasses,
vector<RealVec>& xPrime, RealOpenMM maxStepSize ){
vector<RealVec>& xPrime, RealOpenMM maxStepSize) {
// ---------------------------------------------------------------------------------------
......@@ -148,10 +148,10 @@ void ReferenceVariableStochasticDynamics::updatePart1( int numberOfAtoms, vector
// first-time-through initialization
if( getTimeStep() == 0 ){
if (getTimeStep() == 0) {
// invert masses
for( int ii = 0; ii < numberOfAtoms; ii++ ){
for (int ii = 0; ii < numberOfAtoms; ii++) {
if (masses[ii] == 0)
inverseMasses[ii] = 0;
else
......@@ -208,10 +208,10 @@ void ReferenceVariableStochasticDynamics::updatePart1( int numberOfAtoms, vector
--------------------------------------------------------------------------------------- */
void ReferenceVariableStochasticDynamics::updatePart2( int numberOfAtoms, vector<RealVec>& atomCoordinates,
void ReferenceVariableStochasticDynamics::updatePart2(int numberOfAtoms, vector<RealVec>& atomCoordinates,
vector<RealVec>& velocities,
vector<RealVec>& forces, vector<RealOpenMM>& inverseMasses,
vector<RealVec>& xPrime ){
vector<RealVec>& xPrime) {
// ---------------------------------------------------------------------------------------
......@@ -255,11 +255,11 @@ void ReferenceVariableStochasticDynamics::update(const OpenMM::System& system, v
// 1st update
int numberOfAtoms = system.getNumParticles();
updatePart1( numberOfAtoms, atomCoordinates, velocities, forces, masses, inverseMasses, xPrime, maxStepSize );
updatePart1(numberOfAtoms, atomCoordinates, velocities, forces, masses, inverseMasses, xPrime, maxStepSize);
// 2nd update
updatePart2( numberOfAtoms, atomCoordinates, velocities, forces, inverseMasses, xPrime );
updatePart2(numberOfAtoms, atomCoordinates, velocities, forces, inverseMasses, xPrime);
ReferenceConstraintAlgorithm* referenceConstraintAlgorithm = getReferenceConstraintAlgorithm();
if (referenceConstraintAlgorithm)
......@@ -267,7 +267,7 @@ void ReferenceVariableStochasticDynamics::update(const OpenMM::System& system, v
// copy xPrime -> atomCoordinates
for( int ii = 0; ii < numberOfAtoms; ii++ ) {
for (int ii = 0; ii < numberOfAtoms; ii++) {
if (masses[ii] != 0.0) {
atomCoordinates[ii][0] = xPrime[ii][0];
atomCoordinates[ii][1] = xPrime[ii][1];
......
platforms/reference/src/SimTKReference/ReferenceVariableVerletDynamics.cpp
View file @ 7fb10336
......@@ -44,8 +44,8 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */
ReferenceVariableVerletDynamics::ReferenceVariableVerletDynamics( int numberOfAtoms, RealOpenMM accuracy ) :
ReferenceDynamics( numberOfAtoms, 0.0f, 0.0f ), _accuracy(accuracy) {
ReferenceVariableVerletDynamics::ReferenceVariableVerletDynamics(int numberOfAtoms, RealOpenMM accuracy) :
ReferenceDynamics(numberOfAtoms, 0.0f, 0.0f), _accuracy(accuracy) {
xPrime.resize(numberOfAtoms);
inverseMasses.resize(numberOfAtoms);
}
......@@ -56,7 +56,7 @@ ReferenceVariableVerletDynamics::ReferenceVariableVerletDynamics( int numberOfAt
--------------------------------------------------------------------------------------- */
ReferenceVariableVerletDynamics::~ReferenceVariableVerletDynamics( ){
ReferenceVariableVerletDynamics::~ReferenceVariableVerletDynamics() {
// ---------------------------------------------------------------------------------------
......@@ -74,7 +74,7 @@ ReferenceVariableVerletDynamics::~ReferenceVariableVerletDynamics( ){
--------------------------------------------------------------------------------------- */
RealOpenMM ReferenceVariableVerletDynamics::getAccuracy( void ) const {
RealOpenMM ReferenceVariableVerletDynamics::getAccuracy() const {
return _accuracy;
}
......@@ -84,7 +84,7 @@ RealOpenMM ReferenceVariableVerletDynamics::getAccuracy( void ) const {
--------------------------------------------------------------------------------------- */
void ReferenceVariableVerletDynamics::setAccuracy( RealOpenMM accuracy ) {
void ReferenceVariableVerletDynamics::setAccuracy(RealOpenMM accuracy) {
_accuracy = accuracy;
}
......@@ -118,10 +118,10 @@ void ReferenceVariableVerletDynamics::update(const OpenMM::System& system, vecto
// first-time-through initialization
int numberOfAtoms = system.getNumParticles();
if( getTimeStep() == 0 ){
if (getTimeStep() == 0) {
// invert masses
for( int ii = 0; ii < numberOfAtoms; ii++ ){
for (int ii = 0; ii < numberOfAtoms; ii++) {
if (masses[ii] == zero)
inverseMasses[ii] = zero;
else
......
platforms/reference/src/SimTKReference/ReferenceVerletDynamics.cpp
View file @ 7fb10336
......@@ -46,9 +46,8 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */
ReferenceVerletDynamics::ReferenceVerletDynamics( int numberOfAtoms,
RealOpenMM deltaT ) :
ReferenceDynamics( numberOfAtoms, deltaT, 0.0 ) {
ReferenceVerletDynamics::ReferenceVerletDynamics(int numberOfAtoms, RealOpenMM deltaT) :
ReferenceDynamics(numberOfAtoms, deltaT, 0.0) {
// ---------------------------------------------------------------------------------------
......@@ -69,7 +68,7 @@ ReferenceVerletDynamics::ReferenceVerletDynamics( int numberOfAtoms,
--------------------------------------------------------------------------------------- */
ReferenceVerletDynamics::~ReferenceVerletDynamics( ){
ReferenceVerletDynamics::~ReferenceVerletDynamics() {
// ---------------------------------------------------------------------------------------
......@@ -108,10 +107,10 @@ void ReferenceVerletDynamics::update(const OpenMM::System& system, vector<RealVe
// first-time-through initialization
int numberOfAtoms = system.getNumParticles();
if( getTimeStep() == 0 ){
if (getTimeStep() == 0) {
// invert masses
for( int ii = 0; ii < numberOfAtoms; ii++ ){
for (int ii = 0; ii < numberOfAtoms; ii++) {
if (masses[ii] == zero)
inverseMasses[ii] = zero;
else
......@@ -134,7 +133,7 @@ void ReferenceVerletDynamics::update(const OpenMM::System& system, vector<RealVe
// Update the positions and velocities.
RealOpenMM velocityScale = static_cast<RealOpenMM>( 1.0/getDeltaT() );
RealOpenMM velocityScale = static_cast<RealOpenMM>(1.0/getDeltaT());
for (int i = 0; i < numberOfAtoms; ++i) {
if (masses[i] != zero)
for (int j = 0; j < 3; ++j) {
......
platforms/reference/src/SimTKReference/fftpack.cpp
View file @ 7fb10336
......@@ -672,16 +672,16 @@ fftpack_transpose_2d(t_complex * in_data,
t_complex * src;
int i,j;
if(nx<2 || ny<2)
if (nx<2 || ny<2)
{
if(in_data != out_data)
if (in_data != out_data)
{
memcpy(out_data,in_data,sizeof(t_complex)*nx*ny);
}
return 0;
}
if(in_data == out_data)
if (in_data == out_data)
{
src = (t_complex *)malloc(sizeof(t_complex)*nx*ny);
memcpy(src,in_data,sizeof(t_complex)*nx*ny);
......@@ -691,16 +691,16 @@ fftpack_transpose_2d(t_complex * in_data,
src = in_data;
}
for(i=0;i<nx;i++)
for (i=0;i<nx;i++)
{
for(j=0;j<ny;j++)
for (j=0;j<ny;j++)
{
out_data[j*nx+i].re = src[i*ny+j].re;
out_data[j*nx+i].im = src[i*ny+j].im;
}
}
if(src != in_data)
if (src != in_data)
{
free(src);
}
......@@ -722,16 +722,16 @@ fftpack_transpose_2d_nelem(t_complex * in_data,
ncopy = nelem*sizeof(t_complex);
if(nx<2 || ny<2)
if (nx<2 || ny<2)
{
if(in_data != out_data)
if (in_data != out_data)
{
memcpy(out_data,in_data,nx*ny*ncopy);
}
return 0;
}
if(in_data == out_data)
if (in_data == out_data)
{
src = (t_complex *)malloc(nx*ny*ncopy);
memcpy(src,in_data,nx*ny*ncopy);
......@@ -741,15 +741,15 @@ fftpack_transpose_2d_nelem(t_complex * in_data,
src = in_data;
}
for(i=0;i<nx;i++)
for (i=0;i<nx;i++)
{
for(j=0;j<ny;j++)
for (j=0;j<ny;j++)
{
memcpy(out_data + (j*nx+i)*nelem , src + (i*ny+j)*nelem , ncopy);
}
}
if(src != in_data)
if (src != in_data)
{
free(src);
}
......@@ -767,14 +767,14 @@ fftpack_init_1d(fftpack_t * pfft,
{
fftpack_t fft;
if(pfft==NULL)
if (pfft==NULL)
{
fprintf(stderr,"Fatal error - Invalid FFT opaque type pointer.");
return EINVAL;
}
*pfft = NULL;
if( (fft = (struct fftpack *)malloc(sizeof(struct fftpack))) == NULL)
if ((fft = (struct fftpack *)malloc(sizeof(struct fftpack))) == NULL)
{
return ENOMEM;
}
......@@ -783,13 +783,13 @@ fftpack_init_1d(fftpack_t * pfft,
fft->n = nx;
/* Need 4*n storage for 1D complex FFT */
if( (fft->work = (RealOpenMM *)malloc(sizeof(RealOpenMM)*(4*nx))) == NULL)
if ((fft->work = (RealOpenMM *)malloc(sizeof(RealOpenMM)*(4*nx))) == NULL)
{
free(fft);
return ENOMEM;
}
if(fft->n>1)
if (fft->n>1)
fftpack_cffti1(nx,fft->work,fft->ifac);
*pfft = fft;
......@@ -807,7 +807,7 @@ fftpack_init_2d(fftpack_t * pfft,
fftpack_t fft;
int rc;
if(pfft==NULL)
if (pfft==NULL)
{
fprintf(stderr,"Fatal error - Invalid FFT opaque type pointer.");
return EINVAL;
......@@ -815,13 +815,13 @@ fftpack_init_2d(fftpack_t * pfft,
*pfft = NULL;
/* Create the X transform */
if( (rc = fftpack_init_1d(&fft,nx)) != 0)
if ((rc = fftpack_init_1d(&fft,nx)) != 0)
{
return rc;
}
/* Create Y transform as a link from X */
if( (rc=fftpack_init_1d(&(fft->next),ny)) != 0)
if ((rc=fftpack_init_1d(&(fft->next),ny)) != 0)
{
free(fft);
return rc;
......@@ -842,7 +842,7 @@ fftpack_init_3d(fftpack_t * pfft,
fftpack_t fft;
int rc;
if(pfft==NULL)
if (pfft==NULL)
{
fprintf(stderr,"Fatal error - Invalid FFT opaque type pointer.");
return EINVAL;
......@@ -851,7 +851,7 @@ fftpack_init_3d(fftpack_t * pfft,
/* Create the X transform */
if( (fft = (struct fftpack *)malloc(sizeof(struct fftpack))) == NULL)
if ((fft = (struct fftpack *)malloc(sizeof(struct fftpack))) == NULL)
{
return ENOMEM;
}
......@@ -860,7 +860,7 @@ fftpack_init_3d(fftpack_t * pfft,
/* Need 4*nx storage for 1D complex FFT.
*/
if( (fft->work = (RealOpenMM *)malloc(sizeof(RealOpenMM)*(4*nx))) == NULL)
if ((fft->work = (RealOpenMM *)malloc(sizeof(RealOpenMM)*(4*nx))) == NULL)
{
free(fft);
return ENOMEM;
......@@ -869,7 +869,7 @@ fftpack_init_3d(fftpack_t * pfft,
fftpack_cffti1(nx,fft->work,fft->ifac);
/* Create 2D Y/Z transforms as a link from X */
if( (rc=fftpack_init_2d(&(fft->next),ny,nz)) != 0)
if ((rc=fftpack_init_2d(&(fft->next),ny,nz)) != 0)
{
free(fft);
return rc;
......@@ -893,7 +893,7 @@ fftpack_exec_1d (fftpack_t fft,
n=fft->n;
if(n==1)
if (n==1)
{
p1 = (RealOpenMM *)in_data;
p2 = (RealOpenMM *)out_data;
......@@ -904,13 +904,13 @@ fftpack_exec_1d (fftpack_t fft,
/* FFTPACK only does in-place transforms, so emulate out-of-place
* by copying data to the output array first.
*/
if( in_data != out_data )
if (in_data != out_data)
{
p1 = (RealOpenMM *)in_data;
p2 = (RealOpenMM *)out_data;
/* n complex = 2*n RealOpenMM elements */
for(i=0;i<2*n;i++)
for (i=0;i<2*n;i++)
{
p2[i] = p1[i];
}
......@@ -920,11 +920,11 @@ fftpack_exec_1d (fftpack_t fft,
* Elements 2*n .. 4*n-1 are internal FFTPACK work space.
*/
if(dir == FFTPACK_FORWARD)
if (dir == FFTPACK_FORWARD)
{
fftpack_cfftf1(n,(RealOpenMM *)out_data,fft->work+2*n,fft->work,fft->ifac, -1);
}
else if(dir == FFTPACK_BACKWARD)
else if (dir == FFTPACK_BACKWARD)
{
fftpack_cfftf1(n,(RealOpenMM *)out_data,fft->work+2*n,fft->work,fft->ifac, 1);
}
......@@ -957,7 +957,7 @@ fftpack_exec_2d (fftpack_t fft,
* by copying data to the output array first.
* For 2D there is likely enough data to benefit from memcpy().
*/
if( in_data != out_data )
if (in_data != out_data)
{
memcpy(out_data,in_data,sizeof(t_complex)*nx*ny);
}
......@@ -966,7 +966,7 @@ fftpack_exec_2d (fftpack_t fft,
data = (t_complex *)out_data;
/* y transforms */
for(i=0;i<nx;i++)
for (i=0;i<nx;i++)
{
fftpack_exec_1d(fft->next,dir,data+i*ny,data+i*ny);
}
......@@ -975,7 +975,7 @@ fftpack_exec_2d (fftpack_t fft,
fftpack_transpose_2d(data,data,nx,ny);
/* x transforms */
for(i=0;i<ny;i++)
for (i=0;i<ny;i++)
{
fftpack_exec_1d(fft,dir,data+i*nx,data+i*nx);
}
......@@ -1007,7 +1007,7 @@ fftpack_exec_3d (fftpack_t fft,
* by copying data to the output array first.
* For 3D there is likely enough data to benefit from memcpy().
*/
if( in_data != out_data )
if (in_data != out_data)
{
memcpy(out_data,in_data,sizeof(t_complex)*nx*ny*nz);
}
......@@ -1016,23 +1016,23 @@ fftpack_exec_3d (fftpack_t fft,
data = (t_complex *)out_data;
/* Perform z transforms */
for(i=0;i<nx*ny;i++)
for (i=0;i<nx*ny;i++)
fftpack_exec_1d(fft->next->next,dir,data+i*nz,data+i*nz);
/* For each X slice, transpose the y & z dimensions inside the slice */
for(i=0;i<nx;i++)
for (i=0;i<nx;i++)
{
fftpack_transpose_2d(data+i*ny*nz,data+i*ny*nz,ny,nz);
}
/* Array is now (nx,nz,ny) - perform y transforms */
for(i=0;i<nx*nz;i++)
for (i=0;i<nx*nz;i++)
{
fftpack_exec_1d(fft->next,dir,data+i*ny,data+i*ny);
}
/* Transpose back to (nx,ny,nz) */
for(i=0;i<nx;i++)
for (i=0;i<nx;i++)
{
fftpack_transpose_2d(data+i*ny*nz,data+i*ny*nz,nz,ny);
}
......@@ -1041,26 +1041,26 @@ fftpack_exec_3d (fftpack_t fft,
* (nx,ny,nz) to (ny,nx,nz).
*/
rc=fftpack_transpose_2d_nelem(data,data,nx,ny,nz);
if( rc != 0)
if (rc != 0)
{
fprintf(stderr,"Fatal error - cannot transpose X & Y/Z in fftpack_exec_3d().");
return rc;
}
/* Then go from (ny,nx,nz) to (ny,nz,nx) */
for(i=0;i<ny;i++)
for (i=0;i<ny;i++)
{
fftpack_transpose_2d(data+i*nx*nz,data+i*nx*nz,nx,nz);
}
/* Perform x transforms */
for(i=0;i<ny*nz;i++)
for (i=0;i<ny*nz;i++)
{
fftpack_exec_1d(fft,dir,data+i*nx,data+i*nx);
}
/* Transpose back from (ny,nz,nx) to (ny,nx,nz) */
for(i=0;i<ny;i++)
for (i=0;i<ny;i++)
{
fftpack_transpose_2d(data+i*nz*nx,data+i*nz*nx,nz,nx);
}
......@@ -1068,7 +1068,7 @@ fftpack_exec_3d (fftpack_t fft,
/* Transpose from (ny,nx,nz) to (nx,ny,nz).
*/
rc = fftpack_transpose_2d_nelem(data,data,ny,nx,nz);
if( rc != 0)
if (rc != 0)
{
fprintf(stderr,"Fatal error - cannot transpose Y/Z & X in fftpack_exec_3d().");
return rc;
......@@ -1082,10 +1082,10 @@ fftpack_exec_3d (fftpack_t fft,
void
fftpack_destroy(fftpack_t fft)
{
if(fft != NULL)
if (fft != NULL)
{
free(fft->work);
if(fft->next != NULL)
if (fft->next != NULL)
fftpack_destroy(fft->next);
free(fft);
}
......
platforms/reference/src/SimTKUtilities/SimTKOpenMMCommon.cpp
View file @ 7fb10336
......@@ -30,9 +30,9 @@ using namespace OpenMM;
// initialization of static data members
const std::string SimTKOpenMMCommon::NotSet = std::string( "NotSet" );
const std::string SimTKOpenMMCommon::Comment = std::string( "#" );
const std::string SimTKOpenMMCommon::Tab = std::string( "\t" );
const std::string SimTKOpenMMCommon::NotSet = std::string("NotSet");
const std::string SimTKOpenMMCommon::Comment = std::string("#");
const std::string SimTKOpenMMCommon::Tab = std::string("\t");
const int SimTKOpenMMCommon::DefaultReturn = 0;
const int SimTKOpenMMCommon::ErrorReturn = -1;
......
platforms/reference/src/SimTKUtilities/SimTKOpenMMUtilities.cpp
View file @ 7fb10336
......@@ -59,9 +59,9 @@ OpenMM_SFMT::SFMT SimTKOpenMMUtilities::sfmt;
--------------------------------------------------------------------------------------- */
RealOpenMM* SimTKOpenMMUtilities::allocateOneDRealOpenMMArray( int iSize, RealOpenMM* array1D,
int initialize, RealOpenMM initialValue,
const std::string& idString ){
RealOpenMM* SimTKOpenMMUtilities::allocateOneDRealOpenMMArray(int iSize, RealOpenMM* array1D,
int initialize, RealOpenMM initialValue,
const std::string& idString) {
// ---------------------------------------------------------------------------------------
......@@ -71,17 +71,17 @@ RealOpenMM* SimTKOpenMMUtilities::allocateOneDRealOpenMMArray( int iSize, RealOp
// ---------------------------------------------------------------------------------------
if( array1D == NULL ){
if (array1D == NULL) {
array1D = new RealOpenMM[iSize];
}
if( initialize ){
if( initialValue == zero ){
memset( array1D, 0, iSize*sizeof( RealOpenMM ) );
if (initialize) {
if (initialValue == zero) {
memset(array1D, 0, iSize*sizeof(RealOpenMM));
} else {
for( int ii = 0; ii < iSize; ii++ ){
for (int ii = 0; ii < iSize; ii++) {
array1D[ii] = initialValue;
}
}
......@@ -107,9 +107,9 @@ RealOpenMM* SimTKOpenMMUtilities::allocateOneDRealOpenMMArray( int iSize, RealOp
--------------------------------------------------------------------------------------- */
RealOpenMM** SimTKOpenMMUtilities::allocateTwoDRealOpenMMArray( int iSize, int jSize, RealOpenMM** array2D,
int initialize, RealOpenMM initialValue,
const std::string& idString ){
RealOpenMM** SimTKOpenMMUtilities::allocateTwoDRealOpenMMArray(int iSize, int jSize, RealOpenMM** array2D,
int initialize, RealOpenMM initialValue,
const std::string& idString) {
// ---------------------------------------------------------------------------------------
......@@ -117,22 +117,22 @@ RealOpenMM** SimTKOpenMMUtilities::allocateTwoDRealOpenMMArray( int iSize, int j
// ---------------------------------------------------------------------------------------
if( array2D == NULL ){
if (array2D == NULL) {
array2D = new RealOpenMM*[iSize];
std::string blockString = idString;
blockString.append( "Block" );
blockString.append("Block");
RealOpenMM* block = new RealOpenMM[jSize*iSize];
for( int ii = 0; ii < iSize; ii++ ){
for (int ii = 0; ii < iSize; ii++) {
array2D[ii] = block;
block += jSize;
}
}
if( initialize ){
initialize2DRealOpenMMArray( iSize, jSize, array2D, initialValue );
if (initialize) {
initialize2DRealOpenMMArray(iSize, jSize, array2D, initialValue);
}
return array2D;
......@@ -149,7 +149,7 @@ RealOpenMM** SimTKOpenMMUtilities::allocateTwoDRealOpenMMArray( int iSize, int j
--------------------------------------------------------------------------------------- */
void SimTKOpenMMUtilities::freeTwoDRealOpenMMArray( RealOpenMM** array2D, const std::string& idString ){
void SimTKOpenMMUtilities::freeTwoDRealOpenMMArray(RealOpenMM** array2D, const std::string& idString) {
// ---------------------------------------------------------------------------------------
......@@ -157,10 +157,10 @@ void SimTKOpenMMUtilities::freeTwoDRealOpenMMArray( RealOpenMM** array2D, const
// ---------------------------------------------------------------------------------------
if( array2D != NULL ){
if (array2D != NULL) {
std::string blockString = idString;
blockString.append( "Block" );
blockString.append("Block");
delete[] array2D[0];
delete[] array2D;
......@@ -178,7 +178,7 @@ void SimTKOpenMMUtilities::freeTwoDRealOpenMMArray( RealOpenMM** array2D, const
--------------------------------------------------------------------------------------- */
void SimTKOpenMMUtilities::freeOneDRealOpenMMArray( RealOpenMM* array1D, const std::string& idString ){
void SimTKOpenMMUtilities::freeOneDRealOpenMMArray(RealOpenMM* array1D, const std::string& idString) {
// ---------------------------------------------------------------------------------------
......@@ -186,7 +186,7 @@ void SimTKOpenMMUtilities::freeOneDRealOpenMMArray( RealOpenMM* array1D, const s
// ---------------------------------------------------------------------------------------
if( array1D != NULL ){
if (array1D != NULL) {
delete[] array1D;
}
}
......@@ -204,9 +204,9 @@ void SimTKOpenMMUtilities::freeOneDRealOpenMMArray( RealOpenMM* array1D, const s
--------------------------------------------------------------------------------------- */
void SimTKOpenMMUtilities::initialize2DRealOpenMMArray( int iSize, int jSize,
void SimTKOpenMMUtilities::initialize2DRealOpenMMArray(int iSize, int jSize,
RealOpenMM** array2D,
RealOpenMM initialValue ){
RealOpenMM initialValue) {
// ---------------------------------------------------------------------------------------
......@@ -217,9 +217,9 @@ void SimTKOpenMMUtilities::initialize2DRealOpenMMArray( int iSize, int jSize,
bool useMemset;
bool useMemsetSingleBlock;
if( initialValue == 0.0f ){
if (initialValue == 0.0f) {
useMemset = true;
if( jSize > 1 && (array2D[0] + jSize) == array2D[1] ){
if (jSize > 1 && (array2D[0] + jSize) == array2D[1]) {
useMemsetSingleBlock = true;
} else {
useMemsetSingleBlock = false;
......@@ -229,17 +229,17 @@ void SimTKOpenMMUtilities::initialize2DRealOpenMMArray( int iSize, int jSize,
useMemset = false;
}
if( useMemset ){
if( useMemsetSingleBlock ){
memset( array2D[0], 0, iSize*jSize*sizeof( RealOpenMM ) );
if (useMemset) {
if (useMemsetSingleBlock) {
memset(array2D[0], 0, iSize*jSize*sizeof(RealOpenMM));
} else {
for( int ii = 0; ii < iSize; ii++ ){
memset( array2D[ii], 0, jSize*sizeof( RealOpenMM ) );
for (int ii = 0; ii < iSize; ii++) {
memset(array2D[ii], 0, jSize*sizeof(RealOpenMM));
}
}
} else {
for( int ii = 0; ii < iSize; ii++ ){
for( int jj = 0; jj < jSize; jj++ ){
for (int ii = 0; ii < iSize; ii++) {
for (int jj = 0; jj < jSize; jj++) {
array2D[ii][jj] = initialValue;
}
}
......@@ -260,9 +260,9 @@ void SimTKOpenMMUtilities::initialize2DRealOpenMMArray( int iSize, int jSize,
--------------------------------------------------------------------------------------- */
void SimTKOpenMMUtilities::crossProductVector3( RealOpenMM* vectorX,
RealOpenMM* vectorY,
RealOpenMM* vectorZ ){
void SimTKOpenMMUtilities::crossProductVector3(RealOpenMM* vectorX,
RealOpenMM* vectorY,
RealOpenMM* vectorZ) {
// ---------------------------------------------------------------------------------------
......@@ -285,7 +285,7 @@ void SimTKOpenMMUtilities::crossProductVector3( RealOpenMM* vectorX,
--------------------------------------------------------------------------------------- */
RealOpenMM SimTKOpenMMUtilities::getNormallyDistributedRandomNumber( void ) {
RealOpenMM SimTKOpenMMUtilities::getNormallyDistributedRandomNumber() {
if (nextGaussianIsValid) {
nextGaussianIsValid = false;
return nextGaussian;
......@@ -304,7 +304,7 @@ RealOpenMM SimTKOpenMMUtilities::getNormallyDistributedRandomNumber( void ) {
y = static_cast<RealOpenMM>(2.0 * genrand_real2(sfmt) - 1.0);
r2 = x*x + y*y;
} while (r2 >= 1.0 || r2 == 0.0);
RealOpenMM multiplier = static_cast<RealOpenMM>( sqrt((-2.0*log(r2))/r2) );
RealOpenMM multiplier = static_cast<RealOpenMM>(sqrt((-2.0*log(r2))/r2));
nextGaussian = y*multiplier;
nextGaussianIsValid = true;
return x*multiplier;
......@@ -318,13 +318,13 @@ RealOpenMM SimTKOpenMMUtilities::getNormallyDistributedRandomNumber( void ) {
--------------------------------------------------------------------------------------- */
RealOpenMM SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber( void ) {
RealOpenMM SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber() {
if (!_randomInitialized) {
init_gen_rand(_randomNumberSeed, sfmt);
_randomInitialized = true;
nextGaussianIsValid = false;
}
RealOpenMM value = static_cast<RealOpenMM>( genrand_real2(sfmt) );
RealOpenMM value = static_cast<RealOpenMM>(genrand_real2(sfmt));
return value;
}
......@@ -336,7 +336,7 @@ RealOpenMM SimTKOpenMMUtilities::getUniformlyDistributedRandomNumber( void ) {
--------------------------------------------------------------------------------------- */
uint32_t SimTKOpenMMUtilities::getRandomNumberSeed( void ) {
uint32_t SimTKOpenMMUtilities::getRandomNumberSeed() {
// ---------------------------------------------------------------------------------------
......@@ -355,7 +355,7 @@ uint32_t SimTKOpenMMUtilities::getRandomNumberSeed( void ) {
--------------------------------------------------------------------------------------- */
void SimTKOpenMMUtilities::setRandomNumberSeed( uint32_t seed ) {
void SimTKOpenMMUtilities::setRandomNumberSeed(uint32_t seed) {
// ---------------------------------------------------------------------------------------
......
platforms/reference/src/gbsa/CpuGBVI.cpp
View file @ 7fb10336
......@@ -41,8 +41,8 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */
CpuGBVI::CpuGBVI( GBVIParameters* gbviParameters ) : _gbviParameters(gbviParameters) {
_switchDeriviative.resize( gbviParameters->getNumberOfAtoms() );
CpuGBVI::CpuGBVI(GBVIParameters* gbviParameters) : _gbviParameters(gbviParameters) {
_switchDeriviative.resize(gbviParameters->getNumberOfAtoms());
}
/**---------------------------------------------------------------------------------------
......@@ -51,7 +51,7 @@ CpuGBVI::CpuGBVI( GBVIParameters* gbviParameters ) : _gbviParameters(gbviParamet
--------------------------------------------------------------------------------------- */
CpuGBVI::~CpuGBVI( ){
CpuGBVI::~CpuGBVI() {
}
/**---------------------------------------------------------------------------------------
......@@ -62,7 +62,7 @@ CpuGBVI::~CpuGBVI( ){
--------------------------------------------------------------------------------------- */
GBVIParameters* CpuGBVI::getGBVIParameters( void ) const {
GBVIParameters* CpuGBVI::getGBVIParameters() const {
return _gbviParameters;
}
......@@ -74,7 +74,7 @@ GBVIParameters* CpuGBVI::getGBVIParameters( void ) const {
--------------------------------------------------------------------------------------- */
void CpuGBVI::setGBVIParameters( GBVIParameters* gbviParameters ){
void CpuGBVI::setGBVIParameters(GBVIParameters* gbviParameters) {
_gbviParameters = gbviParameters;
}
......@@ -86,7 +86,7 @@ void CpuGBVI::setGBVIParameters( GBVIParameters* gbviParameters ){
--------------------------------------------------------------------------------------- */
RealOpenMMVector& CpuGBVI::getSwitchDeriviative( void ){
RealOpenMMVector& CpuGBVI::getSwitchDeriviative() {
return _switchDeriviative;
}
......@@ -102,17 +102,17 @@ RealOpenMMVector& CpuGBVI::getSwitchDeriviative( void ){
--------------------------------------------------------------------------------------- */
void CpuGBVI::quinticSpline( RealOpenMM x, RealOpenMM rl, RealOpenMM ru,
RealOpenMM* outValue, RealOpenMM* outDerivative ){
void CpuGBVI::quinticSpline(RealOpenMM x, RealOpenMM rl, RealOpenMM ru,
RealOpenMM* outValue, RealOpenMM* outDerivative) {
// ---------------------------------------------------------------------------------------
static const RealOpenMM one = static_cast<RealOpenMM>( 1.0 );
static const RealOpenMM minusSix = static_cast<RealOpenMM>( -6.0 );
static const RealOpenMM minusTen = static_cast<RealOpenMM>( -10.0 );
static const RealOpenMM minusThirty = static_cast<RealOpenMM>( -30.0 );
static const RealOpenMM fifteen = static_cast<RealOpenMM>( 15.0 );
static const RealOpenMM sixty = static_cast<RealOpenMM>( 60.0 );
static const RealOpenMM one = static_cast<RealOpenMM>( 1.0);
static const RealOpenMM minusSix = static_cast<RealOpenMM>( -6.0);
static const RealOpenMM minusTen = static_cast<RealOpenMM>(-10.0);
static const RealOpenMM minusThirty = static_cast<RealOpenMM>(-30.0);
static const RealOpenMM fifteen = static_cast<RealOpenMM>( 15.0);
static const RealOpenMM sixty = static_cast<RealOpenMM>( 60.0);
// ---------------------------------------------------------------------------------------
......@@ -140,19 +140,19 @@ void CpuGBVI::quinticSpline( RealOpenMM x, RealOpenMM rl, RealOpenMM ru,
--------------------------------------------------------------------------------------- */
void CpuGBVI::computeBornRadiiUsingQuinticSpline( RealOpenMM atomicRadius3, RealOpenMM bornSum,
GBVIParameters* gbviParameters,
RealOpenMM* bornRadius, RealOpenMM* switchDeriviative ){
void CpuGBVI::computeBornRadiiUsingQuinticSpline(RealOpenMM atomicRadius3, RealOpenMM bornSum,
GBVIParameters* gbviParameters,
RealOpenMM* bornRadius, RealOpenMM* switchDeriviative) {
// ---------------------------------------------------------------------------------------
static const RealOpenMM zero = static_cast<RealOpenMM>( 0.0 );
static const RealOpenMM one = static_cast<RealOpenMM>( 1.0 );
static const RealOpenMM minusOne = static_cast<RealOpenMM>( -1.0 );
static const RealOpenMM minusThree = static_cast<RealOpenMM>( -3.0 );
static const RealOpenMM oneEighth = static_cast<RealOpenMM>( 0.125 );
static const RealOpenMM minusOneThird = static_cast<RealOpenMM>( (-1.0/3.0) );
static const RealOpenMM three = static_cast<RealOpenMM>( 3.0 );
static const RealOpenMM zero = static_cast<RealOpenMM>( 0.0);
static const RealOpenMM one = static_cast<RealOpenMM>( 1.0);
static const RealOpenMM minusOne = static_cast<RealOpenMM>(-1.0);
static const RealOpenMM minusThree = static_cast<RealOpenMM>(-3.0);
static const RealOpenMM oneEighth = static_cast<RealOpenMM>( 0.125);
static const RealOpenMM minusOneThird = static_cast<RealOpenMM>((-1.0/3.0));
static const RealOpenMM three = static_cast<RealOpenMM>( 3.0);
// ---------------------------------------------------------------------------------------
......@@ -176,10 +176,10 @@ void CpuGBVI::computeBornRadiiUsingQuinticSpline( RealOpenMM atomicRadius3, Real
RealOpenMM splineL = gbviParameters->getQuinticLowerLimitFactor()*atomicRadius3;
RealOpenMM sum;
if( bornSum > splineL ){
if( bornSum < atomicRadius3 ){
if (bornSum > splineL) {
if (bornSum < atomicRadius3) {
RealOpenMM splineValue, splineDerivative;
quinticSpline( bornSum, splineL, atomicRadius3, &splineValue, &splineDerivative );
quinticSpline(bornSum, splineL, atomicRadius3, &splineValue, &splineDerivative);
sum = (atomicRadius3 - bornSum)*splineValue + gbviParameters->getQuinticUpperBornRadiusLimit();
*switchDeriviative = splineValue - (atomicRadius3 - bornSum)*splineDerivative;
} else {
......@@ -190,7 +190,7 @@ void CpuGBVI::computeBornRadiiUsingQuinticSpline( RealOpenMM atomicRadius3, Real
sum = atomicRadius3 - bornSum;
*switchDeriviative = one;
}
*bornRadius = POW( sum, minusOneThird );
*bornRadius = POW(sum, minusOneThird);
}
/**---------------------------------------------------------------------------------------
......@@ -203,16 +203,16 @@ void CpuGBVI::computeBornRadiiUsingQuinticSpline( RealOpenMM atomicRadius3, Real
--------------------------------------------------------------------------------------- */
void CpuGBVI::computeBornRadii( const vector<RealVec>& atomCoordinates, RealOpenMMVector& bornRadii ){
void CpuGBVI::computeBornRadii(const vector<RealVec>& atomCoordinates, RealOpenMMVector& bornRadii) {
// ---------------------------------------------------------------------------------------
static const RealOpenMM zero = static_cast<RealOpenMM>( 0.0 );
static const RealOpenMM one = static_cast<RealOpenMM>( 1.0 );
static const RealOpenMM minusThree = static_cast<RealOpenMM>( -3.0 );
static const RealOpenMM oneEighth = static_cast<RealOpenMM>( 0.125 );
static const RealOpenMM minusOneThird = static_cast<RealOpenMM>( (-1.0/3.0) );
static const RealOpenMM three = static_cast<RealOpenMM>( 3.0 );
static const RealOpenMM zero = static_cast<RealOpenMM>(0.0);
static const RealOpenMM one = static_cast<RealOpenMM>(1.0);
static const RealOpenMM minusThree = static_cast<RealOpenMM>(-3.0);
static const RealOpenMM oneEighth = static_cast<RealOpenMM>(0.125);
static const RealOpenMM minusOneThird = static_cast<RealOpenMM>((-1.0/3.0));
static const RealOpenMM three = static_cast<RealOpenMM>(3.0);
// ---------------------------------------------------------------------------------------
......@@ -227,42 +227,42 @@ void CpuGBVI::computeBornRadii( const vector<RealVec>& atomCoordinates, RealOpen
// calculate Born radii
for( int atomI = 0; atomI < numberOfAtoms; atomI++ ){
for (int atomI = 0; atomI < numberOfAtoms; atomI++) {
RealOpenMM radiusI = atomicRadii[atomI];
RealOpenMM sum = zero;
// sum over volumes
for( int atomJ = 0; atomJ < numberOfAtoms; atomJ++ ){
for (int atomJ = 0; atomJ < numberOfAtoms; atomJ++) {
if( atomJ != atomI ){
if (atomJ != atomI) {
RealOpenMM deltaR[ReferenceForce::LastDeltaRIndex];
if (_gbviParameters->getPeriodic())
ReferenceForce::getDeltaRPeriodic( atomCoordinates[atomI], atomCoordinates[atomJ], _gbviParameters->getPeriodicBox(), deltaR );
ReferenceForce::getDeltaRPeriodic(atomCoordinates[atomI], atomCoordinates[atomJ], _gbviParameters->getPeriodicBox(), deltaR);
else
ReferenceForce::getDeltaR( atomCoordinates[atomI], atomCoordinates[atomJ], deltaR );
ReferenceForce::getDeltaR(atomCoordinates[atomI], atomCoordinates[atomJ], deltaR);
RealOpenMM r = deltaR[ReferenceForce::RIndex];
if (_gbviParameters->getUseCutoff() && r > _gbviParameters->getCutoffDistance())
continue;
sum += CpuGBVI::getVolume( r, radiusI, scaledRadii[atomJ] );
sum += CpuGBVI::getVolume(r, radiusI, scaledRadii[atomJ]);
}
}
RealOpenMM atomicRadius3 = POW( radiusI, minusThree );
if( _gbviParameters->getBornRadiusScalingMethod() != GBVIParameters::QuinticSpline ){
RealOpenMM atomicRadius3 = POW(radiusI, minusThree);
if (_gbviParameters->getBornRadiusScalingMethod() != GBVIParameters::QuinticSpline) {
sum = atomicRadius3 - sum;
bornRadii[atomI] = POW( sum, minusOneThird );
bornRadii[atomI] = POW(sum, minusOneThird);
switchDeriviatives[atomI] = one;
} else {
RealOpenMM bornRadius, switchDeriviative;
computeBornRadiiUsingQuinticSpline( atomicRadius3, sum, gbviParameters,
&bornRadius, &switchDeriviative );
computeBornRadiiUsingQuinticSpline(atomicRadius3, sum, gbviParameters,
&bornRadius, &switchDeriviative);
bornRadii[atomI] = bornRadius;
switchDeriviatives[atomI] = switchDeriviative;
}
......@@ -281,25 +281,25 @@ void CpuGBVI::computeBornRadii( const vector<RealVec>& atomCoordinates, RealOpen
--------------------------------------------------------------------------------------- */
RealOpenMM CpuGBVI::getVolume( RealOpenMM r, RealOpenMM R, RealOpenMM S ){
RealOpenMM CpuGBVI::getVolume(RealOpenMM r, RealOpenMM R, RealOpenMM S) {
// ---------------------------------------------------------------------------------------
static const RealOpenMM zero = static_cast<RealOpenMM>( 0.0 );
static const RealOpenMM minusThree = static_cast<RealOpenMM>( -3.0 );
static const RealOpenMM zero = static_cast<RealOpenMM>( 0.0);
static const RealOpenMM minusThree = static_cast<RealOpenMM>(-3.0);
RealOpenMM diff = (S - R);
if( FABS( diff ) < r ){
if (FABS(diff) < r) {
RealOpenMM lowerBound = (R > (r - S)) ? R : (r - S);
return (CpuGBVI::getL( r, (r + S), S ) -
CpuGBVI::getL( r, lowerBound, S ));
return (CpuGBVI::getL(r, (r + S), S) -
CpuGBVI::getL(r, lowerBound, S));
} else if( r <= diff ){
} else if (r <= diff) {
return CpuGBVI::getL( r, (r + S), S ) -
CpuGBVI::getL( r, (r - S), S ) +
POW( R, minusThree );
return CpuGBVI::getL(r, (r + S), S) -
CpuGBVI::getL(r, (r - S), S) +
POW(R, minusThree);
} else {
return zero;
......@@ -318,15 +318,15 @@ RealOpenMM CpuGBVI::getVolume( RealOpenMM r, RealOpenMM R, RealOpenMM S ){
--------------------------------------------------------------------------------------- */
RealOpenMM CpuGBVI::getL( RealOpenMM r, RealOpenMM x, RealOpenMM S ){
RealOpenMM CpuGBVI::getL(RealOpenMM r, RealOpenMM x, RealOpenMM S) {
// ---------------------------------------------------------------------------------------
static const RealOpenMM one = static_cast<RealOpenMM>( 1.0 );
static const RealOpenMM threeHalves = static_cast<RealOpenMM>( 1.5 );
static const RealOpenMM third = static_cast<RealOpenMM>( (1.0/3.0) );
static const RealOpenMM fourth = static_cast<RealOpenMM>( 0.25 );
static const RealOpenMM eighth = static_cast<RealOpenMM>( 0.125 );
static const RealOpenMM one = static_cast<RealOpenMM>(1.0);
static const RealOpenMM threeHalves = static_cast<RealOpenMM>(1.5);
static const RealOpenMM third = static_cast<RealOpenMM>((1.0/3.0));
static const RealOpenMM fourth = static_cast<RealOpenMM>(0.25);
static const RealOpenMM eighth = static_cast<RealOpenMM>(0.125);
// ---------------------------------------------------------------------------------------
......@@ -338,7 +338,7 @@ RealOpenMM CpuGBVI::getL( RealOpenMM r, RealOpenMM x, RealOpenMM S ){
RealOpenMM diff2 = (r + S)*(r - S);
return (threeHalves*xInv)*( (xInv*fourth*rInv) - (xInv2*third) + (diff2*xInv3*eighth*rInv) );
return (threeHalves*xInv)*((xInv*fourth*rInv) - (xInv2*third) + (diff2*xInv3*eighth*rInv));
}
/**---------------------------------------------------------------------------------------
......@@ -353,16 +353,16 @@ RealOpenMM CpuGBVI::getL( RealOpenMM r, RealOpenMM x, RealOpenMM S ){
--------------------------------------------------------------------------------------- */
RealOpenMM CpuGBVI::dL_dr( RealOpenMM r, RealOpenMM x, RealOpenMM S ){
RealOpenMM CpuGBVI::dL_dr(RealOpenMM r, RealOpenMM x, RealOpenMM S) {
// ---------------------------------------------------------------------------------------
static const RealOpenMM one = static_cast<RealOpenMM>( 1.0 );
static const RealOpenMM threeHalves = static_cast<RealOpenMM>( 1.5 );
static const RealOpenMM threeEights = static_cast<RealOpenMM>( 0.375 );
static const RealOpenMM third = static_cast<RealOpenMM>( (1.0/3.0) );
static const RealOpenMM fourth = static_cast<RealOpenMM>( 0.25 );
static const RealOpenMM eighth = static_cast<RealOpenMM>( 0.125 );
static const RealOpenMM one = static_cast<RealOpenMM>(1.0);
static const RealOpenMM threeHalves = static_cast<RealOpenMM>(1.5);
static const RealOpenMM threeEights = static_cast<RealOpenMM>(0.375);
static const RealOpenMM third = static_cast<RealOpenMM>((1.0/3.0));
static const RealOpenMM fourth = static_cast<RealOpenMM>(0.25);
static const RealOpenMM eighth = static_cast<RealOpenMM>(0.125);
// ---------------------------------------------------------------------------------------
......@@ -375,7 +375,7 @@ RealOpenMM CpuGBVI::dL_dr( RealOpenMM r, RealOpenMM x, RealOpenMM S ){
RealOpenMM diff2 = (r + S)*(r - S);
return ( (-threeHalves*xInv2*rInv2)*( fourth + eighth*diff2*xInv2 ) + threeEights*xInv3*xInv );
return ((-threeHalves*xInv2*rInv2)*(fourth + eighth*diff2*xInv2) + threeEights*xInv3*xInv);
}
/**---------------------------------------------------------------------------------------
......@@ -390,14 +390,14 @@ RealOpenMM CpuGBVI::dL_dr( RealOpenMM r, RealOpenMM x, RealOpenMM S ){
--------------------------------------------------------------------------------------- */
RealOpenMM CpuGBVI::dL_dx( RealOpenMM r, RealOpenMM x, RealOpenMM S ){
RealOpenMM CpuGBVI::dL_dx(RealOpenMM r, RealOpenMM x, RealOpenMM S) {
// ---------------------------------------------------------------------------------------
static const RealOpenMM one = static_cast<RealOpenMM>( 1.0 );
static const RealOpenMM half = static_cast<RealOpenMM>( 0.5 );
static const RealOpenMM threeHalvesM = static_cast<RealOpenMM>( -1.5 );
static const RealOpenMM third = static_cast<RealOpenMM>( (1.0/3.0) );
static const RealOpenMM one = static_cast<RealOpenMM>( 1.0);
static const RealOpenMM half = static_cast<RealOpenMM>( 0.5);
static const RealOpenMM threeHalvesM = static_cast<RealOpenMM>(-1.5);
static const RealOpenMM third = static_cast<RealOpenMM>( (1.0/3.0));
// ---------------------------------------------------------------------------------------
......@@ -409,7 +409,7 @@ RealOpenMM CpuGBVI::dL_dx( RealOpenMM r, RealOpenMM x, RealOpenMM S ){
RealOpenMM diff = (r + S)*(r - S);
return (threeHalvesM*xInv3)*( (half*rInv) - xInv + (half*diff*xInv2*rInv) );
return (threeHalvesM*xInv3)*((half*rInv) - xInv + (half*diff*xInv2*rInv));
}
/**---------------------------------------------------------------------------------------
......@@ -422,19 +422,19 @@ RealOpenMM CpuGBVI::dL_dx( RealOpenMM r, RealOpenMM x, RealOpenMM S ){
--------------------------------------------------------------------------------------- */
RealOpenMM CpuGBVI::Sgb( RealOpenMM t ){
RealOpenMM CpuGBVI::Sgb(RealOpenMM t) {
// ---------------------------------------------------------------------------------------
// static const char* methodName = "CpuGBVI::Sgb";
static const RealOpenMM zero = static_cast<RealOpenMM>( 0.0 );
static const RealOpenMM one = static_cast<RealOpenMM>( 1.0 );
static const RealOpenMM fourth = static_cast<RealOpenMM>( 0.25 );
static const RealOpenMM zero = static_cast<RealOpenMM>(0.0);
static const RealOpenMM one = static_cast<RealOpenMM>(1.0);
static const RealOpenMM fourth = static_cast<RealOpenMM>(0.25);
// ---------------------------------------------------------------------------------------
return ( (t != zero) ? one/SQRT( (one + (fourth*EXP( -t ))/t) ) : zero);
return ((t != zero) ? one/SQRT((one + (fourth*EXP(-t))/t)) : zero);
}
/**---------------------------------------------------------------------------------------
......@@ -448,18 +448,18 @@ RealOpenMM CpuGBVI::Sgb( RealOpenMM t ){
--------------------------------------------------------------------------------------- */
RealOpenMM CpuGBVI::computeBornEnergy( const vector<RealVec>& atomCoordinates, const RealOpenMMVector& partialCharges ){
RealOpenMM CpuGBVI::computeBornEnergy(const vector<RealVec>& atomCoordinates, const RealOpenMMVector& partialCharges) {
// ---------------------------------------------------------------------------------------
static const RealOpenMM zero = static_cast<RealOpenMM>( 0.0 );
static const RealOpenMM one = static_cast<RealOpenMM>( 1.0 );
static const RealOpenMM two = static_cast<RealOpenMM>( 2.0 );
static const RealOpenMM three = static_cast<RealOpenMM>( 3.0 );
static const RealOpenMM four = static_cast<RealOpenMM>( 4.0 );
static const RealOpenMM half = static_cast<RealOpenMM>( 0.5 );
static const RealOpenMM fourth = static_cast<RealOpenMM>( 0.25 );
static const RealOpenMM eighth = static_cast<RealOpenMM>( 0.125 );
static const RealOpenMM zero = static_cast<RealOpenMM>(0.0);
static const RealOpenMM one = static_cast<RealOpenMM>(1.0);
static const RealOpenMM two = static_cast<RealOpenMM>(2.0);
static const RealOpenMM three = static_cast<RealOpenMM>(3.0);
static const RealOpenMM four = static_cast<RealOpenMM>(4.0);
static const RealOpenMM half = static_cast<RealOpenMM>(0.5);
static const RealOpenMM fourth = static_cast<RealOpenMM>(0.25);
static const RealOpenMM eighth = static_cast<RealOpenMM>(0.125);
// ---------------------------------------------------------------------------------------
......@@ -471,8 +471,8 @@ RealOpenMM CpuGBVI::computeBornEnergy( const vector<RealVec>& atomCoordinates, c
// compute Born radii
RealOpenMMVector bornRadii( numberOfAtoms );
computeBornRadii( atomCoordinates, bornRadii );
RealOpenMMVector bornRadii(numberOfAtoms);
computeBornRadii(atomCoordinates, bornRadii);
// ---------------------------------------------------------------------------------------
......@@ -483,7 +483,7 @@ RealOpenMM CpuGBVI::computeBornEnergy( const vector<RealVec>& atomCoordinates, c
RealOpenMM energy = zero;
RealOpenMM cavityEnergy = zero;
for( int atomI = 0; atomI < numberOfAtoms; atomI++ ){
for (int atomI = 0; atomI < numberOfAtoms; atomI++) {
RealOpenMM partialChargeI = partialCharges[atomI];
......@@ -496,19 +496,19 @@ RealOpenMM CpuGBVI::computeBornEnergy( const vector<RealVec>& atomCoordinates, c
RealOpenMM ratio = (atomicRadii[atomI]/bornRadii[atomI]);
cavityEnergy += gammaParameters[atomI]*ratio*ratio*ratio;
for( int atomJ = atomI + 1; atomJ < numberOfAtoms; atomJ++ ){
for (int atomJ = atomI + 1; atomJ < numberOfAtoms; atomJ++) {
RealOpenMM deltaR[ReferenceForce::LastDeltaRIndex];
if (_gbviParameters->getPeriodic())
ReferenceForce::getDeltaRPeriodic( atomCoordinates[atomI], atomCoordinates[atomJ], _gbviParameters->getPeriodicBox(), deltaR );
ReferenceForce::getDeltaRPeriodic(atomCoordinates[atomI], atomCoordinates[atomJ], _gbviParameters->getPeriodicBox(), deltaR);
else
ReferenceForce::getDeltaR( atomCoordinates[atomI], atomCoordinates[atomJ], deltaR );
ReferenceForce::getDeltaR(atomCoordinates[atomI], atomCoordinates[atomJ], deltaR);
if (_gbviParameters->getUseCutoff() && deltaR[ReferenceForce::RIndex] > _gbviParameters->getCutoffDistance())
continue;
RealOpenMM r2 = deltaR[ReferenceForce::R2Index];
RealOpenMM t = fourth*r2/(bornRadii[atomI]*bornRadii[atomJ]);
atomIEnergy += partialCharges[atomJ]*Sgb( t )/deltaR[ReferenceForce::RIndex];
atomIEnergy += partialCharges[atomJ]*Sgb(t)/deltaR[ReferenceForce::RIndex];
}
energy += two*partialChargeI*atomIEnergy;
......@@ -532,20 +532,20 @@ RealOpenMM CpuGBVI::computeBornEnergy( const vector<RealVec>& atomCoordinates, c
--------------------------------------------------------------------------------------- */
void CpuGBVI::computeBornForces( std::vector<RealVec>& atomCoordinates, const RealOpenMMVector& partialCharges,
std::vector<OpenMM::RealVec>& inputForces){
void CpuGBVI::computeBornForces(std::vector<RealVec>& atomCoordinates, const RealOpenMMVector& partialCharges,
std::vector<OpenMM::RealVec>& inputForces) {
// ---------------------------------------------------------------------------------------
static const RealOpenMM zero = static_cast<RealOpenMM>( 0.0 );
static const RealOpenMM one = static_cast<RealOpenMM>( 1.0 );
static const RealOpenMM two = static_cast<RealOpenMM>( 2.0 );
static const RealOpenMM three = static_cast<RealOpenMM>( 3.0 );
static const RealOpenMM four = static_cast<RealOpenMM>( 4.0 );
static const RealOpenMM half = static_cast<RealOpenMM>( 0.5 );
static const RealOpenMM oneThird = static_cast<RealOpenMM>( (1.0/3.0) );
static const RealOpenMM fourth = static_cast<RealOpenMM>( 0.25 );
static const RealOpenMM eighth = static_cast<RealOpenMM>( 0.125 );
static const RealOpenMM zero = static_cast<RealOpenMM>(0.0);
static const RealOpenMM one = static_cast<RealOpenMM>(1.0);
static const RealOpenMM two = static_cast<RealOpenMM>(2.0);
static const RealOpenMM three = static_cast<RealOpenMM>(3.0);
static const RealOpenMM four = static_cast<RealOpenMM>(4.0);
static const RealOpenMM half = static_cast<RealOpenMM>(0.5);
static const RealOpenMM oneThird = static_cast<RealOpenMM>((1.0/3.0));
static const RealOpenMM fourth = static_cast<RealOpenMM>(0.25);
static const RealOpenMM eighth = static_cast<RealOpenMM>(0.125);
// ---------------------------------------------------------------------------------------
......@@ -564,37 +564,37 @@ void CpuGBVI::computeBornForces( std::vector<RealVec>& atomCoordinates, const Re
// compute Born radii
RealOpenMMVector bornRadii( numberOfAtoms );
computeBornRadii( atomCoordinates, bornRadii );
RealOpenMMVector bornRadii(numberOfAtoms);
computeBornRadii(atomCoordinates, bornRadii);
// set energy/forces to zero
std::vector<OpenMM::RealVec> forces( numberOfAtoms );
for( int ii = 0; ii < numberOfAtoms; ii++ ){
std::vector<OpenMM::RealVec> forces(numberOfAtoms);
for (int ii = 0; ii < numberOfAtoms; ii++) {
forces[ii][0] = zero;
forces[ii][1] = zero;
forces[ii][2] = zero;
}
RealOpenMMVector bornForces( numberOfAtoms, 0.0);
RealOpenMMVector bornForces(numberOfAtoms, 0.0);
// ---------------------------------------------------------------------------------------
// first main loop
for( int atomI = 0; atomI < numberOfAtoms; atomI++ ){
for (int atomI = 0; atomI < numberOfAtoms; atomI++) {
// partial of polar term wrt Born radius
// and (dGpol/dr)(dr/dx)
RealOpenMM partialChargeI = preFactor*partialCharges[atomI];
for( int atomJ = atomI; atomJ < numberOfAtoms; atomJ++ ){
for (int atomJ = atomI; atomJ < numberOfAtoms; atomJ++) {
RealOpenMM deltaR[ReferenceForce::LastDeltaRIndex];
if (_gbviParameters->getPeriodic())
ReferenceForce::getDeltaRPeriodic( atomCoordinates[atomI], atomCoordinates[atomJ], _gbviParameters->getPeriodicBox(), deltaR );
ReferenceForce::getDeltaRPeriodic(atomCoordinates[atomI], atomCoordinates[atomJ], _gbviParameters->getPeriodicBox(), deltaR);
else
ReferenceForce::getDeltaR( atomCoordinates[atomI], atomCoordinates[atomJ], deltaR );
ReferenceForce::getDeltaR(atomCoordinates[atomI], atomCoordinates[atomJ], deltaR);
if (_gbviParameters->getUseCutoff() && deltaR[ReferenceForce::RIndex] > _gbviParameters->getCutoffDistance())
continue;
......@@ -607,16 +607,16 @@ void CpuGBVI::computeBornForces( std::vector<RealVec>& atomCoordinates, const Re
RealOpenMM alpha2_ij = bornRadii[atomI]*bornRadii[atomJ];
RealOpenMM D_ij = r2/(four*alpha2_ij);
RealOpenMM expTerm = EXP( -D_ij );
RealOpenMM expTerm = EXP(-D_ij);
RealOpenMM denominator2 = r2 + alpha2_ij*expTerm;
RealOpenMM denominator = SQRT( denominator2 );
RealOpenMM denominator = SQRT(denominator2);
RealOpenMM Gpol = (partialChargeI*partialCharges[atomJ])/denominator;
RealOpenMM dGpol_dr = -Gpol*( one - fourth*expTerm )/denominator2;
RealOpenMM dGpol_dr = -Gpol*(one - fourth*expTerm)/denominator2;
RealOpenMM dGpol_dalpha2_ij = -half*Gpol*expTerm*( one + D_ij )/denominator2;
RealOpenMM dGpol_dalpha2_ij = -half*Gpol*expTerm*(one + D_ij)/denominator2;
if( atomI != atomJ ){
if (atomI != atomJ) {
bornForces[atomJ] += dGpol_dalpha2_ij*bornRadii[atomI];
......@@ -647,7 +647,7 @@ void CpuGBVI::computeBornForces( std::vector<RealVec>& atomCoordinates, const Re
const RealOpenMMVector& scaledRadii = gbviParameters->getScaledRadii();
const RealOpenMMVector& switchDeriviative = getSwitchDeriviative();
for( int atomI = 0; atomI < numberOfAtoms; atomI++ ){
for (int atomI = 0; atomI < numberOfAtoms; atomI++) {
RealOpenMM R = atomicRadii[atomI];
......@@ -659,9 +659,9 @@ void CpuGBVI::computeBornForces( std::vector<RealVec>& atomCoordinates, const Re
RealOpenMM b2 = bornRadii[atomI]*bornRadii[atomI];
bornForces[atomI] *= switchDeriviative[atomI]*oneThird*b2*b2;
for( int atomJ = 0; atomJ < numberOfAtoms; atomJ++ ){
for (int atomJ = 0; atomJ < numberOfAtoms; atomJ++) {
if( atomJ != atomI ){
if (atomJ != atomI) {
RealOpenMM deltaX = atomCoordinates[atomJ][0] - atomCoordinates[atomI][0];
RealOpenMM deltaY = atomCoordinates[atomJ][1] - atomCoordinates[atomI][1];
......@@ -669,9 +669,9 @@ void CpuGBVI::computeBornForces( std::vector<RealVec>& atomCoordinates, const Re
RealOpenMM deltaR[ReferenceForce::LastDeltaRIndex];
if (_gbviParameters->getPeriodic())
ReferenceForce::getDeltaRPeriodic( atomCoordinates[atomI], atomCoordinates[atomJ], _gbviParameters->getPeriodicBox(), deltaR );
ReferenceForce::getDeltaRPeriodic(atomCoordinates[atomI], atomCoordinates[atomJ], _gbviParameters->getPeriodicBox(), deltaR);
else
ReferenceForce::getDeltaR( atomCoordinates[atomI], atomCoordinates[atomJ], deltaR );
ReferenceForce::getDeltaR(atomCoordinates[atomI], atomCoordinates[atomJ], deltaR);
if (_gbviParameters->getUseCutoff() && deltaR[ReferenceForce::RIndex] > _gbviParameters->getCutoffDistance())
continue;
......@@ -680,7 +680,7 @@ void CpuGBVI::computeBornForces( std::vector<RealVec>& atomCoordinates, const Re
deltaY = deltaR[ReferenceForce::YIndex];
deltaZ = deltaR[ReferenceForce::ZIndex];
RealOpenMM r = SQRT( r2 );
RealOpenMM r = SQRT(r2);
RealOpenMM S = scaledRadii[atomJ];
RealOpenMM diff = (S - R);
......@@ -689,16 +689,16 @@ void CpuGBVI::computeBornForces( std::vector<RealVec>& atomCoordinates, const Re
// find dRb/dr, where Rb is the Born radius
if( FABS( diff ) < r ){
de = CpuGBVI::dL_dr( r, r+S, S ) + CpuGBVI::dL_dx( r, r+S, S );
if( R > (r - S) ){
de -= CpuGBVI::dL_dr( r, R, S );
if (FABS(diff) < r) {
de = CpuGBVI::dL_dr(r, r+S, S) + CpuGBVI::dL_dx(r, r+S, S);
if (R > (r - S)) {
de -= CpuGBVI::dL_dr(r, R, S);
} else {
de -= ( CpuGBVI::dL_dr( r, (r-S), S ) + CpuGBVI::dL_dx( r, (r-S), S ) );
de -= (CpuGBVI::dL_dr(r, (r-S), S) + CpuGBVI::dL_dx(r, (r-S), S));
}
} else if( r < (S - R) ){
de = CpuGBVI::dL_dr( r, r+S, S ) + CpuGBVI::dL_dx( r, r+S, S );
de -= ( CpuGBVI::dL_dr( r, r-S, S ) + CpuGBVI::dL_dx( r, r-S, S ) );
} else if (r < (S - R)) {
de = CpuGBVI::dL_dr(r, r+S, S) + CpuGBVI::dL_dx(r, r+S, S);
de -= (CpuGBVI::dL_dr(r, r-S, S) + CpuGBVI::dL_dx(r, r-S, S));
}
// de = (dG/dRb)(dRb/dr)
......@@ -721,12 +721,12 @@ void CpuGBVI::computeBornForces( std::vector<RealVec>& atomCoordinates, const Re
}
}
//printGbvi( atomCoordinates, partialCharges, bornRadii, bornForces, forces, "GBVI: Post loop2", stderr );
//printGbvi(atomCoordinates, partialCharges, bornRadii, bornForces, forces, "GBVI: Post loop2", stderr);
// convert from cal to Joule & apply prefactor tau = (1/diel_solute - 1/diel_solvent)
RealOpenMM conversion = static_cast<RealOpenMM>(gbviParameters->getTau());
for( int atomI = 0; atomI < numberOfAtoms; atomI++ ){
for (int atomI = 0; atomI < numberOfAtoms; atomI++) {
inputForces[atomI][0] += conversion*forces[atomI][0];
inputForces[atomI][1] += conversion*forces[atomI][1];
inputForces[atomI][2] += conversion*forces[atomI][2];
......@@ -748,11 +748,11 @@ void CpuGBVI::computeBornForces( std::vector<RealVec>& atomCoordinates, const Re
--------------------------------------------------------------------------------------- */
void CpuGBVI::printGbvi( const std::vector<OpenMM::RealVec>& atomCoordinates, const RealOpenMMVector& partialCharges,
const RealOpenMMVector& bornRadii,
const RealOpenMMVector& bornForces,
const std::vector<OpenMM::RealVec>& forces,
const std::string& idString, FILE* log ){
void CpuGBVI::printGbvi(const std::vector<OpenMM::RealVec>& atomCoordinates, const RealOpenMMVector& partialCharges,
const RealOpenMMVector& bornRadii,
const RealOpenMMVector& bornForces,
const std::vector<OpenMM::RealVec>& forces,
const std::string& idString, FILE* log) {
// ---------------------------------------------------------------------------------------
......@@ -775,45 +775,45 @@ void CpuGBVI::printGbvi( const std::vector<OpenMM::RealVec>& atomCoordinates, co
int useComparisonFormat = 1;
(void) fprintf( log, "Reference Gbvi %s atoms=%d\n", idString.c_str(), numberOfAtoms );
(void) fprintf( log, " tau %15.7e\n", tau );
(void) fprintf( log, " scaleMethod %d (QuinticEnum=%d)\n",
_gbviParameters->getBornRadiusScalingMethod(), GBVIParameters::QuinticSpline );
(void) fprintf( log, " preFactor %15.7e)\n", preFactor );
(void) fprintf(log, "Reference Gbvi %s atoms=%d\n", idString.c_str(), numberOfAtoms);
(void) fprintf(log, " tau %15.7e\n", tau);
(void) fprintf(log, " scaleMethod %d (QuinticEnum=%d)\n",
_gbviParameters->getBornRadiusScalingMethod(), GBVIParameters::QuinticSpline);
(void) fprintf(log, " preFactor %15.7e)\n", preFactor);
if( useComparisonFormat ){
(void) fprintf( log, " br bF swd r scR tau*gamma q)\n" );
for( unsigned int atomI = 0; atomI < static_cast<unsigned int>(numberOfAtoms); atomI++ ){
(void) fprintf( log, "%6d ", atomI );
if( bornRadii.size() > atomI ){
(void) fprintf( log, "%15.7e ", bornRadii[atomI] );
if (useComparisonFormat) {
(void) fprintf(log, " br bF swd r scR tau*gamma q)\n");
for (unsigned int atomI = 0; atomI < static_cast<unsigned int>(numberOfAtoms); atomI++) {
(void) fprintf(log, "%6d ", atomI);
if (bornRadii.size() > atomI) {
(void) fprintf(log, "%15.7e ", bornRadii[atomI]);
}
if( bornForces.size() > atomI ){
(void) fprintf( log, "%15.7e ", tau*bornForces[atomI] );
if (bornForces.size() > atomI) {
(void) fprintf(log, "%15.7e ", tau*bornForces[atomI]);
}
(void) fprintf( log, " %15.7e %15.7e %15.7e %15.7e %15.7e",
(void) fprintf(log, " %15.7e %15.7e %15.7e %15.7e %15.7e",
switchDeriviative[atomI],
atomicRadii[atomI],
scaledRadii[atomI],
tau*gammaParameters[atomI],
partialCharges[atomI] );
(void) fprintf( log, "\n" );
partialCharges[atomI]);
(void) fprintf(log, "\n");
}
} else {
for( unsigned int atomI = 0; atomI < static_cast<unsigned int>(numberOfAtoms); atomI++ ){
(void) fprintf( log, "%6d r=%15.7e rSc=%15.7e swd=%15.7e tau*gam=%15.7e q=%15.7e", atomI,
for (unsigned int atomI = 0; atomI < static_cast<unsigned int>(numberOfAtoms); atomI++) {
(void) fprintf(log, "%6d r=%15.7e rSc=%15.7e swd=%15.7e tau*gam=%15.7e q=%15.7e", atomI,
atomicRadii[atomI],
scaledRadii[atomI],
switchDeriviative[atomI],
tau*gammaParameters[atomI],
partialCharges[atomI] );
if( bornRadii.size() > atomI ){
(void) fprintf( log, " bR=%15.7e", bornRadii[atomI] );
partialCharges[atomI]);
if (bornRadii.size() > atomI) {
(void) fprintf(log, " bR=%15.7e", bornRadii[atomI]);
}
if( bornForces.size() > atomI ){
(void) fprintf( log, " tau*bF=%15.7e", tau*bornForces[atomI] );
if (bornForces.size() > atomI) {
(void) fprintf(log, " tau*bF=%15.7e", tau*bornForces[atomI]);
}
(void) fprintf( log, "\n" );
(void) fprintf(log, "\n");
}
}
......@@ -835,7 +835,7 @@ void CpuGBVI::printGbvi( const std::vector<OpenMM::RealVec>& atomCoordinates, co
--------------------------------------------------------------------------------------- */
double CpuGBVI::getVolumeD( double r, double R, double S ){
double CpuGBVI::getVolumeD(double r, double R, double S) {
// ---------------------------------------------------------------------------------------
......@@ -843,18 +843,18 @@ double CpuGBVI::getVolumeD( double r, double R, double S ){
static const double minusThree = -3.0;
double diff = (S - R);
if( fabs( diff ) < r ){
if (fabs(diff) < r) {
double lowerBound = (R > (r - S)) ? R : (r - S);
return (CpuGBVI::getLD( r, (r + S), S ) -
CpuGBVI::getLD( r, lowerBound, S ));
return (CpuGBVI::getLD(r, (r + S), S) -
CpuGBVI::getLD(r, lowerBound, S));
} else if( r < diff ){
} else if (r < diff) {
return CpuGBVI::getLD( r, (r + S), S ) -
CpuGBVI::getLD( r, (r - S), S ) +
pow( R, minusThree );
return CpuGBVI::getLD(r, (r + S), S) -
CpuGBVI::getLD(r, (r - S), S) +
pow(R, minusThree);
} else {
return zero;
......@@ -875,7 +875,7 @@ double CpuGBVI::getVolumeD( double r, double R, double S ){
--------------------------------------------------------------------------------------- */
double CpuGBVI::getLD( double r, double x, double S ){
double CpuGBVI::getLD(double r, double x, double S) {
// ---------------------------------------------------------------------------------------
......@@ -895,7 +895,7 @@ double CpuGBVI::getLD( double r, double x, double S ){
double diff2 = (r + S)*(r - S);
return (threeHalves*xInv)*( (xInv*fourth*rInv) - (xInv2*third) + (diff2*xInv3*eighth*rInv) );
return (threeHalves*xInv)*((xInv*fourth*rInv) - (xInv2*third) + (diff2*xInv3*eighth*rInv));
}
/**---------------------------------------------------------------------------------------
......@@ -912,7 +912,7 @@ double CpuGBVI::getLD( double r, double x, double S ){
--------------------------------------------------------------------------------------- */
double CpuGBVI::dL_drD( double r, double x, double S ){
double CpuGBVI::dL_drD(double r, double x, double S) {
// ---------------------------------------------------------------------------------------
......@@ -934,7 +934,7 @@ double CpuGBVI::dL_drD( double r, double x, double S ){
double diff2 = (r + S)*(r - S);
return ( (-threeHalves*xInv2*rInv2)*( fourth + eighth*diff2*xInv2 ) + threeEights*xInv3*xInv );
return ((-threeHalves*xInv2*rInv2)*(fourth + eighth*diff2*xInv2) + threeEights*xInv3*xInv);
}
/**---------------------------------------------------------------------------------------
......@@ -951,7 +951,7 @@ double CpuGBVI::dL_drD( double r, double x, double S ){
--------------------------------------------------------------------------------------- */
double CpuGBVI::dL_dxD( double r, double x, double S ){
double CpuGBVI::dL_dxD(double r, double x, double S) {
// ---------------------------------------------------------------------------------------
......@@ -970,5 +970,5 @@ double CpuGBVI::dL_dxD( double r, double x, double S ){
double diff = (r + S)*(r - S);
return (threeHalvesM*xInv3)*( (half*rInv) - xInv + (half*diff*xInv2*rInv) );
return (threeHalvesM*xInv3)*((half*rInv) - xInv + (half*diff*xInv2*rInv));
}
platforms/reference/src/gbsa/CpuObc.cpp
View file @ 7fb10336
......@@ -43,7 +43,7 @@ using namespace std;
--------------------------------------------------------------------------------------- */
CpuObc::CpuObc( ObcParameters* obcParameters ) : _obcParameters(obcParameters), _includeAceApproximation(1) {
CpuObc::CpuObc(ObcParameters* obcParameters) : _obcParameters(obcParameters), _includeAceApproximation(1) {
_obcChain.resize(_obcParameters->getNumberOfAtoms());
}
......@@ -53,7 +53,7 @@ CpuObc::CpuObc( ObcParameters* obcParameters ) : _obcParameters(obcParameters),
--------------------------------------------------------------------------------------- */
CpuObc::~CpuObc( ){
CpuObc::~CpuObc() {
}
/**---------------------------------------------------------------------------------------
......@@ -64,7 +64,7 @@ CpuObc::~CpuObc( ){
--------------------------------------------------------------------------------------- */
ObcParameters* CpuObc::getObcParameters( void ) const {
ObcParameters* CpuObc::getObcParameters() const {
return _obcParameters;
}
......@@ -76,7 +76,7 @@ ObcParameters* CpuObc::getObcParameters( void ) const {
--------------------------------------------------------------------------------------- */
void CpuObc::setObcParameters( ObcParameters* obcParameters ){
void CpuObc::setObcParameters( ObcParameters* obcParameters) {
_obcParameters = obcParameters;
}
......@@ -88,7 +88,7 @@ void CpuObc::setObcParameters( ObcParameters* obcParameters ){
--------------------------------------------------------------------------------------- */
int CpuObc::includeAceApproximation( void ) const {
int CpuObc::includeAceApproximation() const {
return _includeAceApproximation;
}
......@@ -100,7 +100,7 @@ int CpuObc::includeAceApproximation( void ) const {
--------------------------------------------------------------------------------------- */
void CpuObc::setIncludeAceApproximation( int includeAceApproximation ){
void CpuObc::setIncludeAceApproximation(int includeAceApproximation) {
_includeAceApproximation = includeAceApproximation;
}
......@@ -112,7 +112,7 @@ void CpuObc::setIncludeAceApproximation( int includeAceApproximation ){
--------------------------------------------------------------------------------------- */
vector<RealOpenMM>& CpuObc::getObcChain( void ){
vector<RealOpenMM>& CpuObc::getObcChain() {
return _obcChain;
}
......@@ -128,16 +128,16 @@ vector<RealOpenMM>& CpuObc::getObcChain( void ){
--------------------------------------------------------------------------------------- */
void CpuObc::computeBornRadii( const vector<RealVec>& atomCoordinates, vector<RealOpenMM>& bornRadii ){
void CpuObc::computeBornRadii(const vector<RealVec>& atomCoordinates, vector<RealOpenMM>& bornRadii) {
// ---------------------------------------------------------------------------------------
static const RealOpenMM zero = static_cast<RealOpenMM>( 0.0 );
static const RealOpenMM one = static_cast<RealOpenMM>( 1.0 );
static const RealOpenMM two = static_cast<RealOpenMM>( 2.0 );
static const RealOpenMM three = static_cast<RealOpenMM>( 3.0 );
static const RealOpenMM half = static_cast<RealOpenMM>( 0.5 );
static const RealOpenMM fourth = static_cast<RealOpenMM>( 0.25 );
static const RealOpenMM zero = static_cast<RealOpenMM>(0.0);
static const RealOpenMM one = static_cast<RealOpenMM>(1.0);
static const RealOpenMM two = static_cast<RealOpenMM>(2.0);
static const RealOpenMM three = static_cast<RealOpenMM>(3.0);
static const RealOpenMM half = static_cast<RealOpenMM>(0.5);
static const RealOpenMM fourth = static_cast<RealOpenMM>(0.25);
// ---------------------------------------------------------------------------------------
......@@ -157,7 +157,7 @@ void CpuObc::computeBornRadii( const vector<RealVec>& atomCoordinates, vector<Re
// calculate Born radii
for( int atomI = 0; atomI < numberOfAtoms; atomI++ ){
for (int atomI = 0; atomI < numberOfAtoms; atomI++) {
RealOpenMM radiusI = atomicRadii[atomI];
RealOpenMM offsetRadiusI = radiusI - dielectricOffset;
......@@ -167,15 +167,15 @@ void CpuObc::computeBornRadii( const vector<RealVec>& atomCoordinates, vector<Re
// HCT code
for( int atomJ = 0; atomJ < numberOfAtoms; atomJ++ ){
for (int atomJ = 0; atomJ < numberOfAtoms; atomJ++) {
if( atomJ != atomI ){
if (atomJ != atomI) {
RealOpenMM deltaR[ReferenceForce::LastDeltaRIndex];
if (_obcParameters->getPeriodic())
ReferenceForce::getDeltaRPeriodic( atomCoordinates[atomI], atomCoordinates[atomJ], _obcParameters->getPeriodicBox(), deltaR );
ReferenceForce::getDeltaRPeriodic(atomCoordinates[atomI], atomCoordinates[atomJ], _obcParameters->getPeriodicBox(), deltaR);
else
ReferenceForce::getDeltaR( atomCoordinates[atomI], atomCoordinates[atomJ], deltaR );
ReferenceForce::getDeltaR(atomCoordinates[atomI], atomCoordinates[atomJ], deltaR);
RealOpenMM r = deltaR[ReferenceForce::RIndex];
if (_obcParameters->getUseCutoff() && r > _obcParameters->getCutoffDistance())
continue;
......@@ -184,9 +184,9 @@ void CpuObc::computeBornRadii( const vector<RealVec>& atomCoordinates, vector<Re
RealOpenMM scaledRadiusJ = offsetRadiusJ*scaledRadiusFactor[atomJ];
RealOpenMM rScaledRadiusJ = r + scaledRadiusJ;
if( offsetRadiusI < rScaledRadiusJ ){
if (offsetRadiusI < rScaledRadiusJ) {
RealOpenMM rInverse = one/r;
RealOpenMM l_ij = offsetRadiusI > FABS( r - scaledRadiusJ ) ? offsetRadiusI : FABS( r - scaledRadiusJ );
RealOpenMM l_ij = offsetRadiusI > FABS(r - scaledRadiusJ) ? offsetRadiusI : FABS(r - scaledRadiusJ);
l_ij = one/l_ij;
RealOpenMM u_ij = one/rScaledRadiusJ;
......@@ -194,15 +194,15 @@ void CpuObc::computeBornRadii( const vector<RealVec>& atomCoordinates, vector<Re
RealOpenMM l_ij2 = l_ij*l_ij;
RealOpenMM u_ij2 = u_ij*u_ij;
RealOpenMM ratio = LN( (u_ij/l_ij) );
RealOpenMM term = l_ij - u_ij + fourth*r*(u_ij2 - l_ij2) + ( half*rInverse*ratio) + (fourth*scaledRadiusJ*scaledRadiusJ*rInverse)*(l_ij2 - u_ij2);
RealOpenMM ratio = LN((u_ij/l_ij));
RealOpenMM term = l_ij - u_ij + fourth*r*(u_ij2 - l_ij2) + (half*rInverse*ratio) + (fourth*scaledRadiusJ*scaledRadiusJ*rInverse)*(l_ij2 - u_ij2);
// this case (atom i completely inside atom j) is not considered in the original paper
// Jay Ponder and the authors of Tinker recognized this and
// worked out the details
if( offsetRadiusI < (scaledRadiusJ - r) ){
term += two*( radiusIInverse - l_ij);
if (offsetRadiusI < (scaledRadiusJ - r)) {
term += two*(radiusIInverse - l_ij);
}
sum += term;
......@@ -215,11 +215,11 @@ void CpuObc::computeBornRadii( const vector<RealVec>& atomCoordinates, vector<Re
sum *= half*offsetRadiusI;
RealOpenMM sum2 = sum*sum;
RealOpenMM sum3 = sum*sum2;
RealOpenMM tanhSum = TANH( alphaObc*sum - betaObc*sum2 + gammaObc*sum3 );
RealOpenMM tanhSum = TANH(alphaObc*sum - betaObc*sum2 + gammaObc*sum3);
bornRadii[atomI] = one/( one/offsetRadiusI - tanhSum/radiusI );
bornRadii[atomI] = one/(one/offsetRadiusI - tanhSum/radiusI);
obcChain[atomI] = offsetRadiusI*( alphaObc - two*betaObc*sum + three*gammaObc*sum2 );
obcChain[atomI] = offsetRadiusI*(alphaObc - two*betaObc*sum + three*gammaObc*sum2);
obcChain[atomI] = (one - tanhSum*tanhSum)*obcChain[atomI]/radiusI;
}
......@@ -236,16 +236,16 @@ void CpuObc::computeBornRadii( const vector<RealVec>& atomCoordinates, vector<Re
--------------------------------------------------------------------------------------- */
void CpuObc::computeAceNonPolarForce( const ObcParameters* obcParameters,
void CpuObc::computeAceNonPolarForce(const ObcParameters* obcParameters,
const RealOpenMMVector& bornRadii,
RealOpenMM* energy,
RealOpenMMVector& forces ) const {
RealOpenMMVector& forces) const {
// ---------------------------------------------------------------------------------------
static const RealOpenMM zero = static_cast<RealOpenMM>( 0.0 );
static const RealOpenMM zero = static_cast<RealOpenMM>(0.0);
static const RealOpenMM minusSix = -6.0;
static const RealOpenMM six = static_cast<RealOpenMM>( 6.0 );
static const RealOpenMM six = static_cast<RealOpenMM>(6.0);
// ---------------------------------------------------------------------------------------
......@@ -271,10 +271,10 @@ void CpuObc::computeAceNonPolarForce( const ObcParameters* obcParameters,
// observed values. He did not think it was important enough to write up, so there is
// no paper to cite.
for( int atomI = 0; atomI < numberOfAtoms; atomI++ ){
if( bornRadii[atomI] > zero ){
for (int atomI = 0; atomI < numberOfAtoms; atomI++) {
if (bornRadii[atomI] > zero) {
RealOpenMM r = atomicRadii[atomI] + probeRadius;
RealOpenMM ratio6 = POW( atomicRadii[atomI]/bornRadii[atomI], six );
RealOpenMM ratio6 = POW(atomicRadii[atomI]/bornRadii[atomI], six);
RealOpenMM saTerm = surfaceAreaFactor*r*r*ratio6;
*energy += saTerm;
forces[atomI] += minusSix*saTerm/bornRadii[atomI];
......@@ -294,19 +294,19 @@ void CpuObc::computeAceNonPolarForce( const ObcParameters* obcParameters,
--------------------------------------------------------------------------------------- */
RealOpenMM CpuObc::computeBornEnergyForces( const vector<RealVec>& atomCoordinates,
const RealOpenMMVector& partialCharges, vector<RealVec>& inputForces ){
RealOpenMM CpuObc::computeBornEnergyForces(const vector<RealVec>& atomCoordinates,
const RealOpenMMVector& partialCharges, vector<RealVec>& inputForces) {
// ---------------------------------------------------------------------------------------
static const RealOpenMM zero = static_cast<RealOpenMM>( 0.0 );
static const RealOpenMM one = static_cast<RealOpenMM>( 1.0 );
static const RealOpenMM two = static_cast<RealOpenMM>( 2.0 );
static const RealOpenMM three = static_cast<RealOpenMM>( 3.0 );
static const RealOpenMM four = static_cast<RealOpenMM>( 4.0 );
static const RealOpenMM half = static_cast<RealOpenMM>( 0.5 );
static const RealOpenMM fourth = static_cast<RealOpenMM>( 0.25 );
static const RealOpenMM eighth = static_cast<RealOpenMM>( 0.125 );
static const RealOpenMM zero = static_cast<RealOpenMM>(0.0);
static const RealOpenMM one = static_cast<RealOpenMM>(1.0);
static const RealOpenMM two = static_cast<RealOpenMM>(2.0);
static const RealOpenMM three = static_cast<RealOpenMM>(3.0);
static const RealOpenMM four = static_cast<RealOpenMM>(4.0);
static const RealOpenMM half = static_cast<RealOpenMM>(0.5);
static const RealOpenMM fourth = static_cast<RealOpenMM>(0.25);
static const RealOpenMM eighth = static_cast<RealOpenMM>(0.125);
// constants
......@@ -325,36 +325,36 @@ RealOpenMM CpuObc::computeBornEnergyForces( const vector<RealVec>& atomCoordinat
// compute Born radii
RealOpenMMVector bornRadii( numberOfAtoms );
computeBornRadii( atomCoordinates, bornRadii );
RealOpenMMVector bornRadii(numberOfAtoms);
computeBornRadii(atomCoordinates, bornRadii);
// set energy/forces to zero
RealOpenMM obcEnergy = zero;
RealOpenMMVector bornForces( numberOfAtoms, 0.0 );
RealOpenMMVector bornForces(numberOfAtoms, 0.0);
// ---------------------------------------------------------------------------------------
// compute the nonpolar solvation via ACE approximation
if( includeAceApproximation() ){
computeAceNonPolarForce( _obcParameters, bornRadii, &obcEnergy, bornForces );
if (includeAceApproximation()) {
computeAceNonPolarForce(_obcParameters, bornRadii, &obcEnergy, bornForces);
}
// ---------------------------------------------------------------------------------------
// first main loop
for( int atomI = 0; atomI < numberOfAtoms; atomI++ ){
for (int atomI = 0; atomI < numberOfAtoms; atomI++) {
RealOpenMM partialChargeI = preFactor*partialCharges[atomI];
for( int atomJ = atomI; atomJ < numberOfAtoms; atomJ++ ){
for (int atomJ = atomI; atomJ < numberOfAtoms; atomJ++) {
RealOpenMM deltaR[ReferenceForce::LastDeltaRIndex];
if (_obcParameters->getPeriodic())
ReferenceForce::getDeltaRPeriodic( atomCoordinates[atomI], atomCoordinates[atomJ], _obcParameters->getPeriodicBox(), deltaR );
ReferenceForce::getDeltaRPeriodic(atomCoordinates[atomI], atomCoordinates[atomJ], _obcParameters->getPeriodicBox(), deltaR);
else
ReferenceForce::getDeltaR( atomCoordinates[atomI], atomCoordinates[atomJ], deltaR );
ReferenceForce::getDeltaR(atomCoordinates[atomI], atomCoordinates[atomJ], deltaR);
if (_obcParameters->getUseCutoff() && deltaR[ReferenceForce::RIndex] > cutoffDistance)
continue;
......@@ -366,18 +366,18 @@ RealOpenMM CpuObc::computeBornEnergyForces( const vector<RealVec>& atomCoordinat
RealOpenMM alpha2_ij = bornRadii[atomI]*bornRadii[atomJ];
RealOpenMM D_ij = r2/(four*alpha2_ij);
RealOpenMM expTerm = EXP( -D_ij );
RealOpenMM expTerm = EXP(-D_ij);
RealOpenMM denominator2 = r2 + alpha2_ij*expTerm;
RealOpenMM denominator = SQRT( denominator2 );
RealOpenMM denominator = SQRT(denominator2);
RealOpenMM Gpol = (partialChargeI*partialCharges[atomJ])/denominator;
RealOpenMM dGpol_dr = -Gpol*( one - fourth*expTerm )/denominator2;
RealOpenMM dGpol_dr = -Gpol*(one - fourth*expTerm)/denominator2;
RealOpenMM dGpol_dalpha2_ij = -half*Gpol*expTerm*( one + D_ij )/denominator2;
RealOpenMM dGpol_dalpha2_ij = -half*Gpol*expTerm*(one + D_ij)/denominator2;
RealOpenMM energy = Gpol;
if( atomI != atomJ ){
if (atomI != atomJ) {
if (_obcParameters->getUseCutoff())
energy -= partialChargeI*partialCharges[atomJ]/cutoffDistance;
......@@ -420,26 +420,26 @@ RealOpenMM CpuObc::computeBornEnergyForces( const vector<RealVec>& atomCoordinat
// compute factor that depends only on the outer loop index
for( int atomI = 0; atomI < numberOfAtoms; atomI++ ){
for (int atomI = 0; atomI < numberOfAtoms; atomI++) {
bornForces[atomI] *= bornRadii[atomI]*bornRadii[atomI]*obcChain[atomI];
}
for( int atomI = 0; atomI < numberOfAtoms; atomI++ ){
for (int atomI = 0; atomI < numberOfAtoms; atomI++) {
// radius w/ dielectric offset applied
RealOpenMM radiusI = atomicRadii[atomI];
RealOpenMM offsetRadiusI = radiusI - dielectricOffset;
for( int atomJ = 0; atomJ < numberOfAtoms; atomJ++ ){
for (int atomJ = 0; atomJ < numberOfAtoms; atomJ++) {
if( atomJ != atomI ){
if (atomJ != atomI) {
RealOpenMM deltaR[ReferenceForce::LastDeltaRIndex];
if (_obcParameters->getPeriodic())
ReferenceForce::getDeltaRPeriodic( atomCoordinates[atomI], atomCoordinates[atomJ], _obcParameters->getPeriodicBox(), deltaR );
ReferenceForce::getDeltaRPeriodic(atomCoordinates[atomI], atomCoordinates[atomJ], _obcParameters->getPeriodicBox(), deltaR);
else
ReferenceForce::getDeltaR( atomCoordinates[atomI], atomCoordinates[atomJ], deltaR );
ReferenceForce::getDeltaR(atomCoordinates[atomI], atomCoordinates[atomJ], deltaR);
if (_obcParameters->getUseCutoff() && deltaR[ReferenceForce::RIndex] > cutoffDistance)
continue;
......@@ -459,9 +459,9 @@ RealOpenMM CpuObc::computeBornEnergyForces( const vector<RealVec>& atomCoordinat
// dL/dr & dU/dr are zero (this can be shown analytically)
// removed from calculation
if( offsetRadiusI < rScaledRadiusJ ){
if (offsetRadiusI < rScaledRadiusJ) {
RealOpenMM l_ij = offsetRadiusI > FABS( r - scaledRadiusJ ) ? offsetRadiusI : FABS( r - scaledRadiusJ );
RealOpenMM l_ij = offsetRadiusI > FABS(r - scaledRadiusJ) ? offsetRadiusI : FABS(r - scaledRadiusJ);
l_ij = one/l_ij;
RealOpenMM u_ij = one/rScaledRadiusJ;
......@@ -473,7 +473,7 @@ RealOpenMM CpuObc::computeBornEnergyForces( const vector<RealVec>& atomCoordinat
RealOpenMM rInverse = one/r;
RealOpenMM r2Inverse = rInverse*rInverse;
RealOpenMM t3 = eighth*(one + scaledRadiusJ2*r2Inverse)*(l_ij2 - u_ij2) + fourth*LN( u_ij/l_ij )*r2Inverse;
RealOpenMM t3 = eighth*(one + scaledRadiusJ2*r2Inverse)*(l_ij2 - u_ij2) + fourth*LN(u_ij/l_ij)*r2Inverse;
RealOpenMM de = bornForces[atomI]*t3*rInverse;
......@@ -495,7 +495,7 @@ RealOpenMM CpuObc::computeBornEnergyForces( const vector<RealVec>& atomCoordinat
}
//printObc( atomCoordinates, partialCharges, bornRadii, bornForces, inputForces, "Obc Post loop2", stderr );
//printObc(atomCoordinates, partialCharges, bornRadii, bornForces, inputForces, "Obc Post loop2", stderr);
return obcEnergy;
}
......@@ -514,12 +514,12 @@ RealOpenMM CpuObc::computeBornEnergyForces( const vector<RealVec>& atomCoordinat
--------------------------------------------------------------------------------------- */
void CpuObc::printObc( const std::vector<OpenMM::RealVec>& atomCoordinates,
const RealOpenMMVector& partialCharges,
const RealOpenMMVector& bornRadii,
const RealOpenMMVector& bornForces,
const std::vector<OpenMM::RealVec>& forces,
const std::string& idString, FILE* log ){
void CpuObc::printObc(const std::vector<OpenMM::RealVec>& atomCoordinates,
const RealOpenMMVector& partialCharges,
const RealOpenMMVector& bornRadii,
const RealOpenMMVector& bornForces,
const std::vector<OpenMM::RealVec>& forces,
const std::string& idString, FILE* log) {
// ---------------------------------------------------------------------------------------
......@@ -538,43 +538,43 @@ void CpuObc::printObc( const std::vector<OpenMM::RealVec>& atomCoordinates,
// ---------------------------------------------------------------------------------------
(void) fprintf( log, "Reference Obc %s atoms=%d\n", idString.c_str(), numberOfAtoms );
if( comparisonFormat ){
(void) fprintf( log, "Reference Obc %s atoms=%d Chain/Radii/Force\n", idString.c_str(), numberOfAtoms );
for( unsigned int atomI = 0; atomI < static_cast<unsigned int>(numberOfAtoms); atomI++ ){
(void) fprintf( log, "%6d ", atomI );
if( obcChain.size() > atomI ){
(void) fprintf( log, " %15.7e", obcChain[atomI] );
(void) fprintf(log, "Reference Obc %s atoms=%d\n", idString.c_str(), numberOfAtoms);
if (comparisonFormat) {
(void) fprintf(log, "Reference Obc %s atoms=%d Chain/Radii/Force\n", idString.c_str(), numberOfAtoms);
for (unsigned int atomI = 0; atomI < static_cast<unsigned int>(numberOfAtoms); atomI++) {
(void) fprintf(log, "%6d ", atomI);
if (obcChain.size() > atomI) {
(void) fprintf(log, " %15.7e", obcChain[atomI]);
}
if( bornRadii.size() > atomI ){
(void) fprintf( log, " %15.7e", bornRadii[atomI] );
if (bornRadii.size() > atomI) {
(void) fprintf(log, " %15.7e", bornRadii[atomI]);
}
if( bornForces.size() > atomI ){
(void) fprintf( log, " %15.7e", bornForces[atomI] );
if (bornForces.size() > atomI) {
(void) fprintf(log, " %15.7e", bornForces[atomI]);
}
(void) fprintf( log, " %15.7e %6.3f", atomicRadii[atomI], partialCharges[atomI] );
(void) fprintf( log, "\n" );
(void) fprintf(log, " %15.7e %6.3f", atomicRadii[atomI], partialCharges[atomI]);
(void) fprintf(log, "\n");
}
} else {
(void) fprintf( log, "Reference Obc %s atoms=%d\n", idString.c_str(), numberOfAtoms );
(void) fprintf( log, " preFactor %15.7e\n", preFactor );
(void) fprintf( log, " alpha %15.7e\n", alphaObc);
(void) fprintf( log, " beta %15.7e\n", betaObc);
(void) fprintf( log, " gamma %15.7e\n", gammaObc );
(void) fprintf(log, "Reference Obc %s atoms=%d\n", idString.c_str(), numberOfAtoms);
(void) fprintf(log, " preFactor %15.7e\n", preFactor);
(void) fprintf(log, " alpha %15.7e\n", alphaObc);
(void) fprintf(log, " beta %15.7e\n", betaObc);
(void) fprintf(log, " gamma %15.7e\n", gammaObc);
for( unsigned int atomI = 0; atomI < static_cast<unsigned int>(numberOfAtoms); atomI++ ){
(void) fprintf( log, "%6d r=%15.7e q=%6.3f", atomI,
atomicRadii[atomI], partialCharges[atomI] );
if( obcChain.size() > atomI ){
(void) fprintf( log, " bChn=%15.7e", obcChain[atomI] );
for (unsigned int atomI = 0; atomI < static_cast<unsigned int>(numberOfAtoms); atomI++) {
(void) fprintf(log, "%6d r=%15.7e q=%6.3f", atomI,
atomicRadii[atomI], partialCharges[atomI]);
if (obcChain.size() > atomI) {
(void) fprintf(log, " bChn=%15.7e", obcChain[atomI]);
}
if( bornRadii.size() > atomI ){
(void) fprintf( log, " bR=%15.7e", bornRadii[atomI] );
if (bornRadii.size() > atomI) {
(void) fprintf(log, " bR=%15.7e", bornRadii[atomI]);
}
if( bornForces.size() > atomI ){
(void) fprintf( log, " bF=%15.7e", bornForces[atomI] );
if (bornForces.size() > atomI) {
(void) fprintf(log, " bF=%15.7e", bornForces[atomI]);
}
(void) fprintf( log, "\n" );
(void) fprintf(log, "\n");
}
}
......
platforms/reference/src/gbsa/GBVIParameters.cpp
View file @ 7fb10336
......@@ -41,19 +41,19 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */
GBVIParameters::GBVIParameters( int numberOfAtoms ) : _numberOfAtoms(numberOfAtoms),
_soluteDielectric(1.0),
_solventDielectric(78.3),
_electricConstant(-0.5*ONE_4PI_EPS0),
_cutoff(false),
_periodic(false),
_bornRadiusScalingMethod(0),
_quinticLowerLimitFactor(0.8),
_quinticUpperBornRadiusLimit(5.0) {
_atomicRadii.resize( numberOfAtoms );
_scaledRadii.resize( numberOfAtoms );
_gammaParameters.resize( numberOfAtoms );
GBVIParameters::GBVIParameters(int numberOfAtoms) : _numberOfAtoms(numberOfAtoms),
_soluteDielectric(1.0),
_solventDielectric(78.3),
_electricConstant(-0.5*ONE_4PI_EPS0),
_cutoff(false),
_periodic(false),
_bornRadiusScalingMethod(0),
_quinticLowerLimitFactor(0.8),
_quinticUpperBornRadiusLimit(5.0) {
_atomicRadii.resize(numberOfAtoms);
_scaledRadii.resize(numberOfAtoms);
_gammaParameters.resize(numberOfAtoms);
}
......@@ -63,7 +63,7 @@ GBVIParameters::GBVIParameters( int numberOfAtoms ) : _numberOfAtoms(numberOfAto
--------------------------------------------------------------------------------------- */
GBVIParameters::~GBVIParameters( ){
GBVIParameters::~GBVIParameters() {
}
/**---------------------------------------------------------------------------------------
......@@ -74,7 +74,7 @@ GBVIParameters::~GBVIParameters( ){
--------------------------------------------------------------------------------------- */
int GBVIParameters::getNumberOfAtoms( void ) const {
int GBVIParameters::getNumberOfAtoms() const {
return _numberOfAtoms;
}
......@@ -86,7 +86,7 @@ int GBVIParameters::getNumberOfAtoms( void ) const {
--------------------------------------------------------------------------------------- */
RealOpenMM GBVIParameters::getElectricConstant( void ) const {
RealOpenMM GBVIParameters::getElectricConstant() const {
return _electricConstant;
}
......@@ -98,7 +98,7 @@ RealOpenMM GBVIParameters::getElectricConstant( void ) const {
--------------------------------------------------------------------------------------- */
RealOpenMM GBVIParameters::getSolventDielectric( void ) const {
RealOpenMM GBVIParameters::getSolventDielectric() const {
return _solventDielectric;
}
......@@ -110,7 +110,7 @@ RealOpenMM GBVIParameters::getSolventDielectric( void ) const {
--------------------------------------------------------------------------------------- */
void GBVIParameters::setSolventDielectric( RealOpenMM solventDielectric ){
void GBVIParameters::setSolventDielectric(RealOpenMM solventDielectric) {
_solventDielectric = solventDielectric;
}
......@@ -122,7 +122,7 @@ void GBVIParameters::setSolventDielectric( RealOpenMM solventDielectric ){
--------------------------------------------------------------------------------------- */
RealOpenMM GBVIParameters::getSoluteDielectric( void ) const {
RealOpenMM GBVIParameters::getSoluteDielectric() const {
return _soluteDielectric;
}
......@@ -134,7 +134,7 @@ RealOpenMM GBVIParameters::getSoluteDielectric( void ) const {
--------------------------------------------------------------------------------------- */
void GBVIParameters::setSoluteDielectric( RealOpenMM soluteDielectric ){
void GBVIParameters::setSoluteDielectric(RealOpenMM soluteDielectric) {
_soluteDielectric = soluteDielectric;
}
......@@ -146,7 +146,7 @@ void GBVIParameters::setSoluteDielectric( RealOpenMM soluteDielectric ){
--------------------------------------------------------------------------------------- */
const RealOpenMMVector& GBVIParameters::getAtomicRadii( void ) const {
const RealOpenMMVector& GBVIParameters::getAtomicRadii() const {
return _atomicRadii;
}
......@@ -158,10 +158,10 @@ const RealOpenMMVector& GBVIParameters::getAtomicRadii( void ) const {
--------------------------------------------------------------------------------------- */
void GBVIParameters::setAtomicRadii( const RealOpenMMVector& atomicRadii ){
void GBVIParameters::setAtomicRadii(const RealOpenMMVector& atomicRadii) {
if( atomicRadii.size() == _atomicRadii.size() ){
for( unsigned int ii = 0; ii < atomicRadii.size(); ii++ ){
if (atomicRadii.size() == _atomicRadii.size()) {
for (unsigned int ii = 0; ii < atomicRadii.size(); ii++) {
_atomicRadii[ii] = atomicRadii[ii];
}
} else {
......@@ -181,7 +181,7 @@ void GBVIParameters::setAtomicRadii( const RealOpenMMVector& atomicRadii ){
--------------------------------------------------------------------------------------- */
const RealOpenMMVector& GBVIParameters::getScaledRadii( void ) const {
const RealOpenMMVector& GBVIParameters::getScaledRadii() const {
return _scaledRadii;
}
......@@ -193,10 +193,10 @@ const RealOpenMMVector& GBVIParameters::getScaledRadii( void ) const {
--------------------------------------------------------------------------------------- */
void GBVIParameters::setScaledRadii( const RealOpenMMVector& scaledRadii ){
void GBVIParameters::setScaledRadii(const RealOpenMMVector& scaledRadii) {
if( scaledRadii.size() == _scaledRadii.size() ){
for( unsigned int ii = 0; ii < scaledRadii.size(); ii++ ){
if (scaledRadii.size() == _scaledRadii.size()) {
for (unsigned int ii = 0; ii < scaledRadii.size(); ii++) {
_scaledRadii[ii] = scaledRadii[ii];
}
} else {
......@@ -218,7 +218,7 @@ void GBVIParameters::setScaledRadii( const RealOpenMMVector& scaledRadii ){
--------------------------------------------------------------------------------------- */
const RealOpenMMVector& GBVIParameters::getGammaParameters( void ) const {
const RealOpenMMVector& GBVIParameters::getGammaParameters() const {
return _gammaParameters;
}
......@@ -230,10 +230,10 @@ const RealOpenMMVector& GBVIParameters::getGammaParameters( void ) const {
--------------------------------------------------------------------------------------- */
void GBVIParameters::setGammaParameters( const RealOpenMMVector& gammas ){
void GBVIParameters::setGammaParameters(const RealOpenMMVector& gammas) {
if( gammas.size() == _gammaParameters.size() ){
for( unsigned int ii = 0; ii < gammas.size(); ii++ ){
if (gammas.size() == _gammaParameters.size()) {
for (unsigned int ii = 0; ii < gammas.size(); ii++) {
_gammaParameters[ii] = gammas[ii];
}
} else {
......@@ -254,7 +254,7 @@ void GBVIParameters::setGammaParameters( const RealOpenMMVector& gammas ){
--------------------------------------------------------------------------------------- */
void GBVIParameters::setUseCutoff( RealOpenMM distance ) {
void GBVIParameters::setUseCutoff(RealOpenMM distance) {
_cutoff = true;
_cutoffDistance = distance;
......@@ -330,7 +330,7 @@ const OpenMM::RealVec* GBVIParameters::getPeriodicBox() {
--------------------------------------------------------------------------------------- */
RealOpenMM GBVIParameters::getTau( void ) const {
RealOpenMM GBVIParameters::getTau() const {
// ---------------------------------------------------------------------------------------
......@@ -340,7 +340,7 @@ RealOpenMM GBVIParameters::getTau( void ) const {
// ---------------------------------------------------------------------------------------
RealOpenMM tau;
if( getSoluteDielectric() != zero && getSolventDielectric() != zero ){
if (getSoluteDielectric() != zero && getSolventDielectric() != zero) {
tau = (one/getSoluteDielectric()) - (one/getSolventDielectric());
} else {
tau = zero;
......@@ -357,7 +357,7 @@ RealOpenMM GBVIParameters::getTau( void ) const {
--------------------------------------------------------------------------------------- */
int GBVIParameters::getBornRadiusScalingMethod( void ) const {
int GBVIParameters::getBornRadiusScalingMethod() const {
return _bornRadiusScalingMethod;
}
......@@ -369,7 +369,7 @@ int GBVIParameters::getBornRadiusScalingMethod( void ) const {
--------------------------------------------------------------------------------------- */
void GBVIParameters::setBornRadiusScalingMethod( int bornRadiusScalingMethod ){
void GBVIParameters::setBornRadiusScalingMethod(int bornRadiusScalingMethod) {
_bornRadiusScalingMethod = bornRadiusScalingMethod;
}
......@@ -381,7 +381,7 @@ void GBVIParameters::setBornRadiusScalingMethod( int bornRadiusScalingMethod ){
--------------------------------------------------------------------------------------- */
RealOpenMM GBVIParameters::getQuinticLowerLimitFactor( void ) const {
RealOpenMM GBVIParameters::getQuinticLowerLimitFactor() const {
return _quinticLowerLimitFactor;
}
......@@ -393,7 +393,7 @@ RealOpenMM GBVIParameters::getQuinticLowerLimitFactor( void ) const {
--------------------------------------------------------------------------------------- */
void GBVIParameters::setQuinticLowerLimitFactor( RealOpenMM quinticLowerLimitFactor ){
void GBVIParameters::setQuinticLowerLimitFactor(RealOpenMM quinticLowerLimitFactor) {
_quinticLowerLimitFactor = quinticLowerLimitFactor;
}
......@@ -405,7 +405,7 @@ void GBVIParameters::setQuinticLowerLimitFactor( RealOpenMM quinticLowerLimitFac
--------------------------------------------------------------------------------------- */
RealOpenMM GBVIParameters::getQuinticUpperBornRadiusLimit( void ) const {
RealOpenMM GBVIParameters::getQuinticUpperBornRadiusLimit() const {
return _quinticUpperBornRadiusLimit;
}
......@@ -417,6 +417,6 @@ RealOpenMM GBVIParameters::getQuinticUpperBornRadiusLimit( void ) const {
--------------------------------------------------------------------------------------- */
void GBVIParameters::setQuinticUpperBornRadiusLimit( RealOpenMM quinticUpperBornRadiusLimit ){
void GBVIParameters::setQuinticUpperBornRadiusLimit(RealOpenMM quinticUpperBornRadiusLimit) {
_quinticUpperBornRadiusLimit = quinticUpperBornRadiusLimit;
}
platforms/reference/src/gbsa/ObcParameters.cpp
View file @ 7fb10336
......@@ -42,21 +42,21 @@ using namespace OpenMM;
--------------------------------------------------------------------------------------- */
ObcParameters::ObcParameters( int numberOfAtoms, ObcParameters::ObcType obcType ) :
_numberOfAtoms(numberOfAtoms),
_solventDielectric( 78.3 ),
_soluteDielectric( 1.0 ),
_electricConstant(-0.5*ONE_4PI_EPS0),
_probeRadius(0.14),
_pi4Asolv( 28.3919551),
_dielectricOffset( 0.009 ),
_obcType( obcType ),
_cutoff(false),
_periodic(false) {
_atomicRadii.resize( numberOfAtoms );
_scaledRadiusFactors.resize( numberOfAtoms );
setObcTypeParameters( obcType );
ObcParameters::ObcParameters(int numberOfAtoms, ObcParameters::ObcType obcType) :
_numberOfAtoms(numberOfAtoms),
_solventDielectric(78.3),
_soluteDielectric(1.0),
_electricConstant(-0.5*ONE_4PI_EPS0),
_probeRadius(0.14),
_pi4Asolv(28.3919551),
_dielectricOffset(0.009),
_obcType(obcType),
_cutoff(false),
_periodic(false) {
_atomicRadii.resize(numberOfAtoms);
_scaledRadiusFactors.resize(numberOfAtoms);
setObcTypeParameters(obcType);
}
......@@ -66,7 +66,7 @@ ObcParameters::ObcParameters( int numberOfAtoms, ObcParameters::ObcType obcType
--------------------------------------------------------------------------------------- */
ObcParameters::~ObcParameters( ){
ObcParameters::~ObcParameters() {
}
/**---------------------------------------------------------------------------------------
......@@ -77,7 +77,7 @@ ObcParameters::~ObcParameters( ){
--------------------------------------------------------------------------------------- */
int ObcParameters::getNumberOfAtoms( void ) const {
int ObcParameters::getNumberOfAtoms() const {
return _numberOfAtoms;
}
......@@ -89,7 +89,7 @@ int ObcParameters::getNumberOfAtoms( void ) const {
--------------------------------------------------------------------------------------- */
ObcParameters::ObcType ObcParameters::getObcType( void ) const {
ObcParameters::ObcType ObcParameters::getObcType() const {
return _obcType;
}
......@@ -101,8 +101,8 @@ ObcParameters::ObcType ObcParameters::getObcType( void ) const {
--------------------------------------------------------------------------------------- */
void ObcParameters::setObcTypeParameters( ObcParameters::ObcType obcType ){
if( obcType == ObcTypeI ){
void ObcParameters::setObcTypeParameters(ObcParameters::ObcType obcType) {
if (obcType == ObcTypeI) {
_alphaObc = 0.8f;
_betaObc = 0.0f;
_gammaObc = 2.91f;
......@@ -122,7 +122,7 @@ void ObcParameters::setObcTypeParameters( ObcParameters::ObcType obcType ){
--------------------------------------------------------------------------------------- */
RealOpenMM ObcParameters::getDielectricOffset( void ) const {
RealOpenMM ObcParameters::getDielectricOffset() const {
return _dielectricOffset;
}
......@@ -134,7 +134,7 @@ RealOpenMM ObcParameters::getDielectricOffset( void ) const {
--------------------------------------------------------------------------------------- */
RealOpenMM ObcParameters::getAlphaObc( void ) const {
RealOpenMM ObcParameters::getAlphaObc() const {
return _alphaObc;
}
......@@ -146,7 +146,7 @@ RealOpenMM ObcParameters::getAlphaObc( void ) const {
--------------------------------------------------------------------------------------- */
RealOpenMM ObcParameters::getBetaObc( void ) const {
RealOpenMM ObcParameters::getBetaObc() const {
return _betaObc;
}
......@@ -158,7 +158,7 @@ RealOpenMM ObcParameters::getBetaObc( void ) const {
--------------------------------------------------------------------------------------- */
RealOpenMM ObcParameters::getGammaObc( void ) const {
RealOpenMM ObcParameters::getGammaObc() const {
return _gammaObc;
}
......@@ -170,7 +170,7 @@ RealOpenMM ObcParameters::getGammaObc( void ) const {
--------------------------------------------------------------------------------------- */
RealOpenMM ObcParameters::getSolventDielectric( void ) const {
RealOpenMM ObcParameters::getSolventDielectric() const {
return _solventDielectric;
}
......@@ -182,7 +182,7 @@ RealOpenMM ObcParameters::getSolventDielectric( void ) const {
--------------------------------------------------------------------------------------- */
void ObcParameters::setSolventDielectric( RealOpenMM solventDielectric ){
void ObcParameters::setSolventDielectric(RealOpenMM solventDielectric) {
_solventDielectric = solventDielectric;
}
/**---------------------------------------------------------------------------------------
......@@ -193,7 +193,7 @@ void ObcParameters::setSolventDielectric( RealOpenMM solventDielectric ){
--------------------------------------------------------------------------------------- */
RealOpenMM ObcParameters::getSoluteDielectric( void ) const {
RealOpenMM ObcParameters::getSoluteDielectric() const {
return _soluteDielectric;
}
......@@ -205,7 +205,7 @@ RealOpenMM ObcParameters::getSoluteDielectric( void ) const {
--------------------------------------------------------------------------------------- */
void ObcParameters::setSoluteDielectric( RealOpenMM soluteDielectric ){
void ObcParameters::setSoluteDielectric(RealOpenMM soluteDielectric) {
_soluteDielectric = soluteDielectric;
}
......@@ -217,7 +217,7 @@ void ObcParameters::setSoluteDielectric( RealOpenMM soluteDielectric ){
--------------------------------------------------------------------------------------- */
RealOpenMM ObcParameters::getElectricConstant( void ) const {
RealOpenMM ObcParameters::getElectricConstant() const {
return _electricConstant;
}
......@@ -229,7 +229,7 @@ RealOpenMM ObcParameters::getElectricConstant( void ) const {
--------------------------------------------------------------------------------------- */
RealOpenMM ObcParameters::getProbeRadius( void ) const {
RealOpenMM ObcParameters::getProbeRadius() const {
return _probeRadius;
}
......@@ -241,7 +241,7 @@ RealOpenMM ObcParameters::getProbeRadius( void ) const {
--------------------------------------------------------------------------------------- */
void ObcParameters::setProbeRadius( RealOpenMM probeRadius ){
void ObcParameters::setProbeRadius(RealOpenMM probeRadius) {
_probeRadius = probeRadius;
}
......@@ -255,7 +255,7 @@ void ObcParameters::setProbeRadius( RealOpenMM probeRadius ){
--------------------------------------------------------------------------------------- */
RealOpenMM ObcParameters::getPi4Asolv( void ) const {
RealOpenMM ObcParameters::getPi4Asolv() const {
return _pi4Asolv;
}
......@@ -271,7 +271,7 @@ void ObcParameters::setPi4Asolv(RealOpenMM pi4Asolv) {
--------------------------------------------------------------------------------------- */
const RealOpenMMVector& ObcParameters::getAtomicRadii( void ) const {
const RealOpenMMVector& ObcParameters::getAtomicRadii() const {
return _atomicRadii;
}
......@@ -283,10 +283,10 @@ const RealOpenMMVector& ObcParameters::getAtomicRadii( void ) const {
--------------------------------------------------------------------------------------- */
void ObcParameters::setAtomicRadii( const RealOpenMMVector& atomicRadii ){
void ObcParameters::setAtomicRadii(const RealOpenMMVector& atomicRadii) {
if( atomicRadii.size() == _atomicRadii.size() ){
for( unsigned int ii = 0; ii < atomicRadii.size(); ii++ ){
if (atomicRadii.size() == _atomicRadii.size()) {
for (unsigned int ii = 0; ii < atomicRadii.size(); ii++) {
_atomicRadii[ii] = atomicRadii[ii];
}
} else {
......@@ -307,7 +307,7 @@ void ObcParameters::setAtomicRadii( const RealOpenMMVector& atomicRadii ){
--------------------------------------------------------------------------------------- */
const RealOpenMMVector& ObcParameters::getScaledRadiusFactors( void ) const {
const RealOpenMMVector& ObcParameters::getScaledRadiusFactors() const {
return _scaledRadiusFactors;
}
......@@ -319,10 +319,10 @@ const RealOpenMMVector& ObcParameters::getScaledRadiusFactors( void ) const {
--------------------------------------------------------------------------------------- */
void ObcParameters::setScaledRadiusFactors( const RealOpenMMVector& scaledRadiusFactors ){
void ObcParameters::setScaledRadiusFactors(const RealOpenMMVector& scaledRadiusFactors) {
if( scaledRadiusFactors.size() == _scaledRadiusFactors.size() ){
for( unsigned int ii = 0; ii < scaledRadiusFactors.size(); ii++ ){
if (scaledRadiusFactors.size() == _scaledRadiusFactors.size()) {
for (unsigned int ii = 0; ii < scaledRadiusFactors.size(); ii++) {
_scaledRadiusFactors[ii] = scaledRadiusFactors[ii];
}
} else {
......@@ -343,7 +343,7 @@ void ObcParameters::setScaledRadiusFactors( const RealOpenMMVector& scaledRadius
--------------------------------------------------------------------------------------- */
void ObcParameters::setUseCutoff( RealOpenMM distance ) {
void ObcParameters::setUseCutoff(RealOpenMM distance) {
_cutoff = true;
_cutoffDistance = distance;
......
platforms/reference/tests/TestReferenceCustomGBForce.cpp
View file @ 7fb10336
......@@ -473,7 +473,7 @@ void testExclusions() {
// create custom GB/VI force
static CustomGBForce* createCustomGBVI( double solventDielectric, double soluteDielectric ) {
static CustomGBForce* createCustomGBVI(double solventDielectric, double soluteDielectric) {
CustomGBForce* customGbviForce = new CustomGBForce();
......@@ -524,7 +524,7 @@ static CustomGBForce* createCustomGBVI( double solventDielectric, double soluteD
// ethance GB/VI test case
static void buildEthane( GBVIForce* gbviForce, std::vector<Vec3>& positions ) {
static void buildEthane(GBVIForce* gbviForce, std::vector<Vec3>& positions) {
const int numParticles = 8;
......@@ -535,7 +535,7 @@ static void buildEthane( GBVIForce* gbviForce, std::vector<Vec3>& positions ) {
int AM1_BCC = 1;
H_charge = -0.053;
C_charge = -3.0*H_charge;
if( AM1_BCC ){
if (AM1_BCC) {
C_radius = 0.180;
C_gamma = -0.2863;
H_radius = 0.125;
......@@ -548,43 +548,43 @@ static void buildEthane( GBVIForce* gbviForce, std::vector<Vec3>& positions ) {
H_gamma = 0.1237;
}
for( int i = 0; i < numParticles; i++ ){
gbviForce->addParticle( H_charge, H_radius, H_gamma);
for (int i = 0; i < numParticles; i++) {
gbviForce->addParticle(H_charge, H_radius, H_gamma);
}
gbviForce->setParticleParameters( 1, C_charge, C_radius, C_gamma);
gbviForce->setParticleParameters( 4, C_charge, C_radius, C_gamma);
gbviForce->setParticleParameters(1, C_charge, C_radius, C_gamma);
gbviForce->setParticleParameters(4, C_charge, C_radius, C_gamma);
gbviForce->addBond( 0, 1, C_HBondDistance );
gbviForce->addBond( 2, 1, C_HBondDistance );
gbviForce->addBond( 3, 1, C_HBondDistance );
gbviForce->addBond( 1, 4, C_CBondDistance );
gbviForce->addBond( 5, 4, C_HBondDistance );
gbviForce->addBond( 6, 4, C_HBondDistance );
gbviForce->addBond( 7, 4, C_HBondDistance );
gbviForce->addBond(0, 1, C_HBondDistance);
gbviForce->addBond(2, 1, C_HBondDistance);
gbviForce->addBond(3, 1, C_HBondDistance);
gbviForce->addBond(1, 4, C_CBondDistance);
gbviForce->addBond(5, 4, C_HBondDistance);
gbviForce->addBond(6, 4, C_HBondDistance);
gbviForce->addBond(7, 4, C_HBondDistance);
std::vector<pair<int, int> > bondExceptions;
std::vector<double> bondDistances;
bondExceptions.push_back(pair<int, int>(0, 1));
bondDistances.push_back( C_HBondDistance );
bondDistances.push_back(C_HBondDistance);
bondExceptions.push_back(pair<int, int>(2, 1));
bondDistances.push_back( C_HBondDistance );
bondDistances.push_back(C_HBondDistance);
bondExceptions.push_back(pair<int, int>(3, 1));
bondDistances.push_back( C_HBondDistance );
bondDistances.push_back(C_HBondDistance);
bondExceptions.push_back(pair<int, int>(1, 4));
bondDistances.push_back( C_CBondDistance );
bondDistances.push_back(C_CBondDistance);
bondExceptions.push_back(pair<int, int>(5, 4));
bondDistances.push_back( C_HBondDistance );
bondDistances.push_back(C_HBondDistance);
bondExceptions.push_back(pair<int, int>(6, 4));
bondDistances.push_back( C_HBondDistance );
bondDistances.push_back(C_HBondDistance);
bondExceptions.push_back(pair<int, int>(7, 4));
bondDistances.push_back( C_HBondDistance );
bondDistances.push_back(C_HBondDistance);
positions.resize(numParticles);
positions[0] = Vec3(0.5480, 1.7661, 0.0000);
......@@ -600,7 +600,7 @@ static void buildEthane( GBVIForce* gbviForce, std::vector<Vec3>& positions ) {
// dimer GB/VI test case
static void buildDimer( GBVIForce* gbviForce, std::vector<Vec3>& positions ) {
static void buildDimer(GBVIForce* gbviForce, std::vector<Vec3>& positions) {
const int numParticles = 2;
......@@ -614,7 +614,7 @@ static void buildDimer( GBVIForce* gbviForce, std::vector<Vec3>& positions ) {
H_charge = 0.0;
C_charge = 0.0;
if( AM1_BCC ){
if (AM1_BCC) {
C_radius = 0.180;
C_gamma = -0.2863;
H_radius = 0.125;
......@@ -627,17 +627,17 @@ static void buildDimer( GBVIForce* gbviForce, std::vector<Vec3>& positions ) {
H_gamma = 0.1237;
}
for( int i = 0; i < numParticles; i++ ){
gbviForce->addParticle( H_charge, H_radius, H_gamma);
for (int i = 0; i < numParticles; i++) {
gbviForce->addParticle(H_charge, H_radius, H_gamma);
}
gbviForce->setParticleParameters( 1, C_charge, C_radius, C_gamma);
gbviForce->setParticleParameters(1, C_charge, C_radius, C_gamma);
gbviForce->addBond( 0, 1, C_HBondDistance );
gbviForce->addBond(0, 1, C_HBondDistance);
std::vector<pair<int, int> > bondExceptions;
std::vector<double> bondDistances;
bondExceptions.push_back(pair<int, int>(0, 1));
bondDistances.push_back( C_HBondDistance );
bondDistances.push_back(C_HBondDistance);
positions.resize(numParticles);
positions[0] = Vec3(0.0, 0.0, 0.0);
......@@ -646,7 +646,7 @@ static void buildDimer( GBVIForce* gbviForce, std::vector<Vec3>& positions ) {
// monomer GB/VI test case
static void buildMonomer( GBVIForce* gbviForce, std::vector<Vec3>& positions ) {
static void buildMonomer(GBVIForce* gbviForce, std::vector<Vec3>& positions) {
const int numParticles = 1;
......@@ -656,8 +656,8 @@ static void buildMonomer( GBVIForce* gbviForce, std::vector<Vec3>& positions ) {
H_radius = 0.125;
H_gamma = 0.2437;
for( int i = 0; i < numParticles; i++ ){
gbviForce->addParticle( H_charge, H_radius, H_gamma);
for (int i = 0; i < numParticles; i++) {
gbviForce->addParticle(H_charge, H_radius, H_gamma);
}
positions.resize(numParticles);
positions[0] = Vec3(0.0, 0.0, 0.0);
......@@ -666,7 +666,7 @@ static void buildMonomer( GBVIForce* gbviForce, std::vector<Vec3>& positions ) {
// taken from gbviForceImpl class
// computes the scaled radii based on covalent info and atomic radii
static void findScaledRadii( GBVIForce& gbviForce, std::vector<double> & scaledRadii) {
static void findScaledRadii(GBVIForce& gbviForce, std::vector<double> & scaledRadii) {
int numberOfParticles = gbviForce.getNumParticles();
int numberOfBonds = gbviForce.getNumBonds();
......@@ -674,15 +674,15 @@ static void findScaledRadii( GBVIForce& gbviForce, std::vector<double> & scaledR
// load 1-2 atom pairs along w/ bond distance using HarmonicBondForce & constraints
// numberOfBonds < 1, indicating they were not set by the user
if( numberOfBonds < 1 && numberOfParticles > 1 ){
(void) fprintf( stderr, "Warning: no covalent bonds set for GB/VI force!\n" );
if (numberOfBonds < 1 && numberOfParticles > 1) {
(void) fprintf(stderr, "Warning: no covalent bonds set for GB/VI force!\n");
}
std::vector< std::vector<int> > bondIndices;
bondIndices.resize( numberOfBonds );
bondIndices.resize(numberOfBonds);
std::vector<double> bondLengths;
bondLengths.resize( numberOfBonds );
bondLengths.resize(numberOfBonds);
scaledRadii.resize(numberOfParticles);
for (int i = 0; i < numberOfParticles; i++) {
......@@ -707,14 +707,14 @@ static void findScaledRadii( GBVIForce& gbviForce, std::vector<double> & scaledR
msg << particle2;
throw OpenMMException(msg.str());
}
if (bondLength < 0 ) {
if (bondLength < 0) {
std::stringstream msg;
msg << "GBVISoftcoreForce: negative bondlength: ";
msg << bondLength;
throw OpenMMException(msg.str());
}
bondIndices[i].push_back( particle1 );
bondIndices[i].push_back( particle2 );
bondIndices[i].push_back(particle1);
bondIndices[i].push_back(particle2);
bondLengths[i] = bondLength;
}
......@@ -732,7 +732,7 @@ static void findScaledRadii( GBVIForce& gbviForce, std::vector<double> & scaledR
// compute scaled radii (Eq. 5 of Labute paper [JCC 29 p. 1693-1698 2008])
for (int j = 0; j < (int) bonded12.size(); ++j){
for (int j = 0; j < (int) bonded12.size(); ++j) {
double charge;
double gamma;
......@@ -741,9 +741,9 @@ static void findScaledRadii( GBVIForce& gbviForce, std::vector<double> & scaledR
gbviForce.getParticleParameters(j, charge, radiusJ, gamma);
if( bonded12[j].size() == 0 ){
if( numberOfParticles > 1 ){
(void) fprintf( stderr, "Warning GBVIForceImpl::findScaledRadii atom %d has no covalent bonds; using atomic radius=%.3f.\n", j, radiusJ );
if ( bonded12[j].size() == 0) {
if (numberOfParticles > 1) {
(void) fprintf(stderr, "Warning GBVIForceImpl::findScaledRadii atom %d has no covalent bonds; using atomic radius=%.3f.\n", j, radiusJ);
}
scaledRadiusJ = radiusJ;
// errors++;
......@@ -755,7 +755,7 @@ static void findScaledRadii( GBVIForce& gbviForce, std::vector<double> & scaledR
// loop over bonded neighbors of atom j, applying Eq. 5 in Labute
scaledRadiusJ = 0.0;
for (int i = 0; i < (int) bonded12[j].size(); ++i){
for (int i = 0; i < (int) bonded12[j].size(); ++i) {
int index = bonded12[j][i];
int bondedAtomIndex = (j == bondIndices[index][0]) ? bondIndices[index][1] : bondIndices[index][0];
......@@ -772,32 +772,32 @@ static void findScaledRadii( GBVIForce& gbviForce, std::vector<double> & scaledR
a_ji *= a_ji;
a_ji = (rI2 - a_ji)/(2.0*bondLengths[index]);
scaledRadiusJ += a_ij*a_ij*(3.0*radiusI - a_ij) + a_ji*a_ji*( 3.0*radiusJ - a_ji );
scaledRadiusJ += a_ij*a_ij*(3.0*radiusI - a_ij) + a_ji*a_ji*(3.0*radiusJ - a_ji);
}
scaledRadiusJ = (radiusJ*radiusJ*radiusJ) - 0.125*scaledRadiusJ;
if( scaledRadiusJ > 0.0 ){
scaledRadiusJ = 0.95*pow( scaledRadiusJ, (1.0/3.0) );
if (scaledRadiusJ > 0.0) {
scaledRadiusJ = 0.95*pow(scaledRadiusJ, (1.0/3.0));
}
else {
scaledRadiusJ = 0.0;
}
}
//(void) fprintf( stderr, "scaledRadii %d %12.4f\n", j, scaledRadiusJ );
//(void) fprintf(stderr, "scaledRadii %d %12.4f\n", j, scaledRadiusJ);
scaledRadii[j] = scaledRadiusJ;
}
// abort if errors
if( errors ){
if (errors) {
throw OpenMMException("GBVIForceImpl::findScaledRadii errors -- aborting");
}
#if GBVIDebug
(void) fprintf( stderr, " R q gamma scaled radii no. bnds\n" );
(void) fprintf(stderr, " R q gamma scaled radii no. bnds\n");
double totalQ = 0.0;
for( int i = 0; i < (int) scaledRadii.size(); i++ ){
for (int i = 0; i < (int) scaledRadii.size(); i++) {
double charge;
double gamma;
......@@ -805,10 +805,10 @@ static void findScaledRadii( GBVIForce& gbviForce, std::vector<double> & scaledR
gbviForce.getParticleParameters(i, charge, radiusI, gamma);
totalQ += charge;
(void) fprintf( stderr, "%4d %14.5e %14.5e %14.5e %14.5e %d\n", i, radiusI, charge, gamma, scaledRadii[i], (int) bonded12[i].size() );
(void) fprintf(stderr, "%4d %14.5e %14.5e %14.5e %14.5e %d\n", i, radiusI, charge, gamma, scaledRadii[i], (int) bonded12[i].size());
}
(void) fprintf( stderr, "Total charge=%e\n", totalQ );
(void) fflush( stderr );
(void) fprintf(stderr, "Total charge=%e\n", totalQ);
(void) fflush(stderr);
#endif
#undef GBVIDebug
......@@ -819,7 +819,7 @@ static void findScaledRadii( GBVIForce& gbviForce, std::vector<double> & scaledR
// findScaledRadii() is called to calculate the scaled radii (S)
// S is derived quantity in GBVIForce, not a parameter is the case here
static void loadGbviParameters( GBVIForce* gbviForce, CustomGBForce* customGbviForce ) {
static void loadGbviParameters(GBVIForce* gbviForce, CustomGBForce* customGbviForce) {
int numParticles = gbviForce->getNumParticles();
......@@ -827,11 +827,11 @@ static void loadGbviParameters( GBVIForce* gbviForce, CustomGBForce* customGbviF
vector<double> params(4);
std::vector<double> scaledRadii;
findScaledRadii( *gbviForce, scaledRadii);
findScaledRadii(*gbviForce, scaledRadii);
for( int ii = 0; ii < numParticles; ii++) {
for (int ii = 0; ii < numParticles; ii++) {
double charge, radius, gamma;
gbviForce->getParticleParameters( ii, charge, radius, gamma );
gbviForce->getParticleParameters(ii, charge, radius, gamma);
params[0] = charge;
params[1] = radius;
params[2] = scaledRadii[ii];
......@@ -852,14 +852,14 @@ void testGBVI(GBVIForce::NonbondedMethod gbviMethod, CustomGBForce::NonbondedMet
// select molecule
if( molecule == "Monomer" ){
buildMonomer( gbvi, positions );
if (molecule == "Monomer") {
buildMonomer(gbvi, positions);
}
else if( molecule == "Dimer" ){
buildDimer( gbvi, positions );
else if (molecule == "Dimer") {
buildDimer(gbvi, positions);
}
else {
buildEthane( gbvi, positions );
buildEthane(gbvi, positions);
}
int numParticles = gbvi->getNumParticles();
......@@ -875,12 +875,12 @@ void testGBVI(GBVIForce::NonbondedMethod gbviMethod, CustomGBForce::NonbondedMet
// create customGbviForce GBVI force
CustomGBForce* customGbviForce = createCustomGBVI( gbvi->getSolventDielectric(), gbvi->getSoluteDielectric() );
CustomGBForce* customGbviForce = createCustomGBVI(gbvi->getSolventDielectric(), gbvi->getSoluteDielectric());
customGbviForce->setCutoffDistance(2.0);
// load parameters from gbvi to customGbviForce
loadGbviParameters( gbvi, customGbviForce );
loadGbviParameters(gbvi, customGbviForce);
OpenMM_SFMT::SFMT sfmt;
init_gen_rand(0, sfmt);
......
platforms/reference/tests/TestReferenceGBVIForce.cpp
View file @ 7fb10336
......@@ -80,20 +80,20 @@ void testSingleParticle() {
double tau = (1.0/forceField->getSoluteDielectric()-1.0/forceField->getSolventDielectric());
double bornEnergy = (-charge*charge/(8*PI_M*eps0))*tau/bornRadius;
double nonpolarEnergy = -gamma*tau*std::pow( radius/bornRadius, 3.0);
double nonpolarEnergy = -gamma*tau*std::pow(radius/bornRadius, 3.0);
double expectedE = (bornEnergy+nonpolarEnergy);
double obtainedE = state.getPotentialEnergy();
double diff = fabs( (obtainedE - expectedE)/expectedE );
if( log ){
(void) fprintf( stderr, "testSingleParticle expected=%14.6e obtained=%14.6e diff=%14.6e breakdown:[%14.6e %14.6e]\n",
expectedE, obtainedE, diff, bornEnergy, nonpolarEnergy );
double diff = fabs((obtainedE - expectedE)/expectedE);
if (log) {
(void) fprintf(stderr, "testSingleParticle expected=%14.6e obtained=%14.6e diff=%14.6e breakdown:[%14.6e %14.6e]\n",
expectedE, obtainedE, diff, bornEnergy, nonpolarEnergy);
}
ASSERT_EQUAL_TOL((bornEnergy+nonpolarEnergy), state.getPotentialEnergy(), 0.01);
}
void testEnergyEthane( int applyBornRadiiScaling ) {
void testEnergyEthane(int applyBornRadiiScaling) {
ReferencePlatform platform;
const int numParticles = 8;
......@@ -123,7 +123,7 @@ void testEnergyEthane( int applyBornRadiiScaling ) {
int AM1_BCC = 1;
H_charge = -0.053;
C_charge = -3.0*H_charge;
if( AM1_BCC ){
if (AM1_BCC) {
C_radius = 0.180;
C_gamma = -0.2863;
H_radius = 0.125;
......@@ -139,59 +139,59 @@ void testEnergyEthane( int applyBornRadiiScaling ) {
NonbondedForce* nonbonded = new NonbondedForce();
nonbonded->setNonbondedMethod(NonbondedForce::NoCutoff);
if( log ){
(void) fprintf( stderr, "Applying GB/VI\n" );
if (log) {
(void) fprintf(stderr, "Applying GB/VI\n");
}
GBVIForce* forceField = new GBVIForce();
if( applyBornRadiiScaling ){
forceField->setBornRadiusScalingMethod( GBVIForce::QuinticSpline );
if (applyBornRadiiScaling) {
forceField->setBornRadiusScalingMethod(GBVIForce::QuinticSpline);
}
else {
forceField->setBornRadiusScalingMethod( GBVIForce::NoScaling );
forceField->setBornRadiusScalingMethod(GBVIForce::NoScaling);
}
for( int i = 0; i < numParticles; i++ ){
for (int i = 0; i < numParticles; i++) {
system.addParticle(1.0);
forceField->addParticle( H_charge, H_radius, H_gamma);
nonbonded->addParticle( H_charge, H_radius, 0.0);
forceField->addParticle(H_charge, H_radius, H_gamma);
nonbonded->addParticle( H_charge, H_radius, 0.0);
}
forceField->setParticleParameters( 1, C_charge, C_radius, C_gamma);
forceField->setParticleParameters( 4, C_charge, C_radius, C_gamma);
forceField->setParticleParameters(1, C_charge, C_radius, C_gamma);
forceField->setParticleParameters(4, C_charge, C_radius, C_gamma);
nonbonded->setParticleParameters( 1, C_charge, C_radius, 0.0);
nonbonded->setParticleParameters( 4, C_charge, C_radius, 0.0);
nonbonded->setParticleParameters( 1, C_charge, C_radius, 0.0);
nonbonded->setParticleParameters( 4, C_charge, C_radius, 0.0);
forceField->addBond( 0, 1, C_HBondDistance );
forceField->addBond( 2, 1, C_HBondDistance );
forceField->addBond( 3, 1, C_HBondDistance );
forceField->addBond( 1, 4, C_CBondDistance );
forceField->addBond( 5, 4, C_HBondDistance );
forceField->addBond( 6, 4, C_HBondDistance );
forceField->addBond( 7, 4, C_HBondDistance );
forceField->addBond(0, 1, C_HBondDistance);
forceField->addBond(2, 1, C_HBondDistance);
forceField->addBond(3, 1, C_HBondDistance);
forceField->addBond(1, 4, C_CBondDistance);
forceField->addBond(5, 4, C_HBondDistance);
forceField->addBond(6, 4, C_HBondDistance);
forceField->addBond(7, 4, C_HBondDistance);
std::vector<pair<int, int> > bondExceptions;
std::vector<double> bondDistances;
bondExceptions.push_back(pair<int, int>(0, 1));
bondDistances.push_back( C_HBondDistance );
bondDistances.push_back(C_HBondDistance);
bondExceptions.push_back(pair<int, int>(2, 1));
bondDistances.push_back( C_HBondDistance );
bondDistances.push_back(C_HBondDistance);
bondExceptions.push_back(pair<int, int>(3, 1));
bondDistances.push_back( C_HBondDistance );
bondDistances.push_back(C_HBondDistance);
bondExceptions.push_back(pair<int, int>(1, 4));
bondDistances.push_back( C_CBondDistance );
bondDistances.push_back(C_CBondDistance);
bondExceptions.push_back(pair<int, int>(5, 4));
bondDistances.push_back( C_HBondDistance );
bondDistances.push_back(C_HBondDistance);
bondExceptions.push_back(pair<int, int>(6, 4));
bondDistances.push_back( C_HBondDistance );
bondDistances.push_back(C_HBondDistance);
bondExceptions.push_back(pair<int, int>(7, 4));
bondDistances.push_back( C_HBondDistance );
bondDistances.push_back(C_HBondDistance);
nonbonded->createExceptionsFromBonds(bondExceptions, 0.0, 0.0);
......@@ -212,8 +212,8 @@ void testEnergyEthane( int applyBornRadiiScaling ) {
context.setPositions(positions);
State state = context.getState(State::Forces | State::Energy);
if( log ){
(void) fprintf( stderr, "Energy %.4e\n", state.getPotentialEnergy() );
if (log) {
(void) fprintf(stderr, "Energy %.4e\n", state.getPotentialEnergy());
}
// Take a small step in the direction of the energy gradient.
......@@ -222,8 +222,8 @@ void testEnergyEthane( int applyBornRadiiScaling ) {
double forceSum[3] = { 0.0, 0.0, 0.0 };
for (int i = 0; i < numParticles; ++i) {
Vec3 f = state.getForces()[i];
if( log ){
(void) fprintf( stderr, "F %d [%14.6e %14.6e %14.6e]\n", i, f[0], f[1], f[2] );
if (log) {
(void) fprintf(stderr, "F %d [%14.6e %14.6e %14.6e]\n", i, f[0], f[1], f[2]);
}
norm += f[0]*f[0] + f[1]*f[1] + f[2]*f[2];
forceSum[0] += f[0];
......@@ -231,8 +231,8 @@ void testEnergyEthane( int applyBornRadiiScaling ) {
forceSum[2] += f[2];
}
norm = std::sqrt(norm);
if( log ){
(void) fprintf( stderr, "Fsum [%14.6e %14.6e %14.6e] norm=%14.6e\n", forceSum[0], forceSum[1], forceSum[2], norm );
if (log) {
(void) fprintf(stderr, "Fsum [%14.6e %14.6e %14.6e] norm=%14.6e\n", forceSum[0], forceSum[1], forceSum[2], norm);
}
const double delta = 1e-4;
......@@ -246,10 +246,10 @@ void testEnergyEthane( int applyBornRadiiScaling ) {
State state2 = context.getState(State::Energy);
if( log ){
double deltaE = fabs( state.getPotentialEnergy() - state2.getPotentialEnergy() )/delta;
if (log) {
double deltaE = fabs(state.getPotentialEnergy() - state2.getPotentialEnergy())/delta;
double diff = (deltaE - norm)/norm;
(void) fprintf( stderr, "Energies %.8e %.8e deltaE=%14.7e %14.7e diff=%14.7e\n", state.getPotentialEnergy(), state2.getPotentialEnergy(), deltaE, norm, diff );
(void) fprintf(stderr, "Energies %.8e %.8e deltaE=%14.7e %14.7e diff=%14.7e\n", state.getPotentialEnergy(), state2.getPotentialEnergy(), deltaE, norm, diff);
}
// See whether the potential energy changed by the expected amount.
......@@ -260,8 +260,8 @@ void testEnergyEthane( int applyBornRadiiScaling ) {
int main() {
try {
testSingleParticle();
testEnergyEthane( 0 );
testEnergyEthane( 1 );
testEnergyEthane(0);
testEnergyEthane(1);
}
catch(const exception& e) {
cout << "exception: " << e.what() << endl;
......
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