Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Fix to the issue #338 and issue #335 #339

Merged
merged 2 commits into from
Apr 12, 2021
Merged

Fix to the issue #338 and issue #335 #339

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
807a318
Fix to the issue #338 and issue #335
msoroush Apr 5, 2021
a90923d
Implement general method to check distance for intra-nonbonded energi…
msoroush Apr 12, 2021
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
26 changes: 7 additions & 19 deletions src/CalculateEnergy.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -710,9 +710,7 @@ void CalculateEnergy::ParticleNonbonded(double* inter,
if (trialMol.AtomExists(*partner)) {
for (uint t = 0; t < trials; ++t) {
double distSq;

if (currentAxes.InRcut(distSq, trialPos, t, trialMol.GetCoords(),
*partner, box)) {
if (currentAxes.InRcut(distSq, trialPos, t, trialMol.GetCoords(), *partner, box)) {
inter[t] += forcefield.particles->CalcEn(distSq,
kind.AtomKind(partIndex),
kind.AtomKind(*partner), 1.0);
Expand Down Expand Up @@ -1066,8 +1064,7 @@ void CalculateEnergy::MolNonbond(double & energy,
for (uint i = 0; i < molKind.nonBonded.count; ++i) {
uint p1 = mols.start[molIndex] + molKind.nonBonded.part1[i];
uint p2 = mols.start[molIndex] + molKind.nonBonded.part2[i];
currentAxes.InRcut(distSq, currentCoords, p1, p2, box);
if (forcefield.rCutSq > distSq) {
if (currentAxes.InRcut(distSq, currentCoords, p1, p2, box)) {
energy += forcefield.particles->CalcEn(distSq, molKind.AtomKind
(molKind.nonBonded.part1[i]),
molKind.AtomKind
Expand Down Expand Up @@ -1102,8 +1099,7 @@ void CalculateEnergy::MolNonbond(double & energy, cbmc::TrialMol const &mol,
uint p1 = molKind.nonBonded.part1[i];
uint p2 = molKind.nonBonded.part2[i];
if(mol.AtomExists(p1) && mol.AtomExists(p2)) {
currentAxes.InRcut(distSq, mol.GetCoords(), p1, p2, mol.GetBox());
if (forcefield.rCutSq > distSq) {
if (currentAxes.InRcut(distSq, mol.GetCoords(), p1, p2, mol.GetBox())) {
energy += forcefield.particles->CalcEn(distSq, molKind.AtomKind(p1),
molKind.AtomKind(p2), 1.0);
if (electrostatic) {
Expand Down Expand Up @@ -1136,8 +1132,7 @@ void CalculateEnergy::MolNonbond_1_4(double & energy,
for (uint i = 0; i < molKind.nonBonded_1_4.count; ++i) {
uint p1 = mols.start[molIndex] + molKind.nonBonded_1_4.part1[i];
uint p2 = mols.start[molIndex] + molKind.nonBonded_1_4.part2[i];
currentAxes.InRcut(distSq, currentCoords, p1, p2, box);
if (forcefield.rCutSq > distSq) {
if (currentAxes.InRcut(distSq, currentCoords, p1, p2, box)) {
forcefield.particles->CalcAdd_1_4(energy, distSq,
molKind.AtomKind
(molKind.nonBonded_1_4.part1[i]),
Expand Down Expand Up @@ -1173,8 +1168,7 @@ void CalculateEnergy::MolNonbond_1_4(double & energy,
uint p1 = molKind.nonBonded_1_4.part1[i];
uint p2 = molKind.nonBonded_1_4.part2[i];
if(mol.AtomExists(p1) && mol.AtomExists(p2)) {
currentAxes.InRcut(distSq, mol.GetCoords(), p1, p2, mol.GetBox());
if (forcefield.rCutSq > distSq) {
if (currentAxes.InRcut(distSq, mol.GetCoords(), p1, p2, mol.GetBox())) {
forcefield.particles->CalcAdd_1_4(energy, distSq,
molKind.AtomKind(p1),
molKind.AtomKind(p2));
Expand Down Expand Up @@ -1207,8 +1201,7 @@ void CalculateEnergy::MolNonbond_1_3(double & energy,
for (uint i = 0; i < molKind.nonBonded_1_3.count; ++i) {
uint p1 = mols.start[molIndex] + molKind.nonBonded_1_3.part1[i];
uint p2 = mols.start[molIndex] + molKind.nonBonded_1_3.part2[i];
currentAxes.InRcut(distSq, currentCoords, p1, p2, box);
if (forcefield.rCutSq > distSq) {
if (currentAxes.InRcut(distSq, currentCoords, p1, p2, box)) {
forcefield.particles->CalcAdd_1_4(energy, distSq,
molKind.AtomKind
(molKind.nonBonded_1_3.part1[i]),
Expand Down Expand Up @@ -1244,8 +1237,7 @@ void CalculateEnergy::MolNonbond_1_3(double & energy,
uint p1 = molKind.nonBonded_1_3.part1[i];
uint p2 = molKind.nonBonded_1_3.part2[i];
if(mol.AtomExists(p1) && mol.AtomExists(p2)) {
currentAxes.InRcut(distSq, mol.GetCoords(), p1, p2, mol.GetBox());
if (forcefield.rCutSq > distSq) {
if (currentAxes.InRcut(distSq, mol.GetCoords(), p1, p2, mol.GetBox())) {
forcefield.particles->CalcAdd_1_4(energy, distSq,
molKind.AtomKind(p1),
molKind.AtomKind(p2));
Expand All @@ -1269,8 +1261,6 @@ double CalculateEnergy::IntraEnergy_1_3(const double distSq, const uint atom1,
{
if(!forcefield.OneThree)
return 0.0;
else if(forcefield.rCutSq < distSq)
return 0.0;

double eng = 0.0;

Expand Down Expand Up @@ -1301,8 +1291,6 @@ double CalculateEnergy::IntraEnergy_1_4(const double distSq, const uint atom1,
{
if(!forcefield.OneFour)
return 0.0;
else if(forcefield.rCutSq < distSq)
return 0.0;

double eng = 0.0;

Expand Down
6 changes: 6 additions & 0 deletions src/FFExp6.h
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -153,6 +153,9 @@ inline void FF_EXP6::Init(ff_setup::Particle const& mie,
inline void FF_EXP6::CalcAdd_1_4(double& en, const double distSq,
const uint kind1, const uint kind2) const
{
if(forcefield.rCutSq < distSq)
return;

uint idx = FlatIndex(kind1, kind2);
if(distSq < rMaxSq_1_4[idx]) {
en += num::BIGNUM;
Expand All @@ -174,6 +177,9 @@ inline void FF_EXP6::CalcCoulombAdd_1_4(double& en, const double distSq,
const double qi_qj_Fact,
const bool NB) const
{
if(forcefield.rCutSq < distSq)
return;

double dist = sqrt(distSq);
if(NB)
en += qi_qj_Fact / dist;
Expand Down
6 changes: 6 additions & 0 deletions src/FFParticle.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -265,6 +265,9 @@ inline double FFParticle::GetRmax_1_4(const uint i, const uint j) const
inline void FFParticle::CalcAdd_1_4(double& en, const double distSq,
const uint kind1, const uint kind2) const
{
if(forcefield.rCutSq < distSq)
return;

uint index = FlatIndex(kind1, kind2);
double rRat2 = sigmaSq_1_4[index] / distSq;
double rRat4 = rRat2 * rRat2;
Expand All @@ -284,6 +287,9 @@ inline void FFParticle::CalcCoulombAdd_1_4(double& en, const double distSq,
const double qi_qj_Fact,
const bool NB) const
{
if(forcefield.rCutSq < distSq)
return;

double dist = sqrt(distSq);
if(NB)
en += qi_qj_Fact / dist;
Expand Down
6 changes: 6 additions & 0 deletions src/FFShift.h
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -127,6 +127,9 @@ inline void FF_SHIFT::Init(ff_setup::Particle const& mie,
inline void FF_SHIFT::CalcAdd_1_4(double& en, const double distSq,
const uint kind1, const uint kind2) const
{
if(forcefield.rCutSq < distSq)
return;

uint index = FlatIndex(kind1, kind2);
double rRat2 = sigmaSq_1_4[index] / distSq;
double rRat4 = rRat2 * rRat2;
Expand All @@ -146,6 +149,9 @@ inline void FF_SHIFT::CalcCoulombAdd_1_4(double& en, const double distSq,
const double qi_qj_Fact,
const bool NB) const
{
if(forcefield.rCutSq < distSq)
return;

double dist = sqrt(distSq);
if(NB)
en += qi_qj_Fact / dist;
Expand Down
6 changes: 6 additions & 0 deletions src/FFSwitch.h
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -118,6 +118,9 @@ inline void FF_SWITCH::Init(ff_setup::Particle const& mie,
inline void FF_SWITCH::CalcAdd_1_4(double& en, const double distSq,
const uint kind1, const uint kind2) const
{
if(forcefield.rCutSq < distSq)
return;

uint index = FlatIndex(kind1, kind2);
double rCutSq_rijSq = forcefield.rCutSq - distSq;
double rCutSq_rijSq_Sq = rCutSq_rijSq * rCutSq_rijSq;
Expand All @@ -144,6 +147,9 @@ inline void FF_SWITCH::CalcCoulombAdd_1_4(double& en, const double distSq,
const double qi_qj_Fact,
const bool NB) const
{
if(forcefield.rCutSq < distSq)
return;

double dist = sqrt(distSq);
if(NB)
en += qi_qj_Fact / dist;
Expand Down
6 changes: 6 additions & 0 deletions src/FFSwitchMartini.h
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -220,6 +220,9 @@ inline void FF_SWITCH_MARTINI::CalcAdd_1_4(double& en, const double distSq,
const uint kind1,
const uint kind2) const
{
if(forcefield.rCutSq < distSq)
return;

uint index = FlatIndex(kind1, kind2);
double r_2 = 1.0 / distSq;
double r_4 = r_2 * r_2;
Expand Down Expand Up @@ -253,6 +256,9 @@ inline void FF_SWITCH_MARTINI::CalcCoulombAdd_1_4(double& en,
const double qi_qj_Fact,
const bool NB) const
{
if(forcefield.rCutSq < distSq)
return;

double dist = sqrt(distSq);
if(NB)
en += qi_qj_Fact / dist;
Expand Down
9 changes: 3 additions & 6 deletions src/cbmc/DCCrankShaftAng.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -394,8 +394,7 @@ void DCCrankShaftAng::ParticleNonbonded1_N(cbmc::TrialMol const& mol,
(std::find(atoms.begin(), atoms.end(), *partner) == atoms.end())) {
for (uint t = 0; t < trials; ++t) {
double distSq;
if(data->axes.InRcut(distSq, trialPos, t, mol.GetCoords(),
*partner, box)) {
if(data->axes.InRcut(distSq, trialPos, t, mol.GetCoords(), *partner, box)) {
nonbonded[t] += data->ff.particles->CalcEn(distSq,
kind.AtomKind(partIndex),
kind.AtomKind(*partner), 1.0);
Expand Down Expand Up @@ -431,8 +430,7 @@ void DCCrankShaftAng::ParticleNonbonded1_4(cbmc::TrialMol const& mol,
(std::find(atoms.begin(), atoms.end(), *partner) == atoms.end())) {
for (uint t = 0; t < trials; ++t) {
double distSq;
if(data->axes.InRcut(distSq, trialPos, t, mol.GetCoords(),
*partner, box)) {
if(data->axes.InRcut(distSq, trialPos, t, mol.GetCoords(), *partner, box)) {
data->ff.particles->CalcAdd_1_4(nonbonded[t], distSq,
kind.AtomKind(partIndex),
kind.AtomKind(*partner));
Expand Down Expand Up @@ -468,8 +466,7 @@ void DCCrankShaftAng::ParticleNonbonded1_3(cbmc::TrialMol const& mol,
(std::find(atoms.begin(), atoms.end(), *partner) == atoms.end())) {
for (uint t = 0; t < trials; ++t) {
double distSq;
if(data->axes.InRcut(distSq, trialPos, t, mol.GetCoords(),
*partner, box)) {
if(data->axes.InRcut(distSq, trialPos, t, mol.GetCoords(), *partner, box)) {
data->ff.particles->CalcAdd_1_4(nonbonded[t], distSq,
kind.AtomKind(partIndex),
kind.AtomKind(*partner));
Expand Down
9 changes: 3 additions & 6 deletions src/cbmc/DCCrankShaftDih.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -404,8 +404,7 @@ void DCCrankShaftDih::ParticleNonbonded1_N(cbmc::TrialMol const& mol,
(std::find(atoms.begin(), atoms.end(), *partner) == atoms.end())) {
for (uint t = 0; t < trials; ++t) {
double distSq;
if(data->axes.InRcut(distSq, trialPos, t, mol.GetCoords(),
*partner, box)) {
if(data->axes.InRcut(distSq, trialPos, t, mol.GetCoords(), *partner, box)) {
nonbonded[t] += data->ff.particles->CalcEn(distSq,
kind.AtomKind(partIndex),
kind.AtomKind(*partner), 1.0);
Expand Down Expand Up @@ -441,8 +440,7 @@ void DCCrankShaftDih::ParticleNonbonded1_4(cbmc::TrialMol const& mol,
(std::find(atoms.begin(), atoms.end(), *partner) == atoms.end())) {
for (uint t = 0; t < trials; ++t) {
double distSq;
if(data->axes.InRcut(distSq, trialPos, t, mol.GetCoords(),
*partner, box)) {
if(data->axes.InRcut(distSq, trialPos, t, mol.GetCoords(), *partner, box)) {
data->ff.particles->CalcAdd_1_4(nonbonded[t], distSq,
kind.AtomKind(partIndex),
kind.AtomKind(*partner));
Expand Down Expand Up @@ -478,8 +476,7 @@ void DCCrankShaftDih::ParticleNonbonded1_3(cbmc::TrialMol const& mol,
(std::find(atoms.begin(), atoms.end(), *partner) == atoms.end())) {
for (uint t = 0; t < trials; ++t) {
double distSq;
if(data->axes.InRcut(distSq, trialPos, t, mol.GetCoords(),
*partner, box)) {
if(data->axes.InRcut(distSq, trialPos, t, mol.GetCoords(), *partner, box)) {
data->ff.particles->CalcAdd_1_4(nonbonded[t], distSq,
kind.AtomKind(partIndex),
kind.AtomKind(*partner));
Expand Down
6 changes: 3 additions & 3 deletions src/cbmc/DCHedronCycle.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -77,10 +77,10 @@ DCHedronCycle::DCHedronCycle(DCData* data, const mol_setup::MolKind& kind,
for (uint a = 0; a < angles.size(); a++) {
sumAngle += data->ff.angles->Angle(angles[a].kind);
}
//If sum of angles = 2*pi = 6.283, it means they are in a plane
//If sum of angles (sumAngle +/- 10) ~ 2*pi = 6.283, it means they are in a plane
//To avoid geometric conflict for flexible angle, we consider it fixed and
//let crankshaft sample it. 0.044 ~= 5 degree
bool angleInPlane = (std::abs(2.0 * M_PI - sumAngle) < 0.044);
//let crankshaft sample it. 0.1745 ~= 10 degree tolerance
bool angleInPlane = (std::abs(2.0 * M_PI - sumAngle) < 0.1745);
bool constrainAngInRing = false;

for (uint i = 0; i < nBonds; ++i) {
Expand Down
9 changes: 3 additions & 6 deletions src/cbmc/DCRotateOnAtom.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -422,8 +422,7 @@ void DCRotateOnAtom::ParticleNonbonded1_N(cbmc::TrialMol const& mol,
(std::find(atoms.begin(), atoms.end(), *partner) == atoms.end())) {
for (uint t = 0; t < trials; ++t) {
double distSq;
if(data->axes.InRcut(distSq, trialPos, t, mol.GetCoords(),
*partner, box)) {
if(data->axes.InRcut(distSq, trialPos, t, mol.GetCoords(), *partner, box)) {
nonbonded[t] += data->ff.particles->CalcEn(distSq,
kind.AtomKind(partIndex),
kind.AtomKind(*partner), 1.0);
Expand Down Expand Up @@ -459,8 +458,7 @@ void DCRotateOnAtom::ParticleNonbonded1_4(cbmc::TrialMol const& mol,
(std::find(atoms.begin(), atoms.end(), *partner) == atoms.end())) {
for (uint t = 0; t < trials; ++t) {
double distSq;
if(data->axes.InRcut(distSq, trialPos, t, mol.GetCoords(),
*partner, box)) {
if(data->axes.InRcut(distSq, trialPos, t, mol.GetCoords(), *partner, box)) {
data->ff.particles->CalcAdd_1_4(nonbonded[t], distSq,
kind.AtomKind(partIndex),
kind.AtomKind(*partner));
Expand Down Expand Up @@ -496,8 +494,7 @@ void DCRotateOnAtom::ParticleNonbonded1_3(cbmc::TrialMol const& mol,
(std::find(atoms.begin(), atoms.end(), *partner) == atoms.end())) {
for (uint t = 0; t < trials; ++t) {
double distSq;
if(data->axes.InRcut(distSq, trialPos, t, mol.GetCoords(),
*partner, box)) {
if(data->axes.InRcut(distSq, trialPos, t, mol.GetCoords(), *partner, box)) {
data->ff.particles->CalcAdd_1_4(nonbonded[t], distSq,
kind.AtomKind(partIndex),
kind.AtomKind(*partner));
Expand Down