/dports/science/gromacs/gromacs-2021.4/api/nblib/listed_forces/ |
H A D | bondtypes.h | 99 return std::tie(a.forceConstant(), a.equilDistance()) 100 < std::tie(b.forceConstant(), b.equilDistance()); 106 return std::tie(a.forceConstant(), a.equilDistance()) 107 == std::tie(b.forceConstant(), b.equilDistance()); 212 return std::tie(a.forceConstant(), a.exponent(), a.equilDistance()) 213 < std::tie(b.forceConstant(), b.exponent(), b.equilDistance()); 218 return std::tie(a.forceConstant(), a.exponent(), a.equilDistance()) 219 == std::tie(b.forceConstant(), b.exponent(), b.equilDistance()); 276 return std::tie(a.equilDistance(), a.forceConstant(), a.multiplicity()) 277 < std::tie(b.equilDistance(), b.forceConstant(), b.multiplicity()); [all …]
|
H A D | kernels.hpp | 117 return harmonicScalarForce(bond.forceConstant(), bond.equilDistance(), dr); in bondKernel() 181 … return g96ScalarForce(bond.forceConstant(), bond.equilDistance() * bond.equilDistance(), dr * dr); in bondKernel() 252 return morseScalarForce(bond.forceConstant(), bond.exponent(), bond.equilDistance(), dr); in bondKernel() 287 return FENEScalarForce(bond.forceConstant(), bond.equilDistance(), dr); in bondKernel() 387 return halfAttractiveScalarForce(bond.forceConstant(), bond.equilDistance(), dr); in bondKernel() 401 return harmonicScalarForce(angle.forceConstant(), angle.equilDistance(), dr); in threeCenterKernel() 410 …const T force = -properDihedral.forceConstant() * properDihedral.multiplicity() * std::sin(deltaPh… in fourCenterKernel() 411 const T ePot = properDihedral.forceConstant() * ( 1 + std::cos(deltaPhi) ); in fourCenterKernel() 448 const T force = -improperDihedral.forceConstant() * deltaPhi; in fourCenterKernel() 449 const T ePot = 0.5 * improperDihedral.forceConstant() * deltaPhi * deltaPhi; in fourCenterKernel()
|
H A D | conversions.hpp | 133 param.harmonic.krA = hbond.forceConstant(); in transferParameters() 145 param.harmonic.krA = angle.forceConstant(); in transferParameters() 158 param.pdihs.cpA = dihedral.forceConstant(); in transferParameters()
|
/dports/biology/protomol/protomol/framework/base/ |
H A D | iSGPAR.cpp | 28 for (unsigned int i=0; i<p.forceConstant.size(); i++) in operator <<() 29 OS <<","<<p.forceConstant[i]<<","<<p.distance[i]; in operator <<() 36 for (unsigned int i=0; i<p.forceConstant.size(); i++) in operator <<() 37 … OS<<","<<p.forceConstant[i]<<","<<p.angleval[i]<<","<<p.ub_flag<<","<<p.k_ub[i]<<","<<p.r_ub[i]; in operator <<() 44 for (unsigned int i=0; i<p.forceConstant.size(); i++) { in operator <<() 46 for(unsigned int j=0;j<p.forceConstant[i].size();++j) in operator <<() 47 OS << ","<<p.forceConstant[i][j]; in operator <<() 58 for (unsigned int i=0; i<p.forceConstant.size(); i++) in operator <<() 59 OS<<","<<p.forceConstant[i]<< ","<<p.periodicity[i]<<","<<p.phaseShift[i]; in operator <<()
|
H A D | iSGPAR.h | 32 forceConstant.resize(a); in Bond() 42 std::vector<Real> forceConstant; member 60 forceConstant.resize(a); in Angle() 74 std::vector<Real> forceConstant; member 104 forceConstant.resize(a); in Dihedral() 121 std::vector< std::vector<Real> > forceConstant; member 143 forceConstant.resize(a); in Improper() 158 std::vector<Real> forceConstant; member
|
H A D | PAR.h | 30 …:string b, std::string c, Real d, Real e):number(a),atom1(b),atom2(c),forceConstant(d),distance(e)… in Bond() 36 Real forceConstant; ///< force constant member 53 number(a),atom1(b),atom2(c),atom3(d),forceConstant(e),angleval(f),ub_flag(g),k_ub(h),r_ub(i){} in Angle() 60 Real forceConstant; ///< force constant member 84 …multiplicity(1),forceConstant(std::vector<Real>(1,f)),periodicity(std::vector<int>(1,g)),phaseShif… in Dihedral() 89 multiplicity(f),forceConstant(g),periodicity(h),phaseShift(i){} in Dihedral() 98 std::vector< Real > forceConstant; ///< force constant member 114 number(a),atom1(b),atom2(c),atom3(d),atom4(e),forceConstant(f),periodicity(g),phaseShift(h){} in Improper() 121 Real forceConstant; ///< force constant member
|
/dports/java/jgraph/jgraph-java-5.13.0.4/src/com/jgraph/layout/organic/ |
H A D | JGraphFastOrganicLayout.java | 52 protected double forceConstant = 50; field in JGraphFastOrganicLayout 167 if (forceConstant < 0.001) in run() 168 forceConstant = 0.001; in run() 169 forceConstantSquared = forceConstant * forceConstant; in run() 320 double force = (deltaLengthSquared) / forceConstant; in calcAttraction() 399 return forceConstant; in getForceConstant() 406 public void setForceConstant(double forceConstant) { in setForceConstant() argument 407 this.forceConstant = forceConstant; in setForceConstant()
|
/dports/science/rdkit/rdkit-Release_2021_03_5/Code/ForceField/Wrap/ |
H A D | ForceField.cpp | 35 self->field.get(), idx1, idx2, minLen, maxLen, forceConstant); in ForceFieldAddDistanceConstraint() 54 double forceConstant) { in UFFAddAngleConstraint() argument 57 forceConstant); in UFFAddAngleConstraint() 65 double forceConstant) { in UFFAddTorsionConstraint() argument 68 maxDihedralDeg, forceConstant); in UFFAddTorsionConstraint() 75 self->field.get(), idx, maxDispl, forceConstant); in UFFAddPositionConstraint() 90 double forceConstant) { in MMFFAddAngleConstraint() argument 93 forceConstant); in MMFFAddAngleConstraint() 101 double forceConstant) { in MMFFAddTorsionConstraint() argument 104 maxDihedralDeg, forceConstant); in MMFFAddTorsionConstraint() [all …]
|
/dports/biology/protomol/protomol/applications/iSGProtomol-app/forces/ |
H A D | iSGAngleSystemForce.h | 100 Real forceConstant = currentAngle.forceConstant; in calcAngle() local 131 Real dpotdtheta = 2.0 * forceConstant * (theta - restAngle); in calcAngle() 160 Real eHarmonic = forceConstant * (theta - restAngle)*(theta - restAngle); in calcAngle() 165 Real DeltaMuHarmonic = eHarmonic * DeltaK / forceConstant - dpotdtheta * DeltaTheta0; in calcAngle() 181 Report::report << "k = " << forceConstant << ", theta0 = " << restAngle << Report::endr; in calcAngle() 211 Real restAngle, forceConstant, ureyBradleyConstant, ureyBradleyRestLength; in calcAngleEnergy() local 219 forceConstant = currentAngle.forceConstant; in calcAngleEnergy() 239 eHarmonic = forceConstant * (theta - restAngle)*(theta - restAngle); in calcAngleEnergy()
|
H A D | iSGMTorsionSystemForce.h | 91 * currTorsion.forceConstant[i] in calcTorsion() 97 Real Vtorsion = currTorsion.forceConstant[i] * ( 1.0 + cos( in calcTorsion() 113 Report::report << "k = " << currTorsion.forceConstant[i] in calcTorsion() 137 Real ftorsion = 2.0 * currTorsion.forceConstant[i] * diff; in calcTorsion() 141 Real Vtorsion = currTorsion.forceConstant[i] * diff * diff; in calcTorsion() 153 Report::report << "k = " << currTorsion.forceConstant[i] in calcTorsion() 279 energy += currTorsion.forceConstant[i] * ( 1.0 + cos( in calcTorsionEnergy() 295 energy += currTorsion.forceConstant[i] * diff * diff; in calcTorsionEnergy()
|
/dports/biology/protomol/protomol/framework/io/ |
H A D | PARWriter.cpp | 83 << par.bonds[i].forceConstant in write() 101 << par.angles[i].forceConstant in write() 128 << par.dihedrals[i].forceConstant[j] in write() 151 << par.impropers[i].forceConstant in write() 234 << par.bonds[i].forceConstant in write() 251 << par.angles[i].forceConstant in write() 275 if(par.dihedrals[i].forceConstant.size() > 1){ in write() 277 << par.dihedrals[i].forceConstant.size(); in write() 280 << par.dihedrals[i].forceConstant[0] in write() 288 << par.dihedrals[i].forceConstant[j] in write() [all …]
|
/dports/biology/protomol/protomol/framework/forces/ |
H A D | AngleSystemForce.h | 102 Real forceConstant = currentAngle.forceConstant; in calcAngle() local 128 Real dpotdtheta = 2.0 * forceConstant * ( theta - restAngle); in calcAngle() 157 Real eHarmonic = forceConstant * (theta - restAngle)*(theta - restAngle); in calcAngle() 185 Real restAngle, forceConstant, ureyBradleyConstant, ureyBradleyRestLength; in calcAngleEnergy() local 193 forceConstant = currentAngle.forceConstant; in calcAngleEnergy() 213 eHarmonic = forceConstant * (theta - restAngle)*(theta - restAngle); in calcAngleEnergy()
|
H A D | MTorsionSystemForce.h | 93 * currTorsion.forceConstant[i] in calcTorsion() 98 energy += currTorsion.forceConstant[i] * ( 1.0 + cos( in calcTorsion() 113 dpotdphi += 2.0 * currTorsion.forceConstant[i] * diff; in calcTorsion() 116 energy += currTorsion.forceConstant[i] * diff * diff; in calcTorsion() 233 energy += currTorsion.forceConstant[i] * ( 1.0 + cos( in calcTorsionEnergy() 249 energy += currTorsion.forceConstant[i] * diff * diff; in calcTorsionEnergy()
|
/dports/java/jgraphx/jgraphx-4.2.2/src/com/mxgraph/layout/ |
H A D | mxFastOrganicLayout.java | 43 protected double forceConstant = 50; field in mxFastOrganicLayout 232 return forceConstant; in getForceConstant() 241 forceConstant = value; in setForceConstant() 346 if (forceConstant < 0.001) in execute() 348 forceConstant = 0.001; in execute() 351 forceConstantSquared = forceConstant * forceConstant; in execute() 589 double force = (deltaLengthSquared) / forceConstant; in calcAttraction()
|
/dports/science/gromacs/gromacs-2021.4/src/gromacs/applied_forces/awh/ |
H A D | dimparams.h | 110 static DimParams pullDimParams(double conversionFactor, double forceConstant, double beta) in pullDimParams() 112 PullDimParams pullDimParams = { forceConstant, forceConstant * beta }; in pullDimParams()
|
/dports/biology/protomol/protomol/applications/iSGProtomol-app/integrators/ |
H A D | ModifierISG.cpp | 398 topo->angles[*iter].forceConstant = angles[myISGAngle].forceConstant[FinalType]; in setForcesAfterTransformation() 424 …topo->dihedrals[*iter].forceConstant[i] = dihedrals[myISGDihedral].forceConstant[FinalType][i]; in setForcesAfterTransformation() 446 topo->impropers[*iter].forceConstant[0] = impropers[myISGImproper].forceConstant[FinalType]; in setForcesAfterTransformation() 623 - bonds[myISGBond].forceConstant[Old]; in pickNewMolecule() 652 - angles[myISGAngle].forceConstant[Old]; in pickNewMolecule() 688 - dihedrals[myISGDihedral].forceConstant[Old][i]; in pickNewMolecule() 719 - impropers[myISGImproper].forceConstant[Old]; in pickNewMolecule() 879 - bonds[myISGBond].forceConstant[Old]; in readXSCs() 908 - angles[myISGAngle].forceConstant[Old]; in readXSCs() 943 - dihedrals[myISGDihedral].forceConstant[Old][i]; in readXSCs() [all …]
|
H A D | iSGIntegrator.cpp | 663 + myBonds[myISGBond].forceConstant[OldType] * (thisStage - myLambda); in modifyForces() 718 …myTopo->angles[*iter].forceConstant = myAngles[myISGAngle].forceConstant[NewType] * (myLambda - ol… in modifyForces() 719 + myAngles[myISGAngle].forceConstant[OldType] * (thisStage - myLambda); in modifyForces() 762 myTopo->dihedrals[*iter].forceConstant[i] = in modifyForces() 805 myTopo->impropers[*iter].forceConstant[0] = in modifyForces() 806 myImpropers[myISGImproper].forceConstant[NewType] * (myLambda - oldStage) in modifyForces() 944 myTopo->bonds[*iter].DeltaK = myBonds[myISGBond].forceConstant[NewType] in checkForTransformation() 945 - myBonds[myISGBond].forceConstant[OldType]; in checkForTransformation() 981 - myAngles[myISGAngle].forceConstant[OldType]; in checkForTransformation() 1022 - myDihedrals[myISGDihedral].forceConstant[OldType][i]; in checkForTransformation() [all …]
|
/dports/science/gromacs/gromacs-2021.4/docs/nblib/ |
H A D | listed-dev.rst | 29 For example, ``NAMED_MEMBERS(forceConstant, equilDistance)`` will expand to 33 inline auto& forceConstant() { return std::get<0>(*this); } 35 inline const auto& forceConstant() const { return std::get<0>(*this); } 44 * V(r; forceConstant, equilDistance, scaleFactor) 45 * = forceConstant * exp( (r - equilDistance) / scaleFactor) 55 NAMED_MEMBERS(forceConstant, equilDistance, scaleFactor) 119 return newBondForce(bond.forceConstant(), bond.equilDistance(), bond.scaleFactor(), dr);
|
/dports/biology/protomol/protomol/framework/topology/ |
H A D | Angle.h | 18 Angle():atom1(-1),atom2(-1),atom3(-1),restAngle(0.0),forceConstant(0.0), in Angle() 38 Real forceConstant; variable
|
H A D | Torsion.h | 24 forceConstant.clear(); in Torsion() 44 std::vector< Real > forceConstant; ///< The force constant ($k$ value) for this interaction. variable
|
/dports/science/gabedit/GabeditSrc251_300720/src/MolecularMechanics/ |
H A D | MolecularMechanics.c | 226 forceConstant[0] = 0.0; in getStretchParameters() 244 forceConstant[0] = amberParameters->bondStretchTerms[i].forceConstant; in getStretchParameters() 256 forceConstant[0] = 0.0; in getBendParameters() 275 forceConstant[0] = amberParameters->angleBendTerms[i].forceConstant; in getBendParameters() 384 forceConstant[0] = 0.0; in getImproperTorsionParameters() 733 forceConstant = 310; in setStretchParameters() 737 forceConstant = 415; in setStretchParameters() 743 forceConstant = 340; in setStretchParameters() 749 forceConstant = 570; in setStretchParameters() 760 forceConstant = 0; in setStretchParameters() [all …]
|
H A D | MolecularMechanics.h | 47 gdouble forceConstant; member 54 gdouble forceConstant; member
|
/dports/biology/protomol/protomol/framework/integrators/ |
H A D | LangevinImpulseIntegrator.cpp | 60 const Real forceConstant = 2*Constant::BOLTZMANN*myLangevinTemperature*myGamma; in fluctuationLI() local 64 Real langDriftVal = sqrt(forceConstant/mass)/myGamma; in fluctuationLI() 79 …(*myVelocities)[i] = (*myVelocities)[i]*exp(-myGamma*dt)+gaussRandCoord1*sqrt(forceConstant/mass)*… in fluctuationLI()
|
H A D | BBKIntegrator.cpp | 66 Real forceConstant =(2*Constant::BOLTZMANN*myLangevinTemperature*myGamma)/dt; in addRandomForceToMyForce() local 75 randomForce *= sqrt(forceConstant*mass); in addRandomForceToMyForce()
|
/dports/biology/protomol/protomol/framework/frontend/ |
H A D | buildTopology.cpp | 177 tempbond.springConstant = currentbond->second->forceConstant; in buildTopology() 246 tempangle.forceConstant = currentangle->second->forceConstant; in buildTopology() 258 if(tempangle.forceConstant == 0.0) in buildTopology() 329 torsion.forceConstant = currentdihedral->second->forceConstant; in buildTopology() 339 torsion.forceConstant.resize(1); in buildTopology() 355 tmp.forceConstant.push_back(torsion.forceConstant[tmp.multiplicity]); in buildTopology() 485 torsion.forceConstant.push_back(currentimproper->second->forceConstant); in buildTopology()
|