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Searched refs:forceConstant (Results 1 – 25 of 50) sorted by relevance

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/dports/science/gromacs/gromacs-2021.4/api/nblib/listed_forces/
H A Dbondtypes.h99 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 Dkernels.hpp117 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 Dconversions.hpp133 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 DiSGPAR.cpp28 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 DiSGPAR.h32 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 DPAR.h30 …: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 DJGraphFastOrganicLayout.java52 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 DForceField.cpp35 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 DiSGAngleSystemForce.h100 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 DiSGMTorsionSystemForce.h91 * 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 DPARWriter.cpp83 << 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 DAngleSystemForce.h102 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 DMTorsionSystemForce.h93 * 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 DmxFastOrganicLayout.java43 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 Ddimparams.h110 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 DModifierISG.cpp398 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 DiSGIntegrator.cpp663 + 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 Dlisted-dev.rst29 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 DAngle.h18 Angle():atom1(-1),atom2(-1),atom3(-1),restAngle(0.0),forceConstant(0.0), in Angle()
38 Real forceConstant; variable
H A DTorsion.h24 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 DMolecularMechanics.c226 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 DMolecularMechanics.h47 gdouble forceConstant; member
54 gdouble forceConstant; member
/dports/biology/protomol/protomol/framework/integrators/
H A DLangevinImpulseIntegrator.cpp60 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 DBBKIntegrator.cpp66 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 DbuildTopology.cpp177 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()

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