Closed nicolasgrimmig closed 10 years ago
<Simulation simName = "TIP3P" inputFromResults = "yes"
<InputWF name = "dummy" cutoff = "5.3" interpolation = "1" selfContribution = "1" weight = "1" /> <Controller dt = "0.0000031" timesteps = "250" statusEvery = "1000" <!--IntegratorScalar species = "H2O" scalar = "s" symbol = "s" /--> <IntegratorVelocityVerletDisp species = "H2O" lambda = "0.5" mass = "18.0" />
<InputWF name = "dummy" cutoff = "5.3" interpolation = "1" selfContribution = "1" weight = "1" />
<Controller dt = "0.0000031" timesteps = "250" statusEvery = "1000"
<!--IntegratorScalar species = "H2O" scalar = "s" symbol = "s" /--> <IntegratorVelocityVerletDisp species = "H2O" lambda = "0.5" mass = "18.0" />
<IntegratorScalar species = "messurePoint" scalar = "dum" symbol = "dum" /> <IntegratorScalarLambda species = "H2O" lambda = "1" scalar = "localdensity" symbol = "localdensity" />
<ParticleTensor stage = "2" species = "H2O" expression = "-uVecX(1)@uVecY(1)" symbol = "Dxy" /> <ParticleTensor stage = "2" species = "H2O" expression = "uVecX(1)@uVecZ(1)" symbol = "Dxz" /> <ParticleTensor stage = "2" species = "H2O" expression = "uVecY(1)@uVecX(1)" symbol = "Dyx" /> <ParticleTensor stage = "2" species = "H2O" expression = "-uVecY(1)@uVecZ(1)" symbol = "Dyz" /> <ParticleTensor stage = "2" species = "H2O" expression = "-uVecZ(1)@uVecX(1)" symbol = "Dzx" /> <ParticleTensor stage = "2" species = "H2O" expression = "uVecZ(1)@uVecY(1)" symbol = "Dzy" />
<ParticleVector symbol = "rH1" species = "H2O" expression = "{rotmat}:(uVecY(0.756950327263661)+uVecZ(0.520784245882929))" stage = "1" />
<ParticleTensor species = "H2O" expression = "{Dxy}zCoord([rH1])+{Dxz}yCoord([rH1])+{Dyx}zCoord([rH1])+{Dyz}xCoord([rH1])+{Dzx}yCoord([rH1])+{Dzy}xCoord([rH1])" symbol = "rH1x" stage = "1" />
<ParticleVector symbol = "rH2" species = "H2O" expression = "{rotmat}:(uVecY(-0.756950327263661)+uVecZ(0.520784245882929))" stage = "1" />
<ParticleTensor species = "H2O" expression = "{Dxy}zCoord([rH2])+{Dxz}yCoord([rH2])+{Dyx}zCoord([rH2])+{Dyz}xCoord([rH2])+{Dzx}yCoord([rH2])+{Dzy}xCoord([rH2])" symbol = "rH2x" stage = "1" />
<ParticleVector symbol = "rM" species = "H2O" expression = "{rotmat}:(uVecZ(-0.0650980307353661))" stage = "1" />
<ParticleTensor species = "H2O" expression = "{Dxy}zCoord([rM])+{Dxz}yCoord([rM])+{Dyx}zCoord([rM])+{Dyz}xCoord([rM])+{Dzx}yCoord([rM])+{Dzy}xCoord([rM])" symbol = "rMx" stage = "1" />
<PairVector species1 = "H2O" species2 = "H2O" symbol = "dH1H1" expression = "[rH1j]+[rj]-([rH1i]+[ri])" cutoff = "5.3" /> <PairParticleVector species1 = "H2O" species2 = "H2O" symbol = "fH1H1" expression = "-0.25*[dH1H1ij]/sqrt([dH1H1ij]:[dH1H1ij])^3" symmetry = "-1" cutoff = "5.3" />
<PairVector species1 = "H2O" species2 = "H2O" symbol = "dH2H2" expression = "[rH2j]+[rj]-([rH2i]+[ri])" cutoff = "5.3" /> <PairParticleVector species1 = "H2O" species2 = "H2O" symbol = "fH2H2" expression = "-0.25*[dH2H2ij]/sqrt([dH2H2ij]:[dH2H2ij])^3" symmetry = "-1" cutoff = "5.3" />
<PairVector species1 = "H2O" species2 = "H2O" symbol = "dH1H2" expression = "[rH2j]+[rj]-([rH1i]+[ri])" cutoff = "5.3" /> <PairParticleVector species1 = "H2O" species2 = "H2O" symbol = "fH1H2" expression = "-0.25*[dH1H2ij]/sqrt([dH1H2ij]:[dH1H2ij])^3" symmetry = "-1" cutoff = "5.3" />
<PairVector species1 = "H2O" species2 = "H2O" symbol = "dH2H1" expression = "[rH1j]+[rj]-([rH2i]+[ri])" cutoff = "5.3" /> <PairParticleVector species1 = "H2O" species2 = "H2O" symbol = "fH2H1" expression = "-0.25*[dH2H1ij]/sqrt([dH2H1ij]:[dH2H1ij])^3" symmetry = "-1" cutoff = "5.3" />
<PairVector species1 = "H2O" species2 = "H2O" symbol = "dH1M" expression = "[rMj]+[rj]-([rH1i]+[ri])" cutoff = "5.3" /> <PairParticleVector species1 = "H2O" species2 = "H2O" symbol = "fH1M" expression = "0.5*[dH1Mij]/sqrt([dH1Mij]:[dH1Mij])^3" symmetry = "-1" cutoff = "5.3" />
<PairVector species1 = "H2O" species2 = "H2O" symbol = "dH2M" expression = "[rMj]+[rj]-([rH2i]+[ri])" cutoff = "5.3" /> <PairParticleVector species1 = "H2O" species2 = "H2O" symbol = "fH2M" expression = "0.5*[dH2Mij]/(sqrt([dH2Mij]:[dH2Mij])^3)" symmetry = "-1" cutoff = "5.3" />
<PairVector species1 = "H2O" species2 = "H2O" symbol = "dMH1" expression = "[rH1j]+[rj]-([rMi]+[ri])" cutoff = "5.3" /> <PairParticleVector species1 = "H2O" species2 = "H2O" symbol = "fMH1" expression = "0.5*[dMH1ij]/sqrt([dMH1ij]:[dMH1ij])^3" symmetry = "-1" cutoff = "5.3" />
<PairVector species1 = "H2O" species2 = "H2O" symbol = "dMH2" expression = "[rH2j]+[rj]-([rMi]+[ri])" cutoff = "5.3" /> <PairParticleVector species1 = "H2O" species2 = "H2O" symbol = "fMH2" expression = "0.5*[dMH2ij]/sqrt([dMH2ij]:[dMH2ij])^3" symmetry = "-1" cutoff = "5.3" />
<PairVector species1 = "H2O" species2 = "H2O" symbol = "dMM" expression = "[rMj]+[rj]-([rMi]+[ri])" cutoff = "5.3" /> <PairParticleVector species1 = "H2O" species2 = "H2O" symbol = "fMM" expression = "-[dMMij]/sqrt([dMMij]:[dMMij])^3" symmetry = "-1" cutoff = "5.3" />
<FParticleVels forceName = "Coulomb" species = "H2O" expression = "([fH1H1]+[fH1H2]+[fH2H1]+[fH2H2]+[fMH1]+[fMH2]+[fH1M]+[fH2M]+[fMM])" />
<FPairVector forceName = "TauH1H1H2O" species1 = "H2O" species2 = "H2O" weightingFunction = "dummy" pairFactor = "idVec(1/26)" particleFactor_i = "{rH1xi}:([fH1H1i]+[fH1H2i]+[fH1Mi])" particleFactor_j = "{rH1xj}:([fH1H1j]+[fH1H2j]+[fH1Mj])" vector = "omega" symmetry = "1" />
<FPairVector forceName = "TauH2H1H2O" species1 = "H2O" species2 = "H2O" weightingFunction = "dummy" pairFactor = "idVec(1/26)" particleFactor_i = "{rH2xi}:([fH2H1i]+[fH2H2i]+[fH2Mi])" particleFactor_j = "{rH2xj}:([fH2H1j]+[fH2H2j]+[fH2Mj])" vector = "omega" symmetry = "1" />
<FPairVector forceName = "TauOH1H2O" species1 = "H2O" species2 = "H2O" weightingFunction = "dummy" pairFactor = "idVec(1/26)" particleFactor_i = "{rMxi}:([fMH1i]+[fMH2i]+[fMMi])" particleFactor_j = "{rMxj}:([fMH1j]+[fMH2j]+[fMMj])" vector = "omega" symmetry = "1" />
<!-- particleFactor_i = "uVecY(0.001)" particleFactor_j = "uVecY(0.001)" particleFactor_i = "{rMxi}:([fMMi])" particleFactor_j = "{rMxj}:([fMMj])" /-->
<PairParticleScalar species1 = "H2O" species2 = "H2O" symbol = "EPotH1H1" expression = "0.25/sqrt([dH1H1ij]:[dH1H1ij])" cutoff = "5.3" /> <PairParticleScalar species1 = "H2O" species2 = "H2O" symbol = "EPotH2H2" expression = "0.25/sqrt([dH2H2ij]:[dH2H2ij])" cutoff = "5.3" /> <PairParticleScalar species1 = "H2O" species2 = "H2O" symbol = "EPotH1H2" expression = "0.25/sqrt([dH1H2ij]:[dH1H2ij])" cutoff = "5.3" /> <PairParticleScalar species1 = "H2O" species2 = "H2O" symbol = "EPotH2H1" expression = "0.25/sqrt([dH2H1ij]:[dH2H1ij])" cutoff = "5.3" /> <PairParticleScalar species1 = "H2O" species2 = "H2O" symbol = "EPotH1M" expression = "-0.5/sqrt([dH1Mij]:[dH1Mij])" cutoff = "5.3" /> <PairParticleScalar species1 = "H2O" species2 = "H2O" symbol = "EPotH2M" expression = "-0.5/sqrt([dH2Mij]:[dH2Mij])" cutoff = "5.3" /> <PairParticleScalar species1 = "H2O" species2 = "H2O" symbol = "EPotMH1" expression = "-0.5/sqrt([dMH1ij]:[dMH1ij])" cutoff = "5.3" /> <PairParticleScalar species1 = "H2O" species2 = "H2O" symbol = "EPotMH2" expression = "-0.5/sqrt([dMH2ij]:[dMH2ij])" cutoff = "5.3" /> <PairParticleScalar species1 = "H2O" species2 = "H2O" symbol = "EPotMM" expression = "1.0/sqrt([dMMij]:[dMMij])" cutoff = "5.3" />
<ParticleScalar species = "H2O" expression ="1.0-sqrt(q0*q0+q1*q1+q2*q2+q3*q3)" symbol = "norm_quater" /> <ParticleScalar species = "H2O" expression = "966.4*(1.77*(xCoord([omega])^2)+0.615*(yCoord([omega])^2)+1.155*(zCoord([omega])^2))/2" symbol = "EKin" /> <ParticleScalar species = "H2O" expression = "966.4*(EPotH1H1+EPotH2H2+EPotH1H2+EPotH2H1+EPotH1M+EPotH2M+EPotMH1+EPotMH2+EPotMM)/2" symbol = "EPot" />
<ParticleScalar species ="H2O" symbol = "Etot" expression = "(EKin+EPot)- 0.6909" /> <ParticleVector species = "H2O" expression = "uVecX(1.770xCoord([omega]))+uVecY(0.615yCoord([omega]))+uVecZ(1.155*zCoord([omega]))" symbol = "AngMom" /> <ParticleVector species = "H2O" expression = "T({rotmat}):[AngMom]" symbol = "AngMomLab" /> <ParticleVector species = "H2O" expression = "T({rotmat}):[omega]" symbol = "OmegaLab" />
<PairParticleScalar species1 = "H2O" species2 = "H2O" symbol = "amountHB" expression = "step(3.1-sqrt([dMMij]:[dMMij]))" cutoff = "5.3" /> <PairParticleScalar species1 = "messurePoint" species2 = "H2O" symbol = "desity" expression = "1/(5.3*5.3*5.3)" cutoff = "5.3" /> <ParticleScalar species = "H2O" symbol = "omegaXDistribution" expression = "exp(-1/2*1.770*xCoord([omega])^2)" /> <ParticleScalar species = "H2O" symbol = "omegaYDistribution" expression = "exp(-1/2*0.615*yCoord([omega])^2)" /> <ParticleScalar species = "messurePoint" symbol = "dum" expression = "1" overwrite = "yes" /> <ParticleScalar species = "H2O" symbol = "omegaZDistribution" expression = "exp(-1/2*1.155*zCoord([omega])^2)" /> <FPairScalar species1 = "H2O" species2 = "H2O" pairFactor = "-([vi]-[vj]):[rij]" weightingFunction = "dummy" symmetry = "1" scalar = "localdensity"
/>
<GridAveragerStructured nX = "10" nY = "10" nZ = "10" measureEvery = "250"
<LocalDensity species = "H2O" densitySymbol = "localdensity" />
<OutputFile nameOutputFile = "results/vels/vels.dat" multipleFiles = "yes" columns = "H2O_velocity_mean|H2O_localdensity_mean"
Hi Nico, do you think it is still worth to look at this? Or might it be a problem caused by redundant contents in the input?
<Simulation simName = "TIP3P" inputFromResults = "yes"
<ParticleTensor stage = "2" species = "H2O" expression = "-uVecX(1)@uVecY(1)" symbol = "Dxy" /> <ParticleTensor stage = "2" species = "H2O" expression = "uVecX(1)@uVecZ(1)" symbol = "Dxz" /> <ParticleTensor stage = "2" species = "H2O" expression = "uVecY(1)@uVecX(1)" symbol = "Dyx" /> <ParticleTensor stage = "2" species = "H2O" expression = "-uVecY(1)@uVecZ(1)" symbol = "Dyz" /> <ParticleTensor stage = "2" species = "H2O" expression = "-uVecZ(1)@uVecX(1)" symbol = "Dzx" /> <ParticleTensor stage = "2" species = "H2O" expression = "uVecZ(1)@uVecY(1)" symbol = "Dzy" />
<ParticleVector symbol = "rH1" species = "H2O" expression = "{rotmat}:(uVecY(0.756950327263661)+uVecZ(0.520784245882929))" stage = "1" />
<ParticleTensor species = "H2O" expression = "{Dxy}zCoord([rH1])+{Dxz}yCoord([rH1])+{Dyx}zCoord([rH1])+{Dyz}xCoord([rH1])+{Dzx}yCoord([rH1])+{Dzy}xCoord([rH1])" symbol = "rH1x" stage = "1" />
<ParticleVector symbol = "rH2" species = "H2O" expression = "{rotmat}:(uVecY(-0.756950327263661)+uVecZ(0.520784245882929))" stage = "1" />
<ParticleTensor species = "H2O" expression = "{Dxy}zCoord([rH2])+{Dxz}yCoord([rH2])+{Dyx}zCoord([rH2])+{Dyz}xCoord([rH2])+{Dzx}yCoord([rH2])+{Dzy}xCoord([rH2])" symbol = "rH2x" stage = "1" />
<ParticleVector symbol = "rM" species = "H2O" expression = "{rotmat}:(uVecZ(-0.0650980307353661))" stage = "1" />
<ParticleTensor species = "H2O" expression = "{Dxy}zCoord([rM])+{Dxz}yCoord([rM])+{Dyx}zCoord([rM])+{Dyz}xCoord([rM])+{Dzx}yCoord([rM])+{Dzy}xCoord([rM])" symbol = "rMx" stage = "1" />
<PairVector species1 = "H2O" species2 = "H2O" symbol = "dH1H1" expression = "[rH1j]+[rj]-([rH1i]+[ri])" cutoff = "5.3" /> <PairParticleVector species1 = "H2O" species2 = "H2O" symbol = "fH1H1" expression = "-0.25*[dH1H1ij]/sqrt([dH1H1ij]:[dH1H1ij])^3" symmetry = "-1" cutoff = "5.3" />
<PairVector species1 = "H2O" species2 = "H2O" symbol = "dH2H2" expression = "[rH2j]+[rj]-([rH2i]+[ri])" cutoff = "5.3" /> <PairParticleVector species1 = "H2O" species2 = "H2O" symbol = "fH2H2" expression = "-0.25*[dH2H2ij]/sqrt([dH2H2ij]:[dH2H2ij])^3" symmetry = "-1" cutoff = "5.3" />
<PairVector species1 = "H2O" species2 = "H2O" symbol = "dH1H2" expression = "[rH2j]+[rj]-([rH1i]+[ri])" cutoff = "5.3" /> <PairParticleVector species1 = "H2O" species2 = "H2O" symbol = "fH1H2" expression = "-0.25*[dH1H2ij]/sqrt([dH1H2ij]:[dH1H2ij])^3" symmetry = "-1" cutoff = "5.3" />
<PairVector species1 = "H2O" species2 = "H2O" symbol = "dH2H1" expression = "[rH1j]+[rj]-([rH2i]+[ri])" cutoff = "5.3" /> <PairParticleVector species1 = "H2O" species2 = "H2O" symbol = "fH2H1" expression = "-0.25*[dH2H1ij]/sqrt([dH2H1ij]:[dH2H1ij])^3" symmetry = "-1" cutoff = "5.3" />
<PairVector species1 = "H2O" species2 = "H2O" symbol = "dH1M" expression = "[rMj]+[rj]-([rH1i]+[ri])" cutoff = "5.3" /> <PairParticleVector species1 = "H2O" species2 = "H2O" symbol = "fH1M" expression = "0.5*[dH1Mij]/sqrt([dH1Mij]:[dH1Mij])^3" symmetry = "-1" cutoff = "5.3" />
<PairVector species1 = "H2O" species2 = "H2O" symbol = "dH2M" expression = "[rMj]+[rj]-([rH2i]+[ri])" cutoff = "5.3" /> <PairParticleVector species1 = "H2O" species2 = "H2O" symbol = "fH2M" expression = "0.5*[dH2Mij]/(sqrt([dH2Mij]:[dH2Mij])^3)" symmetry = "-1" cutoff = "5.3" />
<PairVector species1 = "H2O" species2 = "H2O" symbol = "dMH1" expression = "[rH1j]+[rj]-([rMi]+[ri])" cutoff = "5.3" /> <PairParticleVector species1 = "H2O" species2 = "H2O" symbol = "fMH1" expression = "0.5*[dMH1ij]/sqrt([dMH1ij]:[dMH1ij])^3" symmetry = "-1" cutoff = "5.3" />
<PairVector species1 = "H2O" species2 = "H2O" symbol = "dMH2" expression = "[rH2j]+[rj]-([rMi]+[ri])" cutoff = "5.3" /> <PairParticleVector species1 = "H2O" species2 = "H2O" symbol = "fMH2" expression = "0.5*[dMH2ij]/sqrt([dMH2ij]:[dMH2ij])^3" symmetry = "-1" cutoff = "5.3" />
<PairVector species1 = "H2O" species2 = "H2O" symbol = "dMM" expression = "[rMj]+[rj]-([rMi]+[ri])" cutoff = "5.3" /> <PairParticleVector species1 = "H2O" species2 = "H2O" symbol = "fMM" expression = "-[dMMij]/sqrt([dMMij]:[dMMij])^3" symmetry = "-1" cutoff = "5.3" />
<FParticleVels forceName = "Coulomb" species = "H2O" expression = "([fH1H1]+[fH1H2]+[fH2H1]+[fH2H2]+[fMH1]+[fMH2]+[fH1M]+[fH2M]+[fMM])" />
<FPairVector forceName = "TauH1H1H2O" species1 = "H2O" species2 = "H2O" weightingFunction = "dummy" pairFactor = "idVec(1/26)" particleFactor_i = "{rH1xi}:([fH1H1i]+[fH1H2i]+[fH1Mi])" particleFactor_j = "{rH1xj}:([fH1H1j]+[fH1H2j]+[fH1Mj])" vector = "omega" symmetry = "1" />
<FPairVector forceName = "TauH2H1H2O" species1 = "H2O" species2 = "H2O" weightingFunction = "dummy" pairFactor = "idVec(1/26)" particleFactor_i = "{rH2xi}:([fH2H1i]+[fH2H2i]+[fH2Mi])" particleFactor_j = "{rH2xj}:([fH2H1j]+[fH2H2j]+[fH2Mj])" vector = "omega" symmetry = "1" />
<FPairVector forceName = "TauOH1H2O" species1 = "H2O" species2 = "H2O" weightingFunction = "dummy" pairFactor = "idVec(1/26)" particleFactor_i = "{rMxi}:([fMH1i]+[fMH2i]+[fMMi])" particleFactor_j = "{rMxj}:([fMH1j]+[fMH2j]+[fMMj])" vector = "omega" symmetry = "1" />
<PairParticleScalar species1 = "H2O" species2 = "H2O" symbol = "EPotH1H1" expression = "0.25/sqrt([dH1H1ij]:[dH1H1ij])" cutoff = "5.3" /> <PairParticleScalar species1 = "H2O" species2 = "H2O" symbol = "EPotH2H2" expression = "0.25/sqrt([dH2H2ij]:[dH2H2ij])" cutoff = "5.3" /> <PairParticleScalar species1 = "H2O" species2 = "H2O" symbol = "EPotH1H2" expression = "0.25/sqrt([dH1H2ij]:[dH1H2ij])" cutoff = "5.3" /> <PairParticleScalar species1 = "H2O" species2 = "H2O" symbol = "EPotH2H1" expression = "0.25/sqrt([dH2H1ij]:[dH2H1ij])" cutoff = "5.3" /> <PairParticleScalar species1 = "H2O" species2 = "H2O" symbol = "EPotH1M" expression = "-0.5/sqrt([dH1Mij]:[dH1Mij])" cutoff = "5.3" /> <PairParticleScalar species1 = "H2O" species2 = "H2O" symbol = "EPotH2M" expression = "-0.5/sqrt([dH2Mij]:[dH2Mij])" cutoff = "5.3" /> <PairParticleScalar species1 = "H2O" species2 = "H2O" symbol = "EPotMH1" expression = "-0.5/sqrt([dMH1ij]:[dMH1ij])" cutoff = "5.3" /> <PairParticleScalar species1 = "H2O" species2 = "H2O" symbol = "EPotMH2" expression = "-0.5/sqrt([dMH2ij]:[dMH2ij])" cutoff = "5.3" /> <PairParticleScalar species1 = "H2O" species2 = "H2O" symbol = "EPotMM" expression = "1.0/sqrt([dMMij]:[dMMij])" cutoff = "5.3" />
<ParticleScalar species ="H2O" symbol = "Etot" expression = "(EKin+EPot)- 0.6909" /> <ParticleVector species = "H2O" expression = "uVecX(1.770xCoord([omega]))+uVecY(0.615yCoord([omega]))+uVecZ(1.155*zCoord([omega]))" symbol = "AngMom" /> <ParticleVector species = "H2O" expression = "T({rotmat}):[AngMom]" symbol = "AngMomLab" /> <ParticleVector species = "H2O" expression = "T({rotmat}):[omega]" symbol = "OmegaLab" />
/>
<GridAveragerStructured nX = "10" nY = "10" nZ = "10" measureEvery = "250"
/>