kauzlari / sympler

SYMPLER: SYMbolic ParticLE simulatoR
GNU General Public License v3.0
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Found ValCalculator calculating symbol "desity" at same memory position. #10

Closed nicolasgrimmig closed 10 years ago

nicolasgrimmig commented 11 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"
/>
<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"

/>

kauzlari commented 10 years ago

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?