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more dead code and some whitespace cleanup

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This commit is contained in:
Axel Kohlmeyer
2016-06-08 09:34:39 -04:00
parent 01e94eca90
commit ffc7fbcbd4
6 changed files with 275 additions and 296 deletions
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6
src/RIGID/fix_ehex.cpp
View File

@ -244,13 +244,11 @@ void FixEHEX::end_of_step() {
------------------------------------------------------------------------- */
void FixEHEX::rescale() {
double heat,ke,massone;
double Kr, Ke, escale;
double vsub[3],vcm[3], sfr[3];
double dvcmdt[3];
double mi;
double dt;
double F, mr, Fo2Kr, epsr_ik, sfvr, eta_ik;
double F, mr, epsr_ik, sfvr, eta_ik;
dt = update->dt;
@ -266,8 +264,6 @@ void FixEHEX::rescale() {
mr = masstotal;
Fo2Kr = F / (2.*Kr);
// energy scaling factor
escale = 1. + (F*dt)/Kr;

2
src/USER-DPD/fix_eos_table.cpp
View File

@ -195,7 +195,7 @@ void FixEOStable::read_table(Table *tb, Table *tb2, char *file, char *keyword)
// open file
FILE *fp = fopen(file,"r");
FILE *fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open file %s",file);

124
src/USER-DPD/fix_rx.cpp
View File

@ -137,7 +137,7 @@ void FixRX::post_constructor()
FILE *fp;
fp = NULL;
if (comm->me == 0) {
fp = fopen(kineticsFile,"r");
fp = force->open_potential(kineticsFile);
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open rx file %s",kineticsFile);
@ -147,7 +147,7 @@ void FixRX::post_constructor()
// Assign species names to tmpspecies array and determine the number of unique species
int n,nwords,ispecies;
int n,nwords;
char line[MAXLINE],*ptr;
int eof = 0;
char * word;
@ -179,17 +179,17 @@ void FixRX::post_constructor()
word = strtok(NULL, " \t\n\r\f");
match=false;
for(int jj=0;jj<nUniqueSpecies;jj++){
if(strcmp(word,tmpspecies[jj])==0){
match=true;
break;
}
if(strcmp(word,tmpspecies[jj])==0){
match=true;
break;
}
}
if(!match){
if(nUniqueSpecies+1>=maxspecies)
error->all(FLERR,"Exceeded the maximum number of species permitted in fix rx.");
tmpspecies[nUniqueSpecies] = new char[strlen(word)];
strcpy(tmpspecies[nUniqueSpecies],word);
nUniqueSpecies++;
if(nUniqueSpecies+1>=maxspecies)
error->all(FLERR,"Exceeded the maximum number of species permitted in fix rx.");
tmpspecies[nUniqueSpecies] = new char[strlen(word)];
strcpy(tmpspecies[nUniqueSpecies],word);
nUniqueSpecies++;
}
word = strtok(NULL, " \t\n\r\f");
if(strcmp(word,"+") != 0 && strcmp(word,"=") != 0) break;
@ -292,20 +292,19 @@ void FixRX::setup_pre_force(int vflag)
int nlocal = atom->nlocal;
int nghost = atom->nghost;
int *mask = atom->mask;
double *dpdTheta = atom->dpdTheta;
int newton_pair = force->newton_pair;
double tmp, theta;
double tmp;
int ii;
if(localTempFlag){
if (newton_pair) {
dpdThetaLocal = new double[nlocal+nghost];
for (ii = 0; ii < nlocal+nghost; ii++)
dpdThetaLocal[ii] = double(0.0);
dpdThetaLocal[ii] = double(0.0);
} else {
dpdThetaLocal = new double[nlocal];
for (ii = 0; ii < nlocal; ii++)
dpdThetaLocal[ii] = double(0.0);
dpdThetaLocal[ii] = double(0.0);
}
computeLocalTemperature();
}
@ -317,12 +316,10 @@ void FixRX::setup_pre_force(int vflag)
}
for (int i = 0; i < nlocal; i++)
if (mask[i] & groupbit){
if(localTempFlag) theta = dpdThetaLocal[i];
else theta=dpdTheta[i];
// Set the reaction rate constants to zero: no reactions occur at step 0
for(int irxn=0;irxn<nreactions;irxn++)
kR[irxn] = double(0.0);
kR[irxn] = double(0.0);
if(odeIntegrationFlag==ODE_LAMMPS_RK4) rk4(i);
}
@ -347,14 +344,13 @@ void FixRX::pre_force(int vflag)
if (newton_pair) {
dpdThetaLocal = new double[nlocal+nghost];
for (ii = 0; ii < nlocal+nghost; ii++)
dpdThetaLocal[ii] = double(0.0);
dpdThetaLocal[ii] = double(0.0);
} else {
dpdThetaLocal = new double[nlocal];
for (ii = 0; ii < nlocal; ii++)
dpdThetaLocal[ii] = double(0.0);
dpdThetaLocal[ii] = double(0.0);
}
computeLocalTemperature();
double *dpdTheta = this->dpdThetaLocal;
}
for (int i = 0; i < nlocal; i++)
@ -364,7 +360,7 @@ void FixRX::pre_force(int vflag)
//Compute the reaction rate constants
for(int irxn=0;irxn<nreactions;irxn++)
kR[irxn] = Arr[irxn]*pow(theta,nArr[irxn])*exp(-Ea[irxn]/force->boltz/theta);
kR[irxn] = Arr[irxn]*pow(theta,nArr[irxn])*exp(-Ea[irxn]/force->boltz/theta);
if(odeIntegrationFlag==ODE_LAMMPS_RK4) rk4(i);
}
@ -384,7 +380,7 @@ void FixRX::read_file(char *file)
FILE *fp;
fp = NULL;
if (comm->me == 0) {
fp = fopen(file,"r");
fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open rx file %s",file);
@ -421,7 +417,7 @@ void FixRX::read_file(char *file)
}
// open file on proc 0
if (comm->me == 0) fp = fopen(file,"r");
if (comm->me == 0) fp = force->open_potential(file);
// read each reaction from kinetics file
eof=0;
@ -479,31 +475,37 @@ void FixRX::read_file(char *file)
tmpStoich = atof(word);
word = strtok(NULL, " \t\n\r\f");
for (ispecies = 0; ispecies < nspecies; ispecies++){
if (strcmp(word,&atom->dname[ispecies][0]) == 0){
stoich[nreactions][ispecies] += sign*tmpStoich;
if(sign<double(0.0)) stoichReactants[nreactions][ispecies] += tmpStoich;
else stoichProducts[nreactions][ispecies] += tmpStoich;
break;
}
if (strcmp(word,&atom->dname[ispecies][0]) == 0){
stoich[nreactions][ispecies] += sign*tmpStoich;
if(sign<double(0.0))
stoichReactants[nreactions][ispecies] += tmpStoich;
else stoichProducts[nreactions][ispecies] += tmpStoich;
break;
}
}
if(ispecies==nspecies){
printf("%s mol fraction is not found in data file\n",word);
printf("nspecies=%d ispecies=%d\n",nspecies,ispecies);
error->all(FLERR,"Illegal fix rx command");
if (comm->me) {
fprintf(stderr,"%s mol fraction is not found in data file\n",word);
fprintf(stderr,"nspecies=%d ispecies=%d\n",nspecies,ispecies);
}
error->all(FLERR,"Illegal fix rx command");
}
word = strtok(NULL, " \t\n\r\f");
if(strcmp(word,"=") == 0) sign = double(1.0);
if(strcmp(word,"+") != 0 && strcmp(word,"=") != 0){
if(word==NULL) error->all(FLERR,"Missing parameters in reaction kinetic equation");
Arr[nreactions] = atof(word);
word = strtok(NULL, " \t\n\r\f");
if(word==NULL) error->all(FLERR,"Missing parameters in reaction kinetic equation");
nArr[nreactions] = atof(word);
word = strtok(NULL, " \t\n\r\f");
if(word==NULL) error->all(FLERR,"Missing parameters in reaction kinetic equation");
Ea[nreactions] = atof(word);
sign = double(-1.0);
break;
if(word==NULL)
error->all(FLERR,"Missing parameters in reaction kinetic equation");
Arr[nreactions] = atof(word);
word = strtok(NULL, " \t\n\r\f");
if(word==NULL)
error->all(FLERR,"Missing parameters in reaction kinetic equation");
nArr[nreactions] = atof(word);
word = strtok(NULL, " \t\n\r\f");
if(word==NULL)
error->all(FLERR,"Missing parameters in reaction kinetic equation");
Ea[nreactions] = atof(word);
sign = double(-1.0);
break;
}
word = strtok(NULL, " \t\n\r\f");
}
@ -527,8 +529,8 @@ void FixRX::setupParams()
n = -1;
for (j = 0; j < nreactions; j++) {
if (i == params[j].ispecies) {
if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
n = j;
if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
n = j;
}
}
mol2param[i] = n;
@ -586,7 +588,7 @@ void FixRX::rk4(int id)
for (int ispecies = 0; ispecies < nspecies; ispecies++)
y[ispecies] += h*(k1[ispecies]/6.0 + k2[ispecies]/3.0 +
k3[ispecies]/3.0 + k4[ispecies]/6.0);
k3[ispecies]/3.0 + k4[ispecies]/6.0);
} // end for (int step...
@ -649,7 +651,7 @@ void FixRX::computeLocalTemperature()
int newton_pair = force->newton_pair;
// local temperature variables
double wij, fr, fr4;
double wij;
double *dpdTheta = atom->dpdTheta;
// Initialize the local density and local temperature arrays
@ -690,24 +692,22 @@ void FixRX::computeLocalTemperature()
if (rsq < pairDPDE->cutsq[itype][jtype]) {
double rcut = sqrt(pairDPDE->cutsq[itype][jtype]);
double rij = sqrt(rsq);
double tmpFactor = double(1.0)-rij/rcut;
double tmpFactor4 = tmpFactor*tmpFactor*tmpFactor*tmpFactor;
double ratio = rij/rcut;
double rij = sqrt(rsq);
double ratio = rij/rcut;
// Lucy's Weight Function
if(wtFlag==LUCY){
wij = (double(1.0)+double(3.0)*ratio) * (double(1.0)-ratio)*(double(1.0)-ratio)*(double(1.0)-ratio);
dpdThetaLocal[i] += wij/dpdTheta[j];
if (newton_pair || j < nlocal)
dpdThetaLocal[j] += wij/dpdTheta[i];
}
// Lucy's Weight Function
if(wtFlag==LUCY){
wij = (double(1.0)+double(3.0)*ratio) * (double(1.0)-ratio)*(double(1.0)-ratio)*(double(1.0)-ratio);
dpdThetaLocal[i] += wij/dpdTheta[j];
if (newton_pair || j < nlocal)
dpdThetaLocal[j] += wij/dpdTheta[i];
}
sumWeights[i] += wij;
sumWeights[i] += wij;
if (newton_pair || j < nlocal) {
sumWeights[j] += wij;
}
sumWeights[j] += wij;
}
}
}
}

417
src/USER-DPD/pair_exp6_rx.cpp
View File

@ -66,7 +66,7 @@ void PairExp6rx::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,evdwlOld,fpair;
double rsq,rinv,r2inv,r6inv,forceExp6,factor_lj;
double rsq,r2inv,r6inv,forceExp6,factor_lj;
double rCut,rCutInv,rCut2inv,rCut6inv,rCutExp,urc,durc;
double rm2ij,rm6ij;
double r,rexp;
@ -145,232 +145,229 @@ void PairExp6rx::compute(int eflag, int vflag)
r6inv = r2inv*r2inv*r2inv;
r = sqrt(rsq);
rinv = double(1.0)/r;
rCut2inv = double(1.0)/cutsq[itype][jtype];
rCut6inv = rCut2inv*rCut2inv*rCut2inv;
rCut = sqrt(cutsq[itype][jtype]);
rCutInv = double(1.0)/rCut;
rCut2inv = double(1.0)/cutsq[itype][jtype];
rCut6inv = rCut2inv*rCut2inv*rCut2inv;
rCut = sqrt(cutsq[itype][jtype]);
rCutInv = double(1.0)/rCut;
//
// A. Compute the exp-6 potential
//
//
// A. Compute the exp-6 potential
//
// A1. Get alpha, epsilon and rm for particle j
getParamsEXP6(j,epsilon1_j,alpha1_j,rm1_j,fraction1_j,epsilon2_j,alpha2_j,rm2_j,fraction2_j,epsilonOld1_j,alphaOld1_j,rmOld1_j,fractionOld1_j,epsilonOld2_j,alphaOld2_j,rmOld2_j,fractionOld2_j);
// A1. Get alpha, epsilon and rm for particle j
getParamsEXP6(j,epsilon1_j,alpha1_j,rm1_j,fraction1_j,epsilon2_j,alpha2_j,rm2_j,fraction2_j,epsilonOld1_j,alphaOld1_j,rmOld1_j,fractionOld1_j,epsilonOld2_j,alphaOld2_j,rmOld2_j,fractionOld2_j);
// A2. Apply Lorentz-Berthelot mixing rules for the i-j pair
alphaOld12_ij = sqrt(alphaOld1_i*alphaOld2_j);
rmOld12_ij = 0.5*(rmOld1_i + rmOld2_j);
epsilonOld12_ij = sqrt(epsilonOld1_i*epsilonOld2_j);
alphaOld21_ij = sqrt(alphaOld2_i*alphaOld1_j);
rmOld21_ij = 0.5*(rmOld2_i + rmOld1_j);
epsilonOld21_ij = sqrt(epsilonOld2_i*epsilonOld1_j);
// A2. Apply Lorentz-Berthelot mixing rules for the i-j pair
alphaOld12_ij = sqrt(alphaOld1_i*alphaOld2_j);
rmOld12_ij = 0.5*(rmOld1_i + rmOld2_j);
epsilonOld12_ij = sqrt(epsilonOld1_i*epsilonOld2_j);
alphaOld21_ij = sqrt(alphaOld2_i*alphaOld1_j);
rmOld21_ij = 0.5*(rmOld2_i + rmOld1_j);
epsilonOld21_ij = sqrt(epsilonOld2_i*epsilonOld1_j);
alpha12_ij = sqrt(alpha1_i*alpha2_j);
rm12_ij = 0.5*(rm1_i + rm2_j);
epsilon12_ij = sqrt(epsilon1_i*epsilon2_j);
alpha21_ij = sqrt(alpha2_i*alpha1_j);
rm21_ij = 0.5*(rm2_i + rm1_j);
epsilon21_ij = sqrt(epsilon2_i*epsilon1_j);
alpha12_ij = sqrt(alpha1_i*alpha2_j);
rm12_ij = 0.5*(rm1_i + rm2_j);
epsilon12_ij = sqrt(epsilon1_i*epsilon2_j);
alpha21_ij = sqrt(alpha2_i*alpha1_j);
rm21_ij = 0.5*(rm2_i + rm1_j);
epsilon21_ij = sqrt(epsilon2_i*epsilon1_j);
if(rmOld12_ij!=double(0.0) && rmOld21_ij!=double(0.0)){
if(alphaOld21_ij == double(6.0) || alphaOld12_ij == double(6.0))
error->all(FLERR,"alpha_ij is 6.0 in pair exp6");
if(rmOld12_ij!=double(0.0) && rmOld21_ij!=double(0.0)){
if(alphaOld21_ij == double(6.0) || alphaOld12_ij == double(6.0))
error->all(FLERR,"alpha_ij is 6.0 in pair exp6");
// A3. Compute some convenient quantities for evaluating the force
rminv = 1.0/rmOld12_ij;
buck1 = epsilonOld12_ij / (alphaOld12_ij - 6.0);
rexp = expValue(alphaOld12_ij*(1.0-r*rminv));
rm2ij = rmOld12_ij*rmOld12_ij;
rm6ij = rm2ij*rm2ij*rm2ij;
// A3. Compute some convenient quantities for evaluating the force
rminv = 1.0/rmOld12_ij;
buck1 = epsilonOld12_ij / (alphaOld12_ij - 6.0);
rexp = expValue(alphaOld12_ij*(1.0-r*rminv));
rm2ij = rmOld12_ij*rmOld12_ij;
rm6ij = rm2ij*rm2ij*rm2ij;
// Compute the shifted potential
rCutExp = expValue(alphaOld12_ij*(1.0-rCut*rminv));
buck2 = 6.0*alphaOld12_ij;
urc = buck1*(6.0*rCutExp - alphaOld12_ij*rm6ij*rCut6inv);
durc = -buck1*buck2*(rCutExp* rminv - rCutInv*rm6ij*rCut6inv);
rin1 = shift*rmOld12_ij*func_rin(alphaOld12_ij);
if(r < rin1){
rin6 = rin1*rin1*rin1*rin1*rin1*rin1;
rin6inv = double(1.0)/rin6;
// Compute the shifted potential
rCutExp = expValue(alphaOld12_ij*(1.0-rCut*rminv));
buck2 = 6.0*alphaOld12_ij;
urc = buck1*(6.0*rCutExp - alphaOld12_ij*rm6ij*rCut6inv);
durc = -buck1*buck2*(rCutExp* rminv - rCutInv*rm6ij*rCut6inv);
rin1 = shift*rmOld12_ij*func_rin(alphaOld12_ij);
if(r < rin1){
rin6 = rin1*rin1*rin1*rin1*rin1*rin1;
rin6inv = double(1.0)/rin6;
rin1exp = expValue(alphaOld12_ij*(1.0-rin1*rminv));
rin1exp = expValue(alphaOld12_ij*(1.0-rin1*rminv));
uin1 = buck1*(6.0*rin1exp - alphaOld12_ij*rm6ij*rin6inv) - urc - durc*(rin1-rCut);
uin1 = buck1*(6.0*rin1exp - alphaOld12_ij*rm6ij*rin6inv) - urc - durc*(rin1-rCut);
win1 = buck1*buck2*(rin1*rin1exp*rminv - rm6ij*rin6inv) - rin1*durc;
win1 = buck1*buck2*(rin1*rin1exp*rminv - rm6ij*rin6inv) - rin1*durc;
aRep = double(-1.0)*win1*pow(rin1,nRep)/nRep;
aRep = double(-1.0)*win1*pow(rin1,nRep)/nRep;
uin1rep = aRep/pow(rin1,nRep);
uin1rep = aRep/pow(rin1,nRep);
evdwlOldEXP6_12 = uin1 - uin1rep + aRep/pow(r,nRep);
evdwlOldEXP6_12 = uin1 - uin1rep + aRep/pow(r,nRep);
} else {
evdwlOldEXP6_12 = buck1*(6.0*rexp - alphaOld12_ij*rm6ij*r6inv) - urc - durc*(r-rCut);
}
} else {
evdwlOldEXP6_12 = buck1*(6.0*rexp - alphaOld12_ij*rm6ij*r6inv) - urc - durc*(r-rCut);
}
// A3. Compute some convenient quantities for evaluating the force
rminv = 1.0/rmOld21_ij;
buck1 = epsilonOld21_ij / (alphaOld21_ij - 6.0);
buck2 = 6.0*alphaOld21_ij;
rexp = expValue(alphaOld21_ij*(1.0-r*rminv));
rm2ij = rmOld21_ij*rmOld21_ij;
rm6ij = rm2ij*rm2ij*rm2ij;
// Compute the shifted potential
rCutExp = expValue(alphaOld21_ij*(1.0-rCut*rminv));
buck2 = 6.0*alphaOld21_ij;
urc = buck1*(6.0*rCutExp - alphaOld21_ij*rm6ij*rCut6inv);
durc = -buck1*buck2*(rCutExp* rminv - rCutInv*rm6ij*rCut6inv);
rin1 = shift*rmOld21_ij*func_rin(alphaOld21_ij);
// A3. Compute some convenient quantities for evaluating the force
rminv = 1.0/rmOld21_ij;
buck1 = epsilonOld21_ij / (alphaOld21_ij - 6.0);
buck2 = 6.0*alphaOld21_ij;
rexp = expValue(alphaOld21_ij*(1.0-r*rminv));
rm2ij = rmOld21_ij*rmOld21_ij;
rm6ij = rm2ij*rm2ij*rm2ij;
if(r < rin1){
rin6 = rin1*rin1*rin1*rin1*rin1*rin1;
rin6inv = double(1.0)/rin6;
// Compute the shifted potential
rCutExp = expValue(alphaOld21_ij*(1.0-rCut*rminv));
buck2 = 6.0*alphaOld21_ij;
urc = buck1*(6.0*rCutExp - alphaOld21_ij*rm6ij*rCut6inv);
durc = -buck1*buck2*(rCutExp* rminv - rCutInv*rm6ij*rCut6inv);
rin1 = shift*rmOld21_ij*func_rin(alphaOld21_ij);
rin1exp = expValue(alphaOld21_ij*(1.0-rin1*rminv));
if(r < rin1){
rin6 = rin1*rin1*rin1*rin1*rin1*rin1;
rin6inv = double(1.0)/rin6;
uin1 = buck1*(6.0*rin1exp - alphaOld21_ij*rm6ij*rin6inv) - urc - durc*(rin1-rCut);
rin1exp = expValue(alphaOld21_ij*(1.0-rin1*rminv));
win1 = buck1*buck2*(rin1*rin1exp*rminv - rm6ij*rin6inv) - rin1*durc;
uin1 = buck1*(6.0*rin1exp - alphaOld21_ij*rm6ij*rin6inv) - urc - durc*(rin1-rCut);
aRep = double(-1.0)*win1*pow(rin1,nRep)/nRep;
win1 = buck1*buck2*(rin1*rin1exp*rminv - rm6ij*rin6inv) - rin1*durc;
uin1rep = aRep/pow(rin1,nRep);
aRep = double(-1.0)*win1*pow(rin1,nRep)/nRep;
evdwlOldEXP6_21 = uin1 - uin1rep + aRep/pow(r,nRep);
uin1rep = aRep/pow(rin1,nRep);
} else {
evdwlOldEXP6_21 = buck1*(6.0*rexp - alphaOld21_ij*rm6ij*r6inv) - urc - durc*(r-rCut);
}
evdwlOldEXP6_21 = uin1 - uin1rep + aRep/pow(r,nRep);
if (strcmp(site1,site2) == 0)
evdwlOld = sqrt(fractionOld1_i*fractionOld2_j)*evdwlOldEXP6_12;
else
evdwlOld = sqrt(fractionOld1_i*fractionOld2_j)*evdwlOldEXP6_12 + sqrt(fractionOld2_i*fractionOld1_j)*evdwlOldEXP6_21;
evdwlOld *= factor_lj;
uCG[i] += double(0.5)*evdwlOld;
uCG[j] += double(0.5)*evdwlOld;
}
} else {
evdwlOldEXP6_21 = buck1*(6.0*rexp - alphaOld21_ij*rm6ij*r6inv) - urc - durc*(r-rCut);
}
if(rm12_ij!=double(0.0) && rm21_ij!=double(0.0)){
if(alpha21_ij == double(6.0) || alpha12_ij == double(6.0))
error->all(FLERR,"alpha_ij is 6.0 in pair exp6");
if (strcmp(site1,site2) == 0)
evdwlOld = sqrt(fractionOld1_i*fractionOld2_j)*evdwlOldEXP6_12;
else
evdwlOld = sqrt(fractionOld1_i*fractionOld2_j)*evdwlOldEXP6_12 + sqrt(fractionOld2_i*fractionOld1_j)*evdwlOldEXP6_21;
// A3. Compute some convenient quantities for evaluating the force
rminv = 1.0/rm12_ij;
buck1 = epsilon12_ij / (alpha12_ij - 6.0);
buck2 = 6.0*alpha12_ij;
rexp = expValue(alpha12_ij*(1.0-r*rminv));
rm2ij = rm12_ij*rm12_ij;
rm6ij = rm2ij*rm2ij*rm2ij;
// Compute the shifted potential
rCutExp = expValue(alpha12_ij*(1.0-rCut*rminv));
urc = buck1*(6.0*rCutExp - alpha12_ij*rm6ij*rCut6inv);
durc = -buck1*buck2*(rCutExp*rminv - rCutInv*rm6ij*rCut6inv);
rin1 = shift*rm12_ij*func_rin(alpha12_ij);
evdwlOld *= factor_lj;
if(r < rin1){
rin6 = rin1*rin1*rin1*rin1*rin1*rin1;
rin6inv = double(1.0)/rin6;
uCG[i] += double(0.5)*evdwlOld;
uCG[j] += double(0.5)*evdwlOld;
}
rin1exp = expValue(alpha12_ij*(1.0-rin1*rminv));
if(rm12_ij!=double(0.0) && rm21_ij!=double(0.0)){
if(alpha21_ij == double(6.0) || alpha12_ij == double(6.0))
error->all(FLERR,"alpha_ij is 6.0 in pair exp6");
uin1 = buck1*(6.0*rin1exp - alpha12_ij*rm6ij*rin6inv) - urc - durc*(rin1-rCut);
// A3. Compute some convenient quantities for evaluating the force
rminv = 1.0/rm12_ij;
buck1 = epsilon12_ij / (alpha12_ij - 6.0);
buck2 = 6.0*alpha12_ij;
rexp = expValue(alpha12_ij*(1.0-r*rminv));
rm2ij = rm12_ij*rm12_ij;
rm6ij = rm2ij*rm2ij*rm2ij;
win1 = buck1*buck2*(rin1*rin1exp*rminv - rm6ij*rin6inv) - rin1*durc;
// Compute the shifted potential
rCutExp = expValue(alpha12_ij*(1.0-rCut*rminv));
urc = buck1*(6.0*rCutExp - alpha12_ij*rm6ij*rCut6inv);
durc = -buck1*buck2*(rCutExp*rminv - rCutInv*rm6ij*rCut6inv);
rin1 = shift*rm12_ij*func_rin(alpha12_ij);
aRep = double(-1.0)*win1*pow(rin1,nRep)/nRep;
if(r < rin1){
rin6 = rin1*rin1*rin1*rin1*rin1*rin1;
rin6inv = double(1.0)/rin6;
uin1rep = aRep/pow(rin1,nRep);
rin1exp = expValue(alpha12_ij*(1.0-rin1*rminv));
evdwlEXP6_12 = uin1 - uin1rep + aRep/pow(r,nRep);
uin1 = buck1*(6.0*rin1exp - alpha12_ij*rm6ij*rin6inv) - urc - durc*(rin1-rCut);
forceExp6 = double(-1.0)*nRep*aRep/pow(r,nRep);
fpairEXP6_12 = factor_lj*forceExp6*r2inv;
win1 = buck1*buck2*(rin1*rin1exp*rminv - rm6ij*rin6inv) - rin1*durc;
} else {
aRep = double(-1.0)*win1*pow(rin1,nRep)/nRep;
// A4. Compute the exp-6 force and energy
forceExp6 = buck1*buck2*(r*rexp*rminv - rm6ij*r6inv) + r*durc;
fpairEXP6_12 = factor_lj*forceExp6*r2inv;
evdwlEXP6_12 = buck1*(6.0*rexp - alpha12_ij*rm6ij*r6inv) - urc - durc*(r-rCut);
}
rminv = 1.0/rm21_ij;
buck1 = epsilon21_ij / (alpha21_ij - 6.0);
buck2 = 6.0*alpha21_ij;
rexp = expValue(alpha21_ij*(1.0-r*rminv));
rm2ij = rm21_ij*rm21_ij;
rm6ij = rm2ij*rm2ij*rm2ij;
uin1rep = aRep/pow(rin1,nRep);
// Compute the shifted potential
rCutExp = expValue(alpha21_ij*(1.0-rCut*rminv));
urc = buck1*(6.0*rCutExp - alpha21_ij*rm6ij*rCut6inv);
durc = -buck1*buck2*(rCutExp*rminv - rCutInv*rm6ij*rCut6inv);
rin1 = shift*rm21_ij*func_rin(alpha21_ij);
evdwlEXP6_12 = uin1 - uin1rep + aRep/pow(r,nRep);
if(r < rin1){
rin6 = rin1*rin1*rin1*rin1*rin1*rin1;
rin6inv = double(1.0)/rin6;
forceExp6 = double(-1.0)*nRep*aRep/pow(r,nRep);
fpairEXP6_12 = factor_lj*forceExp6*r2inv;
rin1exp = expValue(alpha21_ij*(1.0-rin1*rminv));
} else {
uin1 = buck1*(6.0*rin1exp - alpha21_ij*rm6ij*rin6inv) - urc - durc*(rin1-rCut);
// A4. Compute the exp-6 force and energy
forceExp6 = buck1*buck2*(r*rexp*rminv - rm6ij*r6inv) + r*durc;
fpairEXP6_12 = factor_lj*forceExp6*r2inv;
evdwlEXP6_12 = buck1*(6.0*rexp - alpha12_ij*rm6ij*r6inv) - urc - durc*(r-rCut);
}
win1 = buck1*buck2*(rin1*rin1exp*rminv - rm6ij*rin6inv) - rin1*durc;
rminv = 1.0/rm21_ij;
buck1 = epsilon21_ij / (alpha21_ij - 6.0);
buck2 = 6.0*alpha21_ij;
rexp = expValue(alpha21_ij*(1.0-r*rminv));
rm2ij = rm21_ij*rm21_ij;
rm6ij = rm2ij*rm2ij*rm2ij;
aRep = double(-1.0)*win1*pow(rin1,nRep)/nRep;
// Compute the shifted potential
rCutExp = expValue(alpha21_ij*(1.0-rCut*rminv));
urc = buck1*(6.0*rCutExp - alpha21_ij*rm6ij*rCut6inv);
durc = -buck1*buck2*(rCutExp*rminv - rCutInv*rm6ij*rCut6inv);
rin1 = shift*rm21_ij*func_rin(alpha21_ij);
uin1rep = aRep/pow(rin1,nRep);
if(r < rin1){
rin6 = rin1*rin1*rin1*rin1*rin1*rin1;
rin6inv = double(1.0)/rin6;
evdwlEXP6_21 = uin1 - uin1rep + aRep/pow(r,nRep);
rin1exp = expValue(alpha21_ij*(1.0-rin1*rminv));
forceExp6 = double(-1.0)*nRep*aRep/pow(r,nRep);
fpairEXP6_21 = factor_lj*forceExp6*r2inv;
uin1 = buck1*(6.0*rin1exp - alpha21_ij*rm6ij*rin6inv) - urc - durc*(rin1-rCut);
} else {
win1 = buck1*buck2*(rin1*rin1exp*rminv - rm6ij*rin6inv) - rin1*durc;
// A4. Compute the exp-6 force and energy
forceExp6 = buck1*buck2*(r*rexp*rminv - rm6ij*r6inv) + r*durc;
fpairEXP6_21 = factor_lj*forceExp6*r2inv;
evdwlEXP6_21 = buck1*(6.0*rexp - alpha21_ij*rm6ij*r6inv) - urc - durc*(r-rCut);
}
aRep = double(-1.0)*win1*pow(rin1,nRep)/nRep;
//
// Apply Mixing Rule to get the overall force for the CG pair
//
if (strcmp(site1,site2) == 0) fpair = sqrt(fractionOld1_i*fractionOld2_j)*fpairEXP6_12;
else fpair = sqrt(fractionOld1_i*fractionOld2_j)*fpairEXP6_12 + sqrt(fractionOld2_i*fractionOld1_j)*fpairEXP6_21;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (strcmp(site1,site2) == 0)
evdwl = sqrt(fraction1_i*fraction2_j)*evdwlEXP6_12;
else
evdwl = sqrt(fraction1_i*fraction2_j)*evdwlEXP6_12 + sqrt(fraction2_i*fraction1_j)*evdwlEXP6_21;
evdwl *= factor_lj;
uCGnew[i] += double(0.5)*evdwl;
uCGnew[j] += double(0.5)*evdwl;
evdwl = evdwlOld;
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
}
uin1rep = aRep/pow(rin1,nRep);
evdwlEXP6_21 = uin1 - uin1rep + aRep/pow(r,nRep);
forceExp6 = double(-1.0)*nRep*aRep/pow(r,nRep);
fpairEXP6_21 = factor_lj*forceExp6*r2inv;
} else {
// A4. Compute the exp-6 force and energy
forceExp6 = buck1*buck2*(r*rexp*rminv - rm6ij*r6inv) + r*durc;
fpairEXP6_21 = factor_lj*forceExp6*r2inv;
evdwlEXP6_21 = buck1*(6.0*rexp - alpha21_ij*rm6ij*r6inv) - urc - durc*(r-rCut);
}
//
// Apply Mixing Rule to get the overall force for the CG pair
//
if (strcmp(site1,site2) == 0) fpair = sqrt(fractionOld1_i*fractionOld2_j)*fpairEXP6_12;
else fpair = sqrt(fractionOld1_i*fractionOld2_j)*fpairEXP6_12 + sqrt(fractionOld2_i*fractionOld1_j)*fpairEXP6_21;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (strcmp(site1,site2) == 0)
evdwl = sqrt(fraction1_i*fraction2_j)*evdwlEXP6_12;
else
evdwl = sqrt(fraction1_i*fraction2_j)*evdwlEXP6_12 + sqrt(fraction2_i*fraction1_j)*evdwlEXP6_21;
evdwl *= factor_lj;
uCGnew[i] += double(0.5)*evdwl;
uCGnew[j] += double(0.5)*evdwl;
evdwl = evdwlOld;
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
}
}
}
}
@ -597,8 +594,8 @@ void PairExp6rx::read_file(char *file)
params[nparams].epsilon = atof(words[3]);
params[nparams].rm = atof(words[4]);
if (params[nparams].epsilon <= 0.0 || params[nparams].rm <= 0.0 ||
params[nparams].alpha < 0.0)
error->all(FLERR,"Illegal exp6/rx parameters. Rm and Epsilon must be greater than zero. Alpha cannot be negative.");
params[nparams].alpha < 0.0)
error->all(FLERR,"Illegal exp6/rx parameters. Rm and Epsilon must be greater than zero. Alpha cannot be negative.");
} else {
error->all(FLERR,"Illegal exp6/rx parameters. Interaction potential does not exist.");
}
@ -624,8 +621,8 @@ void PairExp6rx::setup()
n = -1;
for (j = 0; j < nparams; j++) {
if (i == params[j].ispecies) {
if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
n = j;
if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
n = j;
}
}
mol2param[i] = n;
@ -713,8 +710,8 @@ void PairExp6rx::getParamsEXP6(int id,double &epsilon1,double &alpha1,double &rm
double rmi, rmj, rmij, rm3ij;
double epsiloni, epsilonj, epsilonij;
double alphai, alphaj, alphaij;
double epsilon_old, rm3_old, alpha_old, fraction_old;
double epsilon, rm3, alpha, fraction;
double epsilon_old, rm3_old, alpha_old;
double epsilon, rm3, alpha;
double fractionOFA, fractionOFA_old;
double nTotalOFA, nTotalOFA_old;
double nTotal, nTotal_old;
@ -726,8 +723,6 @@ void PairExp6rx::getParamsEXP6(int id,double &epsilon1,double &alpha1,double &rm
epsilon_old = double(0.0);
rm3_old = double(0.0);
alpha_old = double(0.0);
fraction_old = double(0.0);
fraction = double(0.0);
fractionOFA = double(0.0);
fractionOFA_old = double(0.0);
nTotalOFA = double(0.0);
@ -797,30 +792,30 @@ void PairExp6rx::getParamsEXP6(int id,double &epsilon1,double &alpha1,double &rm
xMolei_old = atom->dvector[ispecies+nspecies][id]/nTotalOFA_old;
for (int jspecies = 0; jspecies < nspecies; jspecies++) {
jparam = mol2param[jspecies];
if (jparam < 0 || strcmp(params[jparam].potential,"exp6") != 0) continue;
if (strcmp(site1,params[jparam].name) == 0 || strcmp(site2,params[jparam].name) == 0) continue;
rmj = params[jparam].rm;
epsilonj = params[jparam].epsilon;
alphaj = params[jparam].alpha;
xMolej = atom->dvector[jspecies][id]/nTotalOFA;
xMolej_old = atom->dvector[jspecies+nspecies][id]/nTotalOFA_old;
jparam = mol2param[jspecies];
if (jparam < 0 || strcmp(params[jparam].potential,"exp6") != 0) continue;
if (strcmp(site1,params[jparam].name) == 0 || strcmp(site2,params[jparam].name) == 0) continue;
rmj = params[jparam].rm;
epsilonj = params[jparam].epsilon;
alphaj = params[jparam].alpha;
xMolej = atom->dvector[jspecies][id]/nTotalOFA;
xMolej_old = atom->dvector[jspecies+nspecies][id]/nTotalOFA_old;
rmij = (rmi+rmj)/2.0;
rm3ij = rmij*rmij*rmij;
epsilonij = sqrt(epsiloni*epsilonj);
alphaij = sqrt(alphai*alphaj);
if(fractionOFA_old > double(0.0)){
rm3_old += xMolei_old*xMolej_old*rm3ij;
epsilon_old += xMolei_old*xMolej_old*rm3ij*epsilonij;
alpha_old += xMolei_old*xMolej_old*rm3ij*epsilonij*alphaij;
}
if(fractionOFA > double(0.0)){
rm3 += xMolei*xMolej*rm3ij;
epsilon += xMolei*xMolej*rm3ij*epsilonij;
alpha += xMolei*xMolej*rm3ij*epsilonij*alphaij;
}
rmij = (rmi+rmj)/2.0;
rm3ij = rmij*rmij*rmij;
epsilonij = sqrt(epsiloni*epsilonj);
alphaij = sqrt(alphai*alphaj);
if(fractionOFA_old > double(0.0)){
rm3_old += xMolei_old*xMolej_old*rm3ij;
epsilon_old += xMolei_old*xMolej_old*rm3ij*epsilonij;
alpha_old += xMolei_old*xMolej_old*rm3ij*epsilonij*alphaij;
}
if(fractionOFA > double(0.0)){
rm3 += xMolei*xMolej*rm3ij;
epsilon += xMolei*xMolej*rm3ij*epsilonij;
alpha += xMolei*xMolej*rm3ij*epsilonij*alphaij;
}
}
}
}
@ -945,12 +940,10 @@ double PairExp6rx::func_rin(double &alpha)
{
double function;
const double alpha_min = double(11.0);
const double alpha_max = double(16.0);
const double a = double(3.7682065);
const double b = double(-1.4308614);
function = a+b*pow(alpha,0.5);
function = a+b*sqrt(alpha);
function = expValue(function);
return function;

13
src/USER-DPD/pair_multi_lucy.cpp
View File

@ -87,12 +87,10 @@ PairMultiLucy::~PairMultiLucy()
void PairMultiLucy::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype,itable;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
double rsq,factor_lj,fraction,value,a,b;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair,rsq;
int *ilist,*jlist,*numneigh,**firstneigh;
Table *tb;
union_int_float_t rsq_lookup;
int tlm1 = tablength - 1;
evdwl = 0.0;
@ -110,7 +108,6 @@ void PairMultiLucy::compute(int eflag, int vflag)
double A_i;
double A_j;
double fraction_i,fraction_j;
double a_i,a_j,b_i,b_j;
int jtable;
double *rho = atom->rho;
@ -134,7 +131,6 @@ void PairMultiLucy::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
@ -293,13 +289,11 @@ void PairMultiLucy::coeff(int narg, char **arg)
// insure cutoff is within table
if (tb->ninput <= 1) error->one(FLERR,"Invalid pair table length");
double rlo,rhi;
double rlo;
if (tb->rflag == 0) {
rlo = tb->rfile[0];
rhi = tb->rfile[tb->ninput-1];
} else {
rlo = tb->rlo;
rhi = tb->rhi;
}
rho_0 = rlo;
@ -390,7 +384,6 @@ void PairMultiLucy::read_table(Table *tb, char *file, char *keyword)
int itmp;
double rtmp;
union_int_float_t rsq_lookup;
fgets(line,MAXLINE,fp);
for (int i = 0; i < tb->ninput; i++) {
@ -733,7 +726,7 @@ void PairMultiLucy::computeLocalDensity()
int *type = atom->type;
int nlocal = atom->nlocal;
int newton_pair = force->newton_pair;
double factor, volume;
double factor;
inum = list->inum;
ilist = list->ilist;

9
src/USER-DPD/pair_multi_lucy_rx.cpp
View File

@ -90,7 +90,7 @@ void PairMultiLucyRX::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype,itable;
double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,evdwlOld,fpair;
double rsq,factor_lj;
double rsq;
int *ilist,*jlist,*numneigh,**firstneigh;
Table *tb;
@ -143,7 +143,6 @@ void PairMultiLucyRX::compute(int eflag, int vflag)
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
@ -352,13 +351,11 @@ void PairMultiLucyRX::coeff(int narg, char **arg)
// insure cutoff is within table
if (tb->ninput <= 1) error->one(FLERR,"Invalid pair table length");
double rlo,rhi;
double rlo;
if (tb->rflag == 0) {
rlo = tb->rfile[0];
rhi = tb->rfile[tb->ninput-1];
} else {
rlo = tb->rlo;
rhi = tb->rhi;
}
rho_0 = rlo;
@ -412,7 +409,7 @@ void PairMultiLucyRX::read_table(Table *tb, char *file, char *keyword)
// open file
FILE *fp = fopen(file,"r");
FILE *fp = force->open_potential(file);
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open file %s",file);