forked from lijiext/lammps
white space cleanup
This commit is contained in:
Axel Kohlmeyer
parent
92395e9bb4
commit
b5e9e90bb6
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@ -71,7 +71,7 @@ enum{ATOM,MOLECULE};
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FixGCMC::FixGCMC(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg),
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idregion(NULL), full_flag(0), ngroups(0), groupstrings(NULL), ngrouptypes(0), grouptypestrings(NULL),
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grouptypebits(NULL), grouptypes(NULL), local_gas_list(NULL), atom_coord(NULL), random_equal(NULL), random_unequal(NULL),
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grouptypebits(NULL), grouptypes(NULL), local_gas_list(NULL), atom_coord(NULL), random_equal(NULL), random_unequal(NULL),
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coords(NULL), imageflags(NULL), fixrigid(NULL), fixshake(NULL), idrigid(NULL), idshake(NULL)
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{
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if (narg < 11) error->all(FLERR,"Illegal fix gcmc command");
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@ -637,7 +637,7 @@ void FixGCMC::init()
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force->boltz*reservoir_temperature));
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zz = exp(beta*chemical_potential)/(pow(lambda,3.0));
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}
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sigma = sqrt(force->boltz*reservoir_temperature*tfac_insert/gas_mass/force->mvv2e);
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if (pressure_flag) zz = pressure*fugacity_coeff*beta/force->nktv2p;
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@ -962,21 +962,21 @@ void FixGCMC::attempt_atomic_insertion()
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zz*volume*exp(-beta*insertion_energy)/(ngas+1)) {
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atom->avec->create_atom(ngcmc_type,coord);
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int m = atom->nlocal - 1;
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// add to groups
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// optionally add to type-based groups
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atom->mask[m] = groupbitall;
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for (int igroup = 0; igroup < ngrouptypes; igroup++) {
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if (ngcmc_type == grouptypes[igroup])
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atom->mask[m] |= grouptypebits[igroup];
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}
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atom->v[m][0] = random_unequal->gaussian()*sigma;
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atom->v[m][1] = random_unequal->gaussian()*sigma;
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atom->v[m][2] = random_unequal->gaussian()*sigma;
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modify->create_attribute(m);
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success = 1;
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}
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}
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@ -1349,7 +1349,7 @@ void FixGCMC::attempt_molecule_insertion()
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if (insertion_energy_sum < MAXENERGYTEST &&
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random_equal->uniform() < zz*volume*natoms_per_molecule*
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exp(-beta*insertion_energy_sum)/(ngas + natoms_per_molecule)) {
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tagint maxmol = 0;
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for (int i = 0; i < atom->nlocal; i++) maxmol = MAX(maxmol,atom->molecule[i]);
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tagint maxmol_all;
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@ -1357,33 +1357,33 @@ void FixGCMC::attempt_molecule_insertion()
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maxmol_all++;
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if (maxmol_all >= MAXTAGINT)
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error->all(FLERR,"Fix gcmc ran out of available molecule IDs");
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tagint maxtag = 0;
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for (int i = 0; i < atom->nlocal; i++) maxtag = MAX(maxtag,atom->tag[i]);
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tagint maxtag_all;
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MPI_Allreduce(&maxtag,&maxtag_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
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int nlocalprev = atom->nlocal;
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double vnew[3];
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vnew[0] = random_equal->gaussian()*sigma;
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vnew[1] = random_equal->gaussian()*sigma;
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vnew[2] = random_equal->gaussian()*sigma;
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for (int i = 0; i < natoms_per_molecule; i++) {
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if (procflag[i]) {
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atom->avec->create_atom(onemols[imol]->type[i],atom_coord[i]);
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int m = atom->nlocal - 1;
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// add to groups
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// optionally add to type-based groups
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atom->mask[m] = groupbitall;
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for (int igroup = 0; igroup < ngrouptypes; igroup++) {
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if (ngcmc_type == grouptypes[igroup])
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atom->mask[m] |= grouptypebits[igroup];
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}
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atom->image[m] = imagezero;
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domain->remap(atom->x[m],atom->image[m]);
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atom->molecule[m] = maxmol_all;
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@ -1393,7 +1393,7 @@ void FixGCMC::attempt_molecule_insertion()
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atom->v[m][0] = vnew[0];
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atom->v[m][1] = vnew[1];
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atom->v[m][2] = vnew[2];
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atom->add_molecule_atom(onemols[imol],i,m,maxtag_all);
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modify->create_attribute(m);
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}
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@ -1494,13 +1494,13 @@ void FixGCMC::attempt_atomic_translation_full()
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energy_stored = energy_after;
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ntranslation_successes += 1.0;
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} else {
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tagint tmptag_all;
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MPI_Allreduce(&tmptag,&tmptag_all,1,MPI_LMP_TAGINT,MPI_MAX,world);
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double xtmp_all[3];
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MPI_Allreduce(&xtmp,&xtmp_all,3,MPI_DOUBLE,MPI_SUM,world);
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for (int i = 0; i < atom->nlocal; i++) {
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if (tmptag_all == atom->tag[i]) {
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x[i][0] = xtmp_all[0];
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@ -1655,7 +1655,7 @@ void FixGCMC::attempt_atomic_insertion_full()
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if (energy_after < MAXENERGYTEST &&
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random_equal->uniform() <
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zz*volume*exp(beta*(energy_before - energy_after))/(ngas+1)) {
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ninsertion_successes += 1.0;
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energy_stored = energy_after;
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} else {
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@ -2150,11 +2150,11 @@ double FixGCMC::energy(int i, int itype, tagint imolecule, double *coord)
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int jtype = type[j];
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// if overlap check requested, if overlap,
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// return signal value for energy
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// return signal value for energy
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if (overlap_flag && rsq < overlap_cutoffsq)
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return MAXENERGYSIGNAL;
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if (rsq < cutsq[itype][jtype])
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total_energy +=
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pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
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@ -2189,7 +2189,7 @@ double FixGCMC::molecule_energy(tagint gas_molecule_id)
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double FixGCMC::energy_full()
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{
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int imolecule;
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if (triclinic) domain->x2lamda(atom->nlocal);
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domain->pbc();
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comm->exchange();
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@ -2202,7 +2202,7 @@ double FixGCMC::energy_full()
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int vflag = 0;
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// if overlap check requested, if overlap,
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// return signal value for energy
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// return signal value for energy
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if (overlap_flag) {
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int overlaptestall;
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@ -2216,12 +2216,12 @@ double FixGCMC::energy_full()
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for (int j = i+1; j < nall; j++) {
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if (mode == MOLECULE)
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if (imolecule == molecule[j]) continue;
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delx = x[i][0] - x[j][0];
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dely = x[i][1] - x[j][1];
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delz = x[i][2] - x[j][2];
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rsq = delx*delx + dely*dely + delz*delz;
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if (rsq < overlap_cutoffsq) {
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overlaptest = 1;
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break;
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@ -2236,7 +2236,7 @@ double FixGCMC::energy_full()
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// clear forces so they don't accumulate over multiple
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// calls within fix gcmc timestep, e.g. for fix shake
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size_t nbytes = sizeof(double) * (atom->nlocal + atom->nghost);
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if (nbytes) memset(&atom->f[0][0],0,3*nbytes);
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@ -2374,7 +2374,7 @@ void FixGCMC::update_gas_atoms_list()
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group->xcm(molecule_group,gas_mass,com);
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// remap unwrapped com into periodic box
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domain->remap(com);
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comx[imolecule] = com[0];
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comy[imolecule] = com[1];
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