forked from lijiext/lammps
Made insertion work correctly for triclinic
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14043 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
athomps
parent
67771a01fb
commit
ed7559f329
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@ -377,6 +377,9 @@ int FixGCMC::setmask()
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void FixGCMC::init()
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{
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triclinic = domain->triclinic;
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// decide whether to switch to the full_energy option
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if (!full_flag) {
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@ -385,7 +388,7 @@ void FixGCMC::init()
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(force->pair->single_enable == 0) ||
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(force->pair_match("hybrid",0)) ||
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(force->pair_match("eam",0)) ||
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(domain->triclinic == 1)
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(triclinic == 1)
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) {
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full_flag = true;
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if (comm->me == 0)
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@ -614,7 +617,7 @@ void FixGCMC::pre_exchange()
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yhi = domain->boxhi[1];
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zlo = domain->boxlo[2];
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zhi = domain->boxhi[2];
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if (domain->triclinic) {
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if (triclinic) {
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sublo = domain->sublo_lamda;
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subhi = domain->subhi_lamda;
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} else {
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@ -625,12 +628,12 @@ void FixGCMC::pre_exchange()
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if (regionflag) volume = region_volume;
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else volume = domain->xprd * domain->yprd * domain->zprd;
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if (domain->triclinic) domain->x2lamda(atom->nlocal);
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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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atom->nghost = 0;
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comm->borders();
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if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
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if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
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update_gas_atoms_list();
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if (full_flag) {
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@ -660,12 +663,12 @@ void FixGCMC::pre_exchange()
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}
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}
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}
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if (domain->triclinic) domain->x2lamda(atom->nlocal);
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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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atom->nghost = 0;
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comm->borders();
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if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
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if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
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} else {
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@ -756,12 +759,12 @@ void FixGCMC::attempt_atomic_translation()
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MPI_Allreduce(&success,&success_all,1,MPI_INT,MPI_MAX,world);
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if (success_all) {
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if (domain->triclinic) domain->x2lamda(atom->nlocal);
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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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atom->nghost = 0;
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comm->borders();
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if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
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if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
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update_gas_atoms_list();
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ntranslation_successes += 1.0;
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}
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@ -809,8 +812,12 @@ void FixGCMC::attempt_atomic_deletion()
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void FixGCMC::attempt_atomic_insertion()
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{
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double lamda[3];
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ninsertion_attempts += 1.0;
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// pick coordinates for insertion point
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double coord[3];
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if (regionflag) {
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int region_attempt = 0;
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@ -824,22 +831,40 @@ void FixGCMC::attempt_atomic_insertion()
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region_attempt++;
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if (region_attempt >= max_region_attempts) return;
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}
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if (triclinic) domain->x2lamda(coord,lamda);
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} else {
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if (triclinic == 0) {
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coord[0] = xlo + random_equal->uniform() * (xhi-xlo);
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coord[1] = ylo + random_equal->uniform() * (yhi-ylo);
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coord[2] = zlo + random_equal->uniform() * (zhi-zlo);
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} else {
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lamda[0] = random_equal->uniform();
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lamda[1] = random_equal->uniform();
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lamda[2] = random_equal->uniform();
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// wasteful, but necessary
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if (lamda[0] == 1.0) lamda[0] = 0.0;
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if (lamda[1] == 1.0) lamda[1] = 0.0;
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if (lamda[2] == 1.0) lamda[2] = 0.0;
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domain->lamda2x(lamda,coord);
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}
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}
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// apply remap to protect against rounding errors
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int proc_flag = 0;
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if (triclinic == 0) {
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domain->remap(coord);
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if (!domain->inside(coord))
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error->one(FLERR,"Fix gcmc put atom outside box");
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int proc_flag = 0;
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if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
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coord[1] >= sublo[1] && coord[1] < subhi[1] &&
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coord[2] >= sublo[2] && coord[2] < subhi[2]) proc_flag = 1;
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} else {
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if (lamda[0] >= sublo[0] && lamda[0] < subhi[0] &&
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lamda[1] >= sublo[1] && lamda[1] < subhi[1] &&
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lamda[2] >= sublo[2] && lamda[2] < subhi[2]) proc_flag = 1;
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}
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int success = 0;
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if (proc_flag) {
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@ -974,12 +999,12 @@ void FixGCMC::attempt_molecule_translation()
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x[i][2] += com_displace[2];
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}
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}
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if (domain->triclinic) domain->x2lamda(atom->nlocal);
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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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atom->nghost = 0;
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comm->borders();
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if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
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if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
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update_gas_atoms_list();
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ntranslation_successes += 1.0;
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}
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@ -1072,12 +1097,12 @@ void FixGCMC::attempt_molecule_rotation()
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n++;
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}
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}
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if (domain->triclinic) domain->x2lamda(atom->nlocal);
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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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atom->nghost = 0;
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comm->borders();
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if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
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if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
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update_gas_atoms_list();
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nrotation_successes += 1.0;
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}
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@ -1120,6 +1145,7 @@ void FixGCMC::attempt_molecule_deletion()
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void FixGCMC::attempt_molecule_insertion()
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{
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double lamda[3];
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ninsertion_attempts += 1.0;
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double com_coord[3];
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@ -1142,10 +1168,25 @@ void FixGCMC::attempt_molecule_insertion()
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region_attempt++;
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if (region_attempt >= max_region_attempts) return;
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}
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if (triclinic) domain->x2lamda(com_coord,lamda);
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} else {
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if (triclinic == 0) {
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com_coord[0] = xlo + random_equal->uniform() * (xhi-xlo);
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com_coord[1] = ylo + random_equal->uniform() * (yhi-ylo);
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com_coord[2] = zlo + random_equal->uniform() * (zhi-zlo);
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} else {
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lamda[0] = random_equal->uniform();
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lamda[1] = random_equal->uniform();
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lamda[2] = random_equal->uniform();
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// wasteful, but necessary
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if (lamda[0] == 1.0) lamda[0] = 0.0;
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if (lamda[1] == 1.0) lamda[1] = 0.0;
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if (lamda[2] == 1.0) lamda[2] = 0.0;
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domain->lamda2x(lamda,com_coord);
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}
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}
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// generate point in unit cube
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@ -1168,7 +1209,6 @@ void FixGCMC::attempt_molecule_insertion()
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double insertion_energy = 0.0;
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bool procflag[natoms_per_molecule];
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for (int i = 0; i < natoms_per_molecule; i++) {
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MathExtra::matvec(rotmat,onemols[imol]->x[i],atom_coord[i]);
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atom_coord[i][0] += com_coord[0];
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@ -1187,10 +1227,18 @@ void FixGCMC::attempt_molecule_insertion()
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error->one(FLERR,"Fix gcmc put atom outside box");
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procflag[i] = false;
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if (triclinic == 0) {
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if (xtmp[0] >= sublo[0] && xtmp[0] < subhi[0] &&
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xtmp[1] >= sublo[1] && xtmp[1] < subhi[1] &&
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xtmp[2] >= sublo[2] && xtmp[2] < subhi[2]) {
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procflag[i] = true;
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xtmp[2] >= sublo[2] && xtmp[2] < subhi[2]) procflag[i] = true;
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} else {
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domain->x2lamda(xtmp,lamda);
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if (lamda[0] >= sublo[0] && lamda[0] < subhi[0] &&
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lamda[1] >= sublo[1] && lamda[1] < subhi[1] &&
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lamda[2] >= sublo[2] && lamda[2] < subhi[2]) procflag[i] = true;
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}
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if (procflag[i]) {
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int ii = -1;
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if (onemols[imol]->qflag == 1) {
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ii = atom->nlocal + atom->nghost;
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@ -1416,6 +1464,7 @@ void FixGCMC::attempt_atomic_deletion_full()
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void FixGCMC::attempt_atomic_insertion_full()
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{
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double lamda[3];
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ninsertion_attempts += 1.0;
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double energy_before = energy_stored;
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@ -1433,30 +1482,42 @@ void FixGCMC::attempt_atomic_insertion_full()
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region_attempt++;
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if (region_attempt >= max_region_attempts) return;
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}
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if (triclinic) domain->x2lamda(coord,lamda);
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} else {
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if (triclinic == 0) {
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coord[0] = xlo + random_equal->uniform() * (xhi-xlo);
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coord[1] = ylo + random_equal->uniform() * (yhi-ylo);
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coord[2] = zlo + random_equal->uniform() * (zhi-zlo);
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} else {
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lamda[0] = random_equal->uniform();
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lamda[1] = random_equal->uniform();
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lamda[2] = random_equal->uniform();
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// wasteful, but necessary
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if (lamda[0] == 1.0) lamda[0] = 0.0;
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if (lamda[1] == 1.0) lamda[1] = 0.0;
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if (lamda[2] == 1.0) lamda[2] = 0.0;
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domain->lamda2x(lamda,coord);
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}
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// apply remap to protect against rounding errors
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domain->remap(coord);
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if (!domain->inside(coord))
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error->one(FLERR,"Fix gcmc put atom outside box");
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// if triclinic, convert to lamda coords (0-1)
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double lamda[3];
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if (domain->triclinic) {
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domain->x2lamda(coord,coord);
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}
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int proc_flag = 0;
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if (triclinic == 0) {
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domain->remap(coord);
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if (!domain->inside(coord))
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error->one(FLERR,"Fix gcmc put atom outside box");
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if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
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coord[1] >= sublo[1] && coord[1] < subhi[1] &&
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coord[2] >= sublo[2] && coord[2] < subhi[2]) {
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proc_flag = 1;
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coord[2] >= sublo[2] && coord[2] < subhi[2]) proc_flag = 1;
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} else {
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if (lamda[0] >= sublo[0] && lamda[0] < subhi[0] &&
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lamda[1] >= sublo[1] && lamda[1] < subhi[1] &&
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lamda[2] >= sublo[2] && lamda[2] < subhi[2]) proc_flag = 1;
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}
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if (proc_flag) {
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atom->avec->create_atom(ngcmc_type,coord);
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int m = atom->nlocal - 1;
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@ -1755,6 +1816,7 @@ void FixGCMC::attempt_molecule_deletion_full()
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void FixGCMC::attempt_molecule_insertion_full()
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{
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double lamda[3];
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ninsertion_attempts += 1.0;
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double energy_before = energy_stored;
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@ -1795,10 +1857,26 @@ void FixGCMC::attempt_molecule_insertion_full()
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region_attempt++;
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if (region_attempt >= max_region_attempts) return;
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}
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if (triclinic) domain->x2lamda(com_coord,lamda);
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} else {
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if (triclinic == 0) {
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com_coord[0] = xlo + random_equal->uniform() * (xhi-xlo);
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com_coord[1] = ylo + random_equal->uniform() * (yhi-ylo);
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com_coord[2] = zlo + random_equal->uniform() * (zhi-zlo);
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} else {
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lamda[0] = random_equal->uniform();
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lamda[1] = random_equal->uniform();
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lamda[2] = random_equal->uniform();
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// wasteful, but necessary
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if (lamda[0] == 1.0) lamda[0] = 0.0;
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if (lamda[1] == 1.0) lamda[1] = 0.0;
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if (lamda[2] == 1.0) lamda[2] = 0.0;
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domain->lamda2x(lamda,com_coord);
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}
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}
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// generate point in unit cube
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@ -1837,10 +1915,19 @@ void FixGCMC::attempt_molecule_insertion_full()
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if (!domain->inside(xtmp))
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error->one(FLERR,"Fix gcmc put atom outside box");
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int proc_flag = 0;
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if (triclinic == 0) {
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if (xtmp[0] >= sublo[0] && xtmp[0] < subhi[0] &&
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xtmp[1] >= sublo[1] && xtmp[1] < subhi[1] &&
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xtmp[2] >= sublo[2] && xtmp[2] < subhi[2]) {
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xtmp[2] >= sublo[2] && xtmp[2] < subhi[2]) proc_flag = 1;
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} else {
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domain->x2lamda(xtmp,lamda);
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if (lamda[0] >= sublo[0] && lamda[0] < subhi[0] &&
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lamda[1] >= sublo[1] && lamda[1] < subhi[1] &&
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lamda[2] >= sublo[2] && lamda[2] < subhi[2]) proc_flag = 1;
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}
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if (proc_flag) {
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atom->avec->create_atom(onemols[imol]->type[i],xtmp);
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int m = atom->nlocal - 1;
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@ -1980,12 +2067,12 @@ double FixGCMC::molecule_energy(tagint gas_molecule_id)
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double FixGCMC::energy_full()
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{
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if (domain->triclinic) domain->x2lamda(atom->nlocal);
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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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atom->nghost = 0;
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comm->borders();
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if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
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if (triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
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if (modify->n_pre_neighbor) modify->pre_neighbor();
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neighbor->build();
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int eflag = 1;
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@ -128,6 +128,7 @@ class FixGCMC : public Fix {
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class Fix *fixshake;
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int shakeflag;
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char *idshake;
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int triclinic; // 0 = orthog box, 1 = triclinic
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class Compute *c_pe;
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