git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@2589 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -121,10 +121,10 @@ FixShake::FixShake(LAMMPS *lmp, int narg, char **arg) :
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type_flag[i] = 1;
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} else if (mode == 'm') {
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double rmass = atof(arg[next]);
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if (rmass == 0.0) error->all("Invalid atom mass for fix shake");
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double massone = atof(arg[next]);
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if (massone == 0.0) error->all("Invalid atom mass for fix shake");
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if (nmass == atom->ntypes) error->all("Too many masses for fix shake");
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mass_list[nmass++] = rmass;
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mass_list[nmass++] = massone;
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} else error->all("Illegal fix shake command");
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next++;
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@ -428,6 +428,7 @@ void FixShake::pre_neighbor()
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v = atom->v;
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f = atom->f;
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mass = atom->mass;
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rmass = atom->rmass;
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type = atom->type;
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nlocal = atom->nlocal;
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@ -562,7 +563,7 @@ void FixShake::find_clusters()
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{
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int i,j,m,n;
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int flag,flag_all,messtag,loop,nbuf,nbufmax,size;
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double imass,jmass,rmass;
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double massone;
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int *buf,*bufcopy;
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MPI_Request request;
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MPI_Status status;
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@ -575,6 +576,7 @@ void FixShake::find_clusters()
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int *type = atom->type;
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int *mask = atom->mask;
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double *mass = atom->mass;
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double *rmass = atom->rmass;
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int **bond_type = atom->bond_type;
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int **angle_type = atom->angle_type;
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int **nspecial = atom->nspecial;
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@ -596,6 +598,7 @@ void FixShake::find_clusters()
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// partner_tag[i][] = global IDs of each partner
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// partner_mask[i][] = mask of each partner
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// partner_type[i][] = type of each partner
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// partner_massflag[i][] = 1 if partner meets mass criterion, 0 if not
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// partner_bondtype[i][] = type of bond attached to each partner
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// partner_shake[i][] = 1 if SHAKE bonded to partner, 0 if not
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// partner_nshake[i][] = nshake value for each partner
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@ -614,6 +617,8 @@ void FixShake::find_clusters()
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memory->create_2d_int_array(nlocal,max,"shake:partner_mask");
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int **partner_type =
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memory->create_2d_int_array(nlocal,max,"shake:partner_type");
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int **partner_massflag =
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memory->create_2d_int_array(nlocal,max,"shake:partner_massflag");
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int **partner_bondtype =
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memory->create_2d_int_array(nlocal,max,"shake:partner_bondtype");
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int **partner_shake =
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@ -631,33 +636,42 @@ void FixShake::find_clusters()
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}
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// -----------------------------------------------------
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// set partner_mask, partner_type, partner_bondtype for bonded partners
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// set partner_mask, partner_type, partner_massflag, partner_bondtype
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// for bonded partners
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// requires communication for off-proc partners
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// -----------------------------------------------------
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// fill in mask, type, bondtype if own bond partner
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// info to store in buf for each off-proc bond =
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// 2 atoms IDs in bond, space for mask, type, bondtype
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// fill in mask, type, massflag, bondtype if own bond partner
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// info to store in buf for each off-proc bond = nper = 6
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// 2 atoms IDs in bond, space for mask, type, massflag, bondtype
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// nbufmax = largest buffer needed to hold info from any proc
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int nper = 6;
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nbuf = 0;
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for (i = 0; i < nlocal; i++) {
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for (j = 0; j < npartner[i]; j++) {
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partner_mask[i][j] = 0;
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partner_type[i][j] = 0;
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partner_massflag[i][j] = 0;
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partner_bondtype[i][j] = 0;
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m = atom->map(partner_tag[i][j]);
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if (m >= 0 && m < nlocal) {
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partner_mask[i][j] = mask[m];
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partner_type[i][j] = type[m];
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if (nmass) {
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if (rmass) massone = rmass[m];
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else massone = mass[type[m]];
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partner_massflag[i][j] = masscheck(massone);
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}
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n = bondfind(i,tag[i],partner_tag[i][j]);
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if (n >= 0) partner_bondtype[i][j] = bond_type[i][n];
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else {
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n = bondfind(m,tag[i],partner_tag[i][j]);
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if (n >= 0) partner_bondtype[i][j] = bond_type[m][n];
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}
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} else nbuf += 5;
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} else nbuf += nper;
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}
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}
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@ -677,18 +691,20 @@ void FixShake::find_clusters()
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buf[size+1] = partner_tag[i][j];
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buf[size+2] = 0;
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buf[size+3] = 0;
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buf[size+4] = 0;
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n = bondfind(i,tag[i],partner_tag[i][j]);
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if (n >= 0) buf[size+4] = bond_type[i][n];
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else buf[size+4] = 0;
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size += 5;
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if (n >= 0) buf[size+5] = bond_type[i][n];
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else buf[size+5] = 0;
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size += nper;
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}
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}
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}
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// cycle buffer around ring of procs back to self
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// when receive buffer, scan bond partner IDs for atoms I own
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// if I own partner, fill in mask and type, search for bond with 1st atom
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// and fill in bondtype
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// if I own partner:
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// fill in mask and type and massflag
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// search for bond with 1st atom and fill in bondtype
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messtag = 1;
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for (loop = 0; loop < nprocs; loop++) {
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@ -698,12 +714,17 @@ void FixShake::find_clusters()
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if (m >= 0 && m < nlocal) {
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buf[i+2] = mask[m];
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buf[i+3] = type[m];
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if (buf[i+4] == 0) {
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if (nmass) {
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if (rmass) massone = rmass[m];
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else massone = mass[type[m]];
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buf[i+4] = masscheck(massone);
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}
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if (buf[i+5] == 0) {
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n = bondfind(m,buf[i],buf[i+1]);
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if (n >= 0) buf[i+4] = bond_type[m][n];
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if (n >= 0) buf[i+5] = bond_type[m][n];
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}
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}
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i += 5;
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i += nper;
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}
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if (me != next) {
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MPI_Irecv(bufcopy,nbufmax,MPI_INT,prev,messtag,world,&request);
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@ -723,8 +744,9 @@ void FixShake::find_clusters()
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if (buf[m+1] == partner_tag[i][j]) break;
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partner_mask[i][j] = buf[m+2];
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partner_type[i][j] = buf[m+3];
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partner_bondtype[i][j] = buf[m+4];
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m += 5;
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partner_massflag[i][j] = buf[m+4];
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partner_bondtype[i][j] = buf[m+5];
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m += nper;
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}
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delete [] buf;
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@ -780,15 +802,17 @@ void FixShake::find_clusters()
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continue;
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}
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if (nmass) {
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imass = mass[type[i]];
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jmass = mass[partner_type[i][j]];
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for (m = 0; m < nmass; m++) {
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rmass = mass_list[m];
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if (fabs(rmass-imass) <= MASSDELTA ||
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fabs(rmass-jmass) <= MASSDELTA) {
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if (partner_massflag[i][j]) {
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partner_shake[i][j] = 1;
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nshake[i]++;
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continue;
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} else {
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if (rmass) massone = rmass[i];
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else massone = mass[type[i]];
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if (masscheck(massone)) {
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partner_shake[i][j] = 1;
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nshake[i]++;
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break;
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continue;
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}
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}
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}
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@ -1049,6 +1073,7 @@ void FixShake::find_clusters()
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memory->destroy_2d_int_array(partner_tag);
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memory->destroy_2d_int_array(partner_mask);
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memory->destroy_2d_int_array(partner_type);
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memory->destroy_2d_int_array(partner_massflag);
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memory->destroy_2d_int_array(partner_bondtype);
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memory->destroy_2d_int_array(partner_shake);
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memory->destroy_2d_int_array(partner_nshake);
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@ -1124,6 +1149,18 @@ void FixShake::find_clusters()
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}
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}
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/* ----------------------------------------------------------------------
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check if massone is within MASSDELTA of any mass in mass_list
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return 1 if yes, 0 if not
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------------------------------------------------------------------------- */
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int FixShake::masscheck(double massone)
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{
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for (int i = 0; i < nmass; i++)
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if (fabs(mass_list[i]-massone) <= MASSDELTA) return 1;
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return 0;
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}
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/* ----------------------------------------------------------------------
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update the unconstrained position of each atom
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only for SHAKE clusters, else set to 0.0
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@ -1134,13 +1171,24 @@ void FixShake::unconstrained_update()
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{
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double dtfmsq;
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for (int i = 0; i < nlocal; i++) {
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if (shake_flag[i]) {
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dtfmsq = dtfsq / mass[type[i]];
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xshake[i][0] = x[i][0] + dtv*v[i][0] + dtfmsq*f[i][0];
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xshake[i][1] = x[i][1] + dtv*v[i][1] + dtfmsq*f[i][1];
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xshake[i][2] = x[i][2] + dtv*v[i][2] + dtfmsq*f[i][2];
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} else xshake[i][2] = xshake[i][1] = xshake[i][0] = 0.0;
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if (rmass) {
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for (int i = 0; i < nlocal; i++) {
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if (shake_flag[i]) {
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dtfmsq = dtfsq / rmass[i];
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xshake[i][0] = x[i][0] + dtv*v[i][0] + dtfmsq*f[i][0];
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xshake[i][1] = x[i][1] + dtv*v[i][1] + dtfmsq*f[i][1];
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xshake[i][2] = x[i][2] + dtv*v[i][2] + dtfmsq*f[i][2];
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} else xshake[i][2] = xshake[i][1] = xshake[i][0] = 0.0;
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}
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} else {
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for (int i = 0; i < nlocal; i++) {
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if (shake_flag[i]) {
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dtfmsq = dtfsq / mass[type[i]];
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xshake[i][0] = x[i][0] + dtv*v[i][0] + dtfmsq*f[i][0];
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xshake[i][1] = x[i][1] + dtv*v[i][1] + dtfmsq*f[i][1];
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xshake[i][2] = x[i][2] + dtv*v[i][2] + dtfmsq*f[i][2];
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} else xshake[i][2] = xshake[i][1] = xshake[i][0] = 0.0;
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}
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}
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}
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@ -1150,6 +1198,7 @@ void FixShake::shake2(int m)
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{
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int nlist,list[2];
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double v[6];
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double invmass0,invmass1;
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// local atom IDs and constraint distances
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@ -1180,8 +1229,13 @@ void FixShake::shake2(int m)
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// a,b,c = coeffs in quadratic equation for lamda
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double invmass0 = 1.0/mass[type[i0]];
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double invmass1 = 1.0/mass[type[i1]];
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if (rmass) {
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invmass0 = 1.0/rmass[i0];
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invmass1 = 1.0/rmass[i1];
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} else {
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invmass0 = 1.0/mass[type[i0]];
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invmass1 = 1.0/mass[type[i1]];
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}
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double a = (invmass0+invmass1)*(invmass0+invmass1) * r01sq;
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double b = 2.0 * (invmass0+invmass1) *
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@ -1243,6 +1297,7 @@ void FixShake::shake3(int m)
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{
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int nlist,list[3];
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double v[6];
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double invmass0,invmass1,invmass2;
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// local atom IDs and constraint distances
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@ -1289,9 +1344,15 @@ void FixShake::shake3(int m)
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// matrix coeffs and rhs for lamda equations
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double invmass0 = 1.0/mass[type[i0]];
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double invmass1 = 1.0/mass[type[i1]];
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double invmass2 = 1.0/mass[type[i2]];
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if (rmass) {
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invmass0 = 1.0/rmass[i0];
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invmass1 = 1.0/rmass[i1];
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invmass2 = 1.0/rmass[i2];
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} else {
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invmass0 = 1.0/mass[type[i0]];
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invmass1 = 1.0/mass[type[i1]];
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invmass2 = 1.0/mass[type[i2]];
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}
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double a11 = 2.0 * (invmass0+invmass1) *
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(s01[0]*r01[0] + s01[1]*r01[1] + s01[2]*r01[2]);
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@ -1401,6 +1462,7 @@ void FixShake::shake4(int m)
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{
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int nlist,list[4];
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double v[6];
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double invmass0,invmass1,invmass2,invmass3;
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// local atom IDs and constraint distances
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@ -1463,10 +1525,17 @@ void FixShake::shake4(int m)
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// matrix coeffs and rhs for lamda equations
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double invmass0 = 1.0/mass[type[i0]];
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double invmass1 = 1.0/mass[type[i1]];
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double invmass2 = 1.0/mass[type[i2]];
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double invmass3 = 1.0/mass[type[i3]];
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if (rmass) {
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invmass0 = 1.0/rmass[i0];
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invmass1 = 1.0/rmass[i1];
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invmass2 = 1.0/rmass[i2];
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invmass3 = 1.0/rmass[i3];
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} else {
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invmass0 = 1.0/mass[type[i0]];
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invmass1 = 1.0/mass[type[i1]];
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invmass2 = 1.0/mass[type[i2]];
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invmass3 = 1.0/mass[type[i3]];
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}
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double a11 = 2.0 * (invmass0+invmass1) *
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(s01[0]*r01[0] + s01[1]*r01[1] + s01[2]*r01[2]);
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@ -1636,6 +1705,7 @@ void FixShake::shake3angle(int m)
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{
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int nlist,list[3];
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double v[6];
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double invmass0,invmass1,invmass2;
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// local atom IDs and constraint distances
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@ -1697,9 +1767,15 @@ void FixShake::shake3angle(int m)
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// matrix coeffs and rhs for lamda equations
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double invmass0 = 1.0/mass[type[i0]];
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double invmass1 = 1.0/mass[type[i1]];
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double invmass2 = 1.0/mass[type[i2]];
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if (rmass) {
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invmass0 = 1.0/rmass[i0];
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invmass1 = 1.0/rmass[i1];
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invmass2 = 1.0/rmass[i2];
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} else {
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invmass0 = 1.0/mass[type[i0]];
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invmass1 = 1.0/mass[type[i1]];
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invmass2 = 1.0/mass[type[i2]];
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}
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double a11 = 2.0 * (invmass0+invmass1) *
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(s01[0]*r01[0] + s01[1]*r01[1] + s01[2]*r01[2]);
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@ -2204,20 +2280,39 @@ void FixShake::post_force_respa(int vflag, int ilevel, int iloop)
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double invmass,dtfmsq;
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int jlevel;
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for (int i = 0; i < nlocal; i++) {
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if (shake_flag[i]) {
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invmass = 1.0 / mass[type[i]];
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dtfmsq = dtfsq * invmass;
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xshake[i][0] = x[i][0] + dtv*v[i][0] + dtfmsq*f[i][0];
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xshake[i][1] = x[i][1] + dtv*v[i][1] + dtfmsq*f[i][1];
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xshake[i][2] = x[i][2] + dtv*v[i][2] + dtfmsq*f[i][2];
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for (jlevel = 0; jlevel < ilevel; jlevel++) {
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dtfmsq = dtf_innerhalf * step_respa[jlevel] * invmass;
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xshake[i][0] += dtfmsq*f_level[i][jlevel][0];
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xshake[i][1] += dtfmsq*f_level[i][jlevel][1];
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xshake[i][2] += dtfmsq*f_level[i][jlevel][2];
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}
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} else xshake[i][2] = xshake[i][1] = xshake[i][0] = 0.0;
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if (rmass) {
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for (int i = 0; i < nlocal; i++) {
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if (shake_flag[i]) {
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invmass = 1.0 / rmass[i];
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dtfmsq = dtfsq * invmass;
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xshake[i][0] = x[i][0] + dtv*v[i][0] + dtfmsq*f[i][0];
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xshake[i][1] = x[i][1] + dtv*v[i][1] + dtfmsq*f[i][1];
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xshake[i][2] = x[i][2] + dtv*v[i][2] + dtfmsq*f[i][2];
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for (jlevel = 0; jlevel < ilevel; jlevel++) {
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dtfmsq = dtf_innerhalf * step_respa[jlevel] * invmass;
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xshake[i][0] += dtfmsq*f_level[i][jlevel][0];
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xshake[i][1] += dtfmsq*f_level[i][jlevel][1];
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xshake[i][2] += dtfmsq*f_level[i][jlevel][2];
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}
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} else xshake[i][2] = xshake[i][1] = xshake[i][0] = 0.0;
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}
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} else {
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for (int i = 0; i < nlocal; i++) {
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if (shake_flag[i]) {
|
||||
invmass = 1.0 / mass[type[i]];
|
||||
dtfmsq = dtfsq * invmass;
|
||||
xshake[i][0] = x[i][0] + dtv*v[i][0] + dtfmsq*f[i][0];
|
||||
xshake[i][1] = x[i][1] + dtv*v[i][1] + dtfmsq*f[i][1];
|
||||
xshake[i][2] = x[i][2] + dtv*v[i][2] + dtfmsq*f[i][2];
|
||||
for (jlevel = 0; jlevel < ilevel; jlevel++) {
|
||||
dtfmsq = dtf_innerhalf * step_respa[jlevel] * invmass;
|
||||
xshake[i][0] += dtfmsq*f_level[i][jlevel][0];
|
||||
xshake[i][1] += dtfmsq*f_level[i][jlevel][1];
|
||||
xshake[i][2] += dtfmsq*f_level[i][jlevel][2];
|
||||
}
|
||||
} else xshake[i][2] = xshake[i][1] = xshake[i][0] = 0.0;
|
||||
}
|
||||
}
|
||||
|
||||
// communicate results if necessary
|
||||
|
||||
Reference in New Issue
Block a user