forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@12859 f3b2605a-c512-4ea7-a41b-209d697bcdaa
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sjplimp
parent
32f47e4a99
commit
1aefa8d624
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@ -26,6 +26,7 @@
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#include "error.h"
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#include "neighbor.h"
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#include "atom_vec.h"
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#include "modify.h"
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using namespace LAMMPS_NS;
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using namespace FixConst;
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@ -66,11 +67,11 @@ FixSRP::FixSRP(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
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array[i][m] = 0.0;
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// assume setup of fix is needed to insert particles
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// yes if reading datafile
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// maybe if reading restart
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// a datafile cannot contain BPs
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// a restart file written during the run has BPs as per atom data
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// a restart file written after the run does not have BPs
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// is true if reading from datafile
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// since a datafile cannot contain bond particles
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// might be true if reading from restart
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// a restart file written during the run has bond particles as per atom data
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// a restart file written after the run does not have bond particles
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setup = 1;
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}
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@ -80,7 +81,7 @@ FixSRP::~FixSRP()
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{
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// unregister callbacks to this fix from Atom class
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atom->delete_callback(id,0);
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atom->delete_callback(id,1); // for restart
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atom->delete_callback(id,1);
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atom->delete_callback(id,2);
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memory->destroy(array);
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}
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@ -104,18 +105,16 @@ void FixSRP::init()
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if (force->pair_match("hybrid",1) == NULL)
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error->all(FLERR,"Cannot use pair srp without pair_style hybrid");
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// reserve the highest numbered atom type for bond particles (BPs)
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// set bptype if not read from restart
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// the highest numbered atom type should be reserved for bond particles (bptype)
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// set bptype, unless it will be read from restart
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if(!restart_reset) bptype = atom->ntypes;
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// check for prescense of extra atom type for bond particle
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// if reading a rst file written in the middle of run
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// then bond particles are already present
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// otherwise need to insert particles in setup
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// check if bptype is already in use
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for(int i=0; i < atom->nlocal; i++)
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if(atom->type[i] == bptype){
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// error if missing extra atom type in either
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// data file or rst file without this fix
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// error if bptype is already in use
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// unless starting from a rst file
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// since rst can contain the bond particles as per atom data
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if(!restart_reset)
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error->all(FLERR,"Fix SRP requires an extra atom type");
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else
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@ -123,7 +122,7 @@ void FixSRP::init()
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}
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// setup neigh exclusions for diff atom types
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// BPs do not interact with other types
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// bond particles do not interact with other types
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// type bptype only interacts with itself
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char* arg1[4];
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arg1[0] = (char *) "exclude";
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@ -155,8 +154,8 @@ void FixSRP::setup_pre_force(int zz)
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bigint nall = atom->nlocal + atom->nghost;
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double xold[nall][3];
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// make a copy of coordinates and tags
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// create_atom overwrites ghost atoms
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// make a copy of all coordinates and tags
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// need this because create_atom overwrites ghost atoms
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for(int i = 0; i < nall; i++){
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xold[i][0] = x[i][0];
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xold[i][1] = x[i][1];
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@ -189,7 +188,8 @@ void FixSRP::setup_pre_force(int zz)
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xone[1] = (xold[i][1] + xold[j][1])*0.5;
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xone[2] = (xold[i][2] + xold[j][2])*0.5;
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// record longest bond for ghostcut
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// record longest bond
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// this used to set ghost cutoff
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delx = xold[j][0] - xold[i][0];
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dely = xold[j][1] - xold[i][1];
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delz = xold[j][2] - xold[i][2];
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@ -262,11 +262,20 @@ void FixSRP::setup_pre_force(int zz)
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// move owned to new procs
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// get ghosts
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// build neigh lists again
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// if triclinic, lambda coords needed for pbc, exchange, borders
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if (domain->triclinic) domain->x2lamda(atom->nlocal);
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domain->pbc();
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comm->setup();
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if (neighbor->style) neighbor->setup_bins();
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comm->exchange();
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if (atom->sortfreq > 0) atom->sort();
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comm->borders();
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// back to box coords
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if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
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domain->image_check();
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domain->box_too_small_check();
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modify->setup_pre_neighbor();
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neighbor->build();
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neighbor->ncalls = 0;
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@ -295,7 +304,7 @@ void FixSRP::pre_exchange()
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comm->forward_comm();
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// reassign bond particle coordinates to midpoint of bonds
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// only needed before neigh rebuild
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// only need to do this before neigh rebuild
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double **x=atom->x;
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int i,j;
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int nlocal = atom->nlocal;
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@ -422,7 +431,7 @@ void FixSRP::post_run()
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{
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// all bond particles are removed after each run
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// useful for write_data and write_restart commands
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// since it occurs between runs
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// since those commands occur between runs
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bigint natoms_previous = atom->natoms;
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int nlocal = atom->nlocal;
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@ -481,11 +490,16 @@ void FixSRP::post_run()
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// verlet calls box_too_small_check() in post_run
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// this check maps all bond partners
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// therefore need ghosts
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// need to convert to lambda coords before apply pbc
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if (domain->triclinic) domain->x2lamda(atom->nlocal);
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domain->pbc();
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comm->setup();
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comm->exchange();
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if (atom->sortfreq > 0) atom->sort();
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comm->borders();
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// change back to box coordinates
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if (domain->triclinic) domain->lamda2x(atom->nlocal+atom->nghost);
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}
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/* ----------------------------------------------------------------------
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@ -572,8 +586,8 @@ void FixSRP::restart(char *buf)
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}
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/* ----------------------------------------------------------------------
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interface with other classes
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pair srp sets the bond type for this fix
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interface with pair class
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pair srp sets the bond type in this fix
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------------------------------------------------------------------------- */
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int FixSRP::modify_param(int narg, char **arg)
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@ -45,7 +45,7 @@ Please contact Timothy Sirk for questions (tim.sirk@us.army.mil).
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using namespace LAMMPS_NS;
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#define SMALL 1.0e-3
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#define SMALL 1.0e-10
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#define BIG 1e10
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#define ONETWOBIT 0x40000000
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@ -155,8 +155,9 @@ void PairSRP::compute(int eflag, int vflag)
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}
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// this pair style only used with hybrid
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// so each atom i is type bptype
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// each neigh j is type bptype due to exclusions
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// due to exclusions
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// each atom i is type bptype
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// each neigh j is type bptype
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// using midpoint distance option
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if(midpoint){
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@ -179,7 +180,7 @@ void PairSRP::compute(int eflag, int vflag)
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continue;
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j &= NEIGHMASK;
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//atoms inside bond particle
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//retrieve atoms from bond particle
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i1 = segment[j][0];
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j1 = segment[j][1];
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@ -190,13 +191,13 @@ void PairSRP::compute(int eflag, int vflag)
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dijsq = dx*dx + dy*dy + dz*dz;
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if (dijsq < cutsq[bptype][bptype]){
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dij = pow(dijsq, 0.5);
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dij = sqrt(dijsq);
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if (dij < SMALL)
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dij = SMALL; // prevent explosions
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if (dij < SMALL)
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continue; // dij can be 0.0 with soft potentials
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wd = 1.0 - dij / cut[bptype][bptype];
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fpair = 0.5 * a0[bptype][bptype] * wd / dij;
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fpair = 0.5 * a0[bptype][bptype] * wd / dij; // 0.5 factor for lever rule
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// force for bond 0, beads 0,1
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//force between bonds
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@ -266,13 +267,13 @@ void PairSRP::compute(int eflag, int vflag)
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if (dijsq < cutsq[bptype][bptype]){
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dij = pow(dijsq, 0.5);
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dij = sqrt(dijsq);
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if (dij < SMALL)
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dij = SMALL; // prevent explosions
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if (dij < SMALL)
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continue; // dij can be 0.0 with soft potentials
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wd = 1.0 - dij / cut[bptype][bptype];
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fpair = a0[bptype][bptype] * wd / dij;
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fpair = a0[bptype][bptype] * wd / dij;
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// force for bond 0, beads 0,1
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lever0 = 0.5 + ti; // assign force according to lever rule
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@ -281,6 +282,7 @@ void PairSRP::compute(int eflag, int vflag)
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fx = fpair * dx;
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fy = fpair * dy;
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fz = fpair * dz;
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//decompose onto atoms
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fxlever0 = fx * lever0;
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fylever0 = fy * lever0;
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@ -353,16 +355,18 @@ void PairSRP::settings(int narg, char **arg)
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while (iarg < narg) {
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if (strcmp(arg[iarg],"exclude") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal pair srp exclude command");
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if (iarg+2 > narg) error->all(FLERR,"Illegal pair srp command");
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if (strcmp(arg[iarg+1],"yes") == 0)
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exclude = 1;
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if (strcmp(arg[iarg+1],"no") == 0)
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exclude = 0;
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exclude = 1;
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if (strcmp(arg[iarg+1],"no") == 0){
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if (min) error->all(FLERR,"Illegal exclude option in pair srp command");
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exclude = 0;
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}
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iarg += 2;
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} else error->all(FLERR,"Illegal pair srp command");
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}
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// highest atom type is saved for bond particles (BPs)
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// highest atom type is saved for bond particles
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bptype = atom->ntypes;
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// reset cutoffs if explicitly set
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@ -372,7 +376,6 @@ void PairSRP::settings(int narg, char **arg)
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for (j = i+1; j <= bptype; j++)
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if (setflag[i][j]) cut[i][j] = cut_global;
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}
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}
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/* ----------------------------------------------------------------------
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@ -422,16 +425,16 @@ void PairSRP::init_style()
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// need fix srp
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// invoke here instead of constructor
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// to make restart possible
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char **newarg = new char*[3];
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newarg[0] = (char *) "pair_srp";
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newarg[1] = (char *) "all";
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newarg[2] = (char *) "SRP";
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modify->add_fix(3,newarg);
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char **fixarg = new char*[3];
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fixarg[0] = (char *) "mysrp";
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fixarg[1] = (char *) "all";
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fixarg[2] = (char *) "SRP";
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modify->add_fix(3,fixarg);
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f_srp = (FixSRP *) modify->fix[modify->nfix-1];
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delete [] newarg;
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delete [] fixarg;
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// set bond type in fix srp
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// bonds of this type will be represented by bond particles (BPs)
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// bonds of this type will be represented by bond particles
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// btype = bond type
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// bptype = bond particle type
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char c0[20];
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@ -441,10 +444,10 @@ void PairSRP::init_style()
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arg0[1] = c0;
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f_srp->modify_params(2, arg0);
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// BPs do not contribute to energy or virial
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// BPs do not belong to group all
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// but thermo normalization is by nall
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// turn off normalization
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// bond particles do not contribute to energy or virial
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// bond particles do not belong to group all
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// but thermo normalization is by nall
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// therefore should turn off normalization
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int me;
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MPI_Comm_rank(world,&me);
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char *arg1[2];
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