forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@4528 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
41d9b859e4
commit
f4f39a21d8
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@ -5,7 +5,9 @@
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if (test $1 = 1) then
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cp fix_qeq.cpp ..
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cp pair_airebo.cpp ..
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cp pair_comb.cpp ..
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cp pair_eam.cpp ..
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cp pair_eam_alloy.cpp ..
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cp pair_eam_fs.cpp ..
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@ -13,7 +15,9 @@ if (test $1 = 1) then
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cp pair_tersoff.cpp ..
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cp pair_tersoff_zbl.cpp ..
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cp fix_qeq.h ..
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cp pair_airebo.h ..
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cp pair_comb.h ..
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cp pair_eam.h ..
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cp pair_eam_alloy.h ..
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cp pair_eam_fs.h ..
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@ -27,7 +31,9 @@ if (test $1 = 1) then
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elif (test $1 = 0) then
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rm ../fix_qeq.cpp
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rm ../pair_airebo.cpp
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rm ../pair_comb.cpp
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rm ../pair_eam.cpp
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rm ../pair_eam_alloy.cpp
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rm ../pair_eam_fs.cpp
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@ -35,7 +41,9 @@ elif (test $1 = 0) then
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rm ../pair_tersoff.cpp
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rm ../pair_tersoff_zbl.cpp
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rm ../pair_qeq.h
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rm ../pair_airebo.h
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rm ../pair_comb.h
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rm ../pair_eam.h
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rm ../pair_eam_alloy.h
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rm ../pair_eam_fs.h
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@ -0,0 +1,248 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Tzu-Ray Shan (U Florida, rayshan@ufl.edu)
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------------------------------------------------------------------------- */
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#include "mpi.h"
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#include "math.h"
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#include "stdlib.h"
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#include "string.h"
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#include "fix_qeq.h"
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#include "atom.h"
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#include "force.h"
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#include "group.h"
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#include "respa.h"
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#include "pair_comb.h"
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#include "update.h"
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#include "memory.h"
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#include "error.h"
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using namespace LAMMPS_NS;
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#define MIN(A,B) ((A) < (B)) ? (A) : (B)
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#define MAX(A,B) ((A) > (B)) ? (A) : (B)
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/* ---------------------------------------------------------------------- */
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FixQEQ::FixQEQ(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
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{
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if (narg < 5) error->all("Illegal fix qeq command");
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peratom_flag = 1;
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size_peratom_cols = 0;
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peratom_freq = 1;
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nevery = force->inumeric(arg[3]);
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precision = force->numeric(arg[4]);
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if (nevery <= 0 || precision <= 0.0) error->all("Illegal fix qeq command");
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MPI_Comm_rank(world,&me);
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// optional args
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fp = NULL;
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int iarg = 5;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"file") == 0) {
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if (iarg+2 > narg) error->all("Illegal fix qeq command");
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if (me == 0) {
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fp = fopen(arg[iarg+1],"w");
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if (fp == NULL) {
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char str[128];
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sprintf(str,"Cannot open fix qeq file %s",arg[iarg+1]);
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error->one(str);
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}
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}
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iarg += 2;
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} else error->all("Illegal fix qeq command");
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}
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nmax = atom->nmax;
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qf = (double *) memory->smalloc(nmax*sizeof(double),"qeq:qf");
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q1 = (double *) memory->smalloc(nmax*sizeof(double),"qeq:q1");
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q2 = (double *) memory->smalloc(nmax*sizeof(double),"qeq:q2");
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vector_atom = qf;
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// zero the vector since dump may access it on timestep 0
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// zero the vector since a variable may access it before first run
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int nlocal = atom->nlocal;
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for (int i = 0; i < nlocal; i++) qf[i] = 0.0;
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}
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/* ---------------------------------------------------------------------- */
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FixQEQ::~FixQEQ()
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{
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if (me == 0 && fp) fclose(fp);
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memory->sfree(qf);
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memory->sfree(q1);
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memory->sfree(q2);
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}
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/* ---------------------------------------------------------------------- */
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int FixQEQ::setmask()
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{
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int mask = 0;
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mask |= POST_FORCE;
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mask |= POST_FORCE_RESPA;
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return mask;
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}
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/* ---------------------------------------------------------------------- */
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void FixQEQ::init()
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{
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if (atom->q == NULL) error->all("Must use atom style charge with fix qeq");
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comb = (PairComb *) force->pair_match("comb",1);
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if (comb == NULL) error->all("Fix qeq must be used with pair_style comb");
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if (strcmp(update->integrate_style,"respa") == 0)
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nlevels_respa = ((Respa *) update->integrate)->nlevels;
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ngroup = group->count(igroup);
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if (ngroup == 0.0) error->all("Fix qeq group has no atoms");
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}
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/* ---------------------------------------------------------------------- */
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void FixQEQ::setup(int vflag)
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{
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firstflag = 1;
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if (strcmp(update->integrate_style,"verlet") == 0)
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post_force(vflag);
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else {
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((Respa *) update->integrate)->copy_flevel_f(nlevels_respa-1);
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post_force_respa(vflag,nlevels_respa-1,0);
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((Respa *) update->integrate)->copy_f_flevel(nlevels_respa-1);
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}
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firstflag = 0;
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}
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/* ---------------------------------------------------------------------- */
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void FixQEQ::post_force(int vflag)
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{
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int i,iloop,loopmax;
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double heatpq,qmass,dtq,dtq2;
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double enegchkall,enegmaxall;
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if (update->ntimestep % nevery) return;
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// reallocate work arrays if necessary
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// qf = charge force
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// q1 = charge displacement
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// q2 = tmp storage of charge force for next iteration
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if (atom->nmax > nmax) {
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memory->sfree(qf);
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memory->sfree(q1);
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memory->sfree(q2);
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nmax = atom->nmax;
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qf = (double *) memory->smalloc(nmax*sizeof(double),"qeq:qf");
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q1 = (double *) memory->smalloc(nmax*sizeof(double),"qeq:q1");
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q2 = (double *) memory->smalloc(nmax*sizeof(double),"qeq:q2");
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vector_atom = qf;
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}
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// more loops for first-time charge equilibrium
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iloop = 0;
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if (firstflag) loopmax = 1000;
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else loopmax = 500;
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// charge-equilibration loop
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heatpq = 0.01;
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qmass = 0.06;
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dtq = 0.040;
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dtq2 = 0.5*dtq*dtq/qmass;
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double enegchk = 0.0;
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double enegtot = 0.0;
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double enegmax = 0.0;
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double *q = atom->q;
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int *mask = atom->mask;
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int nlocal = atom->nlocal;
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for (i = 0; i < nlocal; i++)
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q1[i] = q2[i] = qf[i] = 0.0;
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for (iloop = 0; iloop < loopmax; iloop ++ ) {
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit) {
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q1[i] = qf[i]*dtq2 - heatpq*q1[i];
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q[i] += q1[i];
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}
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enegtot = comb->yasu_char(qf,igroup);
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enegtot /= ngroup;
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enegchk = enegmax = 0.0;
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for (i = 0; i < nlocal ; i++)
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if (mask[i] & groupbit) {
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q2[i] = enegtot-qf[i];
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enegmax = MAX(enegmax,fabs(q2[i]));
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enegchk += fabs(q2[i]);
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qf[i] = q2[i];
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}
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MPI_Allreduce(&enegchk,&enegchkall,1,MPI_DOUBLE,MPI_SUM,world);
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enegchk = enegchkall/ngroup;
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MPI_Allreduce(&enegmax,&enegmaxall,1,MPI_DOUBLE,MPI_MAX,world);
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enegmax = enegmaxall;
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if (enegchk <= precision && enegmax <= 10.0*precision) break;
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if (me == 0 && fp)
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fprintf(fp,"Step: %d, loop: %d, enegtot %.6g, "
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"enegmax %.6g, fq deviation: %.6g\n",
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update->ntimestep,iloop,enegtot,enegmax,enegchk);
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for (i = 0; i < nlocal; i++)
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if (mask[i] & groupbit)
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q1[i] += qf[i]*dtq2 - heatpq*q1[i];
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}
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if (me == 0 && fp) {
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if (iloop == loopmax)
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fprintf(fp,"Charges did not converge in %d iterations\n",iloop);
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else
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fprintf(fp,"Charges converged in %d iterations to %.10f\n",
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iloop,enegchk);
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}
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}
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/* ---------------------------------------------------------------------- */
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void FixQEQ::post_force_respa(int vflag, int ilevel, int iloop)
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{
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if (ilevel == nlevels_respa-1) post_force(vflag);
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}
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/* ----------------------------------------------------------------------
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memory usage of local atom-based arrays
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------------------------------------------------------------------------- */
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double FixQEQ::memory_usage()
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{
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double bytes = atom->nmax*3 * sizeof(double);
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return bytes;
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}
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@ -0,0 +1,54 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#ifdef FIX_CLASS
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FixStyle(qeq,FixQEQ)
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#else
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#ifndef LMP_FIX_QEQ_H
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#define LMP_FIX_QEQ_H
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#include "stdio.h"
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#include "fix.h"
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namespace LAMMPS_NS {
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class FixQEQ : public Fix {
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public:
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FixQEQ(class LAMMPS *, int, char **);
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~FixQEQ();
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int setmask();
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void init();
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void setup(int);
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void post_force(int);
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void post_force_respa(int,int,int);
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double memory_usage();
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private:
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int me,firstflag;
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double precision;
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int nlevels_respa;
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double ngroup;
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FILE *fp;
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class PairComb *comb;
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int nmax;
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double *qf,*q1,*q2;
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};
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}
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#endif
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#endif
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File diff suppressed because it is too large
Load Diff
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@ -0,0 +1,150 @@
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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http://lammps.sandia.gov, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||
certain rights in this software. This software is distributed under
|
||||
the GNU General Public License.
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|
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#ifdef PAIR_CLASS
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PairStyle(comb,PairComb)
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#else
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#ifndef LMP_PAIR_COMB_H
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#define LMP_PAIR_COMB_H
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#include "pair.h"
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namespace LAMMPS_NS {
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class PairComb : public Pair {
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friend class FixQEQ;
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public:
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PairComb(class LAMMPS *);
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virtual ~PairComb();
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void compute(int, int);
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void settings(int, char **);
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void coeff(int, char **);
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void init_style();
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double init_one(int, int);
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double memory_usage();
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private:
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struct Param {
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double lam11,lam12,lam21,lam22;
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double c,d,h;
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double gamma,powerm;
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double powern,beta;
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double biga1,biga2,bigb1,bigb2;
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double bigd,bigr;
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double cut,cutsq;
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double c1,c2,c3,c4;
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double plp1,plp3,plp6,a123,aconf;
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double rlm1,rlm2;
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double romiga,romigb,romigc,romigd,addrep;
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double QU1,QL1,DU1,DL1,Qo1,dQ1,aB1,bB1,nD1,bD1;
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double QU2,QL2,DU2,DL2,Qo2,dQ2,aB2,bB2,nD2,bD2;
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double chi,dj,dk,dl,dm,esm1,esm2,cmn1,cmn2,cml1,cml2;
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double coulcut, lcut, lcutsq, hfocor;
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int ielement,jelement,kelement;
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int powermint;
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};
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double PI,PI2,PI4,PIsq;
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double cutmax; // max cutoff for all elements
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int nelements; // # of unique elements
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char **elements; // names of unique elements
|
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int ***elem2param; // mapping from element triplets to parameters
|
||||
int *map; // mapping from atom types to elements
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int nparams; // # of stored parameter sets
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int maxparam; // max # of parameter sets
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double precision;
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Param *params; // parameter set for an I-J-K interaction
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int nmax;
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double *qf;
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double *esm, **fafb, **dfafb, **ddfafb, **phin, **dphin, **erpaw;
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double *charge;
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int **intype, *typeno;
|
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int *NCo, cor_flag, cuo_flag, cuo_flag1, cuo_flag2;
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||||
|
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void allocate();
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virtual void read_file(char *);
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void setup();
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virtual void repulsive(Param *, double, double &, int,
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double &, double, double);
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double zeta(Param *, double, double, double *, double *);
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void force_zeta(Param *, double, double, double &, double &,
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int, double &, double,double);
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void attractive(Param *, double, double, double, double *, double *,
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double *, double *, double *);
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double elp(Param *, double, double, double *, double *);
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void flp(Param *, double, double, double *, double *, double *,
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double *, double *);
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double comb_fc(double, Param *);
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double comb_fc_d(double, Param *);
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double comb_fc2(double);
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double comb_fc2_d(double);
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double comb_fc3(double);
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double comb_fc3_d(double);
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virtual double comb_fa(double, Param *, double,double);
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virtual double comb_fa_d(double, Param *, double,double);
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double comb_bij(double, Param *);
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double comb_bij_d(double, Param *);
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double comb_gijk(double, Param *);
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double comb_gijk_d(double, Param *);
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void comb_zetaterm_d(double, double *, double, double *, double,
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double *, double *, double *, Param *);
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void costheta_d(double *, double, double *, double,
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double *, double *, double *);
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double self(Param *, double, double);
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void sm_table();
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void potal_calc(double &, double &, double &);
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void tri_point(double, int &, int &, int &, double &, double &,
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double &, int &);
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void direct(int,int,int,int,double,double,double,double,double,double,
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double,double,double,double &,double &);
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void field(Param *,double,double,double,double &,double &);
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double qfo_self(Param *, double, double);
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void qfo_short(Param *, double, double, double, double, double &, double &);
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void qfo_direct (int, int, int, int, double, double, double, double,
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double, double &);
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void qfo_field(Param *, double,double ,double ,double &, double &);
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void qsolve(double *);
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// double yasu_char(double *);
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double yasu_char(double *, int &);
|
||||
void Over_cor(Param *, double, int, double &, double &);
|
||||
int pack_reverse_comm(int, int, double *);
|
||||
void unpack_reverse_comm(int, int *, double *);
|
||||
int pack_comm(int , int *, double *, int, int *);
|
||||
void unpack_comm(int , int , double *);
|
||||
|
||||
// vector functions, inline for efficiency
|
||||
|
||||
inline double vec3_dot(double *x, double *y) {
|
||||
return x[0]*y[0] + x[1]*y[1] + x[2]*y[2];
|
||||
}
|
||||
inline void vec3_add(double *x, double *y, double *z) {
|
||||
z[0] = x[0]+y[0]; z[1] = x[1]+y[1]; z[2] = x[2]+y[2];
|
||||
}
|
||||
inline void vec3_scale(double k, double *x, double *y) {
|
||||
y[0] = k*x[0]; y[1] = k*x[1]; y[2] = k*x[2];
|
||||
}
|
||||
inline void vec3_scaleadd(double k, double *x, double *y, double *z) {
|
||||
z[0] = k*x[0]+y[0]; z[1] = k*x[1]+y[1]; z[2] = k*x[2]+y[2];
|
||||
}
|
||||
};
|
||||
|
||||
}
|
||||
|
||||
#endif
|
||||
#endif
|
||||
Loading…
Reference in New Issue