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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13731 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2015-07-27 15:00:00 +00:00
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2
src/Makefile
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@ -46,7 +46,7 @@ PACKAGE = asphere body class2 colloid coreshell dipole fld gpu granular kim \
python qeq reax replica rigid shock snap srd voronoi xtc
PACKUSER = user-atc user-awpmd user-cg-cmm user-colvars user-cuda \
user-diffraction user-eff user-fep user-intel user-lb \
user-diffraction user-drude user-eff user-fep user-intel user-lb \
user-misc user-molfile user-omp user-phonon user-qmmm user-qtb \
user-quip user-reaxc user-sph

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src/USER-DRUDE/README Normal file
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This package implements Drude oscillator methods for simulating
polarizable systems in LAMMPS. The package provides the following
features:
* tagging particles as cores or Drude particles
* thermostating the Drude oscillators at a distinct temperature
using Langevin or Nosé-Hoover thermostats
* computation of the atom and dipole temperatures
* damping induced dipole interactions using Thole's function
See the file doc/drude_tutorial.html for getting started.
There are auxiliary tools for using this package in tools/drude.
There are example scripts for using this package in examples/USER/drude.
The person who created this package is Alain Dequidt at the
Chemistry Institute of Clermont-Ferrand, Clermont University, France
(alain.dequidt at univ-bpclermont.fr). Contact him directly if you
have questions. Co-authors: Julien Devémy, Agilio Padua.

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src/USER-DRUDE/compute_temp_drude.cpp Normal file
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
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.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "mpi.h"
#include "stdlib.h"
#include "string.h"
#include "compute_temp_drude.h"
#include "atom.h"
#include "update.h"
#include "force.h"
#include "group.h"
#include "modify.h"
#include "fix.h"
#include "domain.h"
#include "lattice.h"
#include "memory.h"
#include "error.h"
#include "comm.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
ComputeTempDrude::ComputeTempDrude(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg != 3) error->all(FLERR,"Illegal compute temp command");
vector_flag = 1;
size_vector = 6;
extscalar = 0;
extvector = -1;
extlist = new int[6];
extlist[0] = extlist[1] = 0;
extlist[2] = extlist[3] = extlist[4] = extlist[5] = 1;
tempflag = 0; // because does not compute a single temperature (scalar and vector)
vector = new double[6];
fix_drude = NULL;
id_temp = NULL;
temperature = NULL;
}
/* ---------------------------------------------------------------------- */
ComputeTempDrude::~ComputeTempDrude()
{
delete [] vector;
delete [] extlist;
delete [] id_temp;
}
/* ---------------------------------------------------------------------- */
void ComputeTempDrude::init()
{
int ifix;
for (ifix = 0; ifix < modify->nfix; ifix++)
if (strcmp(modify->fix[ifix]->style,"drude") == 0) break;
if (ifix == modify->nfix) error->all(FLERR, "compute temp/drude requires fix drude");
fix_drude = (FixDrude *) modify->fix[ifix];
if (!comm->ghost_velocity)
error->all(FLERR,"compute temp/drude requires ghost velocities. Use comm_modify vel yes");
}
/* ---------------------------------------------------------------------- */
void ComputeTempDrude::setup()
{
dof_compute();
}
/* ---------------------------------------------------------------------- */
void ComputeTempDrude::dof_compute()
{
int nlocal = atom->nlocal;
int *type = atom->type;
int dim = domain->dimension;
int *drudetype = fix_drude->drudetype;
fix_dof = 0;
for (int i = 0; i < modify->nfix; i++)
fix_dof += modify->fix[i]->dof(igroup);
bigint dof_core_loc = 0, dof_drude_loc = 0;
for (int i = 0; i < nlocal; i++) {
if (atom->mask[i] & groupbit) {
if (drudetype[type[i]] == DRUDE_TYPE) // Non-polarizable atom
dof_drude_loc++;
else
dof_core_loc++;
}
}
dof_core_loc *= dim;
dof_drude_loc *= dim;
MPI_Allreduce(&dof_core_loc, &dof_core, 1, MPI_LMP_BIGINT, MPI_SUM, world);
MPI_Allreduce(&dof_drude_loc, &dof_drude, 1, MPI_LMP_BIGINT, MPI_SUM, world);
dof_core -= fix_dof;
vector[2] = dof_core;
vector[3] = dof_drude;
}
/* ---------------------------------------------------------------------- */
int ComputeTempDrude::modify_param(int narg, char **arg)
{
if (strcmp(arg[0],"temp") == 0) {
if (narg < 2) error->all(FLERR,"Illegal fix_modify command");
delete [] id_temp;
int n = strlen(arg[1]) + 1;
id_temp = new char[n];
strcpy(id_temp,arg[1]);
int icompute = modify->find_compute(id_temp);
if (icompute < 0)
error->all(FLERR,"Could not find fix_modify temperature ID");
temperature = modify->compute[icompute];
if (temperature->tempflag == 0)
error->all(FLERR,
"Fix_modify temperature ID does not compute temperature");
if (temperature->igroup != igroup && comm->me == 0)
error->warning(FLERR,"Group for fix_modify temp != fix group");
return 2;
}
return 0;
}
/* ---------------------------------------------------------------------- */
void ComputeTempDrude::compute_vector()
{
invoked_vector = update->ntimestep;
int nlocal = atom->nlocal;
int *mask = atom->mask;
int *type = atom->type;
double *rmass = atom->rmass, *mass = atom->mass;
double **v = atom->v;
tagint *drudeid = fix_drude->drudeid;
int *drudetype = fix_drude->drudetype;
int dim = domain->dimension;
double mvv2e = force->mvv2e, kb = force->boltz;
double mcore, mdrude;
double ecore, edrude;
double *vcore, *vdrude;
double kineng_core_loc = 0., kineng_drude_loc = 0.;
for (int i=0; i<nlocal; i++){
if (groupbit & mask[i] && drudetype[type[i]] != DRUDE_TYPE){
if (drudetype[type[i]] == NOPOL_TYPE) {
ecore = 0.;
vcore = v[i];
if (temperature) temperature->remove_bias(i, vcore);
for (int k=0; k<dim; k++) ecore += vcore[k]*vcore[k];
if (temperature) temperature->restore_bias(i, vcore);
if (rmass) mcore = rmass[i];
else mcore = mass[type[i]];
kineng_core_loc += mcore * ecore;
} else { // CORE_TYPE
int j = atom->map(drudeid[i]);
if (rmass) {
mcore = rmass[i];
mdrude = rmass[j];
} else {
mcore = mass[type[i]];
mdrude = mass[type[j]];
}
double mtot_inv = 1. / (mcore + mdrude);
ecore = 0.;
edrude = 0.;
vcore = v[i];
vdrude = v[j];
if (temperature) {
temperature->remove_bias(i, vcore);
temperature->remove_bias(j, vdrude);
}
for (int k=0; k<dim; k++) {
double v1 = mdrude * vdrude[k] + mcore * vcore[k];
ecore += v1 * v1;
double v2 = vdrude[k] - vcore[k];
edrude += v2 * v2;
}
if (temperature) {
temperature->restore_bias(i, vcore);
temperature->restore_bias(j, vdrude);
}
kineng_core_loc += mtot_inv * ecore;
kineng_drude_loc += mtot_inv * mcore * mdrude * edrude;
}
}
}
if (dynamic) dof_compute();
kineng_core_loc *= 0.5 * mvv2e;
kineng_drude_loc *= 0.5 * mvv2e;
MPI_Allreduce(&kineng_core_loc,&kineng_core,1,MPI_DOUBLE,MPI_SUM,world);
MPI_Allreduce(&kineng_drude_loc,&kineng_drude,1,MPI_DOUBLE,MPI_SUM,world);
temp_core = 2.0 * kineng_core / (dof_core * kb);
temp_drude = 2.0 * kineng_drude / (dof_drude * kb);
vector[0] = temp_core;
vector[1] = temp_drude;
vector[4] = kineng_core;
vector[5] = kineng_drude;
}

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src/USER-DRUDE/compute_temp_drude.h Normal file
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/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
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.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef COMPUTE_CLASS
ComputeStyle(temp/drude,ComputeTempDrude)
#else
#ifndef LMP_COMPUTE_TEMP_DRUDE_H
#define LMP_COMPUTE_TEMP_DRUDE_H
#include "compute.h"
#include "fix_drude.h"
namespace LAMMPS_NS {
class ComputeTempDrude : public Compute {
public:
ComputeTempDrude(class LAMMPS *, int, char **);
~ComputeTempDrude();
void init();
void setup();
void compute_vector();
int modify_param(int, char **);
private:
int fix_dof;
FixDrude * fix_drude;
char *id_temp;
class Compute *temperature;
bigint dof_core, dof_drude;
double kineng_core, kineng_drude;
double temp_core, temp_drude;
void dof_compute();
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
*/

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src/USER-DRUDE/fix_drude.cpp Normal file
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
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.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "string.h"
#include "stdlib.h"
#include "fix_drude.h"
#include "atom.h"
#include "comm.h"
#include "modify.h"
#include "error.h"
#include "memory.h"
#include <set>
#include <vector>
using namespace LAMMPS_NS;
using namespace FixConst;
FixDrude *FixDrude::sptr = NULL;
/* ---------------------------------------------------------------------- */
FixDrude::FixDrude(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg != 3 + atom->ntypes) error->all(FLERR,"Illegal fix drude command");
comm_border = 1; // drudeid
special_alter_flag = 1;
create_attribute = 1;
memory->create(drudetype, atom->ntypes+1, "fix_drude::drudetype");
for (int i=3; i<narg; i++) {
if (arg[i][0] == 'n' || arg[i][0] == 'N' || arg[i][0] == '0')
drudetype[i-2] = NOPOL_TYPE;
else if (arg[i][0] == 'c' || arg[i][0] == 'C' || arg[i][0] == '1')
drudetype[i-2] = CORE_TYPE;
else if (arg[i][0] == 'd' || arg[i][0] == 'D' || arg[i][0] == '2')
drudetype[i-2] = DRUDE_TYPE;
else
error->all(FLERR, "Illegal fix drude command");
}
drudeid = NULL;
grow_arrays(atom->nmax);
atom->add_callback(0);
atom->add_callback(1);
atom->add_callback(2);
// one-time assignment of Drude partners
build_drudeid();
// set rebuildflag = 0 to indicate special lists have never been rebuilt
rebuildflag = 0;
}
/* ---------------------------------------------------------------------- */
FixDrude::~FixDrude()
{
atom->delete_callback(id,2);
atom->delete_callback(id,1);
atom->delete_callback(id,0);
memory->destroy(drudetype);
memory->destroy(drudeid);
}
/* ---------------------------------------------------------------------- */
void FixDrude::init()
{
int count = 0;
for (int i = 0; i < modify->nfix; i++)
if (strcmp(modify->fix[i]->style,"drude") == 0) count++;
if (count > 1) error->all(FLERR,"More than one fix drude");
if (!rebuildflag) rebuild_special();
}
/* ---------------------------------------------------------------------- */
int FixDrude::setmask()
{
int mask = 0;
return mask;
}
/* ----------------------------------------------------------------------
look in bond lists for Drude partner tags and fill drudeid
------------------------------------------------------------------------- */
void FixDrude::build_drudeid(){
int nlocal = atom->nlocal;
int *type = atom->type;
std::vector<tagint> drude_vec; // list of my Drudes' tags
std::vector<tagint> core_drude_vec;
partner_set = new std::set<tagint>[nlocal]; // Temporary sets of bond partner tags
sptr = this;
// Build list of my atoms' bond partners
for (int i=0; i<nlocal; i++){
if (drudetype[type[i]] == NOPOL_TYPE) continue;
drudeid[i] = 0;
for (int k=0; k<atom->num_bond[i]; k++){
core_drude_vec.push_back(atom->tag[i]);
core_drude_vec.push_back(atom->bond_atom[i][k]);
}
}
// Loop on procs to fill my atoms' sets of bond partners
comm->ring(core_drude_vec.size(), sizeof(tagint),
(char *) core_drude_vec.data(),
4, ring_build_partner, NULL, 1);
// Build the list of my Drudes' tags
// The only bond partners of a Drude particle is its core,
// so fill drudeid for my Drudes.
for (int i=0; i<nlocal; i++){
if (drudetype[type[i]] == DRUDE_TYPE){
drude_vec.push_back(atom->tag[i]);
drudeid[i] = *partner_set[i].begin(); // only one 1-2 neighbor, the core
}
}
// At this point each of my Drudes knows its core.
// Send my list of Drudes to other procs and myself
// so that each core finds its Drude.
comm->ring(drude_vec.size(), sizeof(tagint),
(char *) drude_vec.data(),
3, ring_search_drudeid, NULL, 1);
delete [] partner_set;
}
/* ----------------------------------------------------------------------
* when receive buffer, build the set of received Drude tags.
* Look in my cores' bond partner tags if there is a Drude tag.
* If so fill this core's dureid.
------------------------------------------------------------------------- */
void FixDrude::ring_search_drudeid(int size, char *cbuf){
// Search for the drude partner of my cores
Atom *atom = sptr->atom;
int nlocal = atom->nlocal;
int *type = atom->type;
std::set<tagint> *partner_set = sptr->partner_set;
tagint *drudeid = sptr->drudeid;
int *drudetype = sptr->drudetype;
tagint *first = (tagint *) cbuf;
tagint *last = first + size;
std::set<tagint> drude_set(first, last);
std::set<tagint>::iterator it;
for (int i=0; i<nlocal; i++) {
if (drudetype[type[i]] != CORE_TYPE || drudeid[i] > 0) continue;
for (it = partner_set[i].begin(); it != partner_set[i].end(); it++) { // Drude-core are 1-2 neighbors
if (drude_set.count(*it) > 0){
drudeid[i] = *it;
break;
}
}
}
}
/* ----------------------------------------------------------------------
* buffer contains bond partners. Look for my atoms and add their partner's
* tag in its set of bond partners.
------------------------------------------------------------------------- */
void FixDrude::ring_build_partner(int size, char *cbuf){
// Add partners from incoming list
Atom *atom = sptr->atom;
int nlocal = atom->nlocal;
std::set<tagint> *partner_set = sptr->partner_set;
tagint *it = (tagint *) cbuf;
tagint *last = it + size;
while (it < last) {
int j = atom->map(*it);
if (j >= 0 && j < nlocal)
partner_set[j].insert(*(it+1));
j = atom->map(*(it+1));
if (j >= 0 && j < nlocal)
partner_set[j].insert(*it);
it += 2;
}
}
/* ----------------------------------------------------------------------
allocate atom-based array for drudeid
------------------------------------------------------------------------- */
void FixDrude::grow_arrays(int nmax)
{
memory->grow(drudeid,nmax,"fix_drude:drudeid");
}
/* ----------------------------------------------------------------------
copy values within local atom-based array
------------------------------------------------------------------------- */
void FixDrude::copy_arrays(int i, int j, int delflag)
{
drudeid[j] = drudeid[i];
}
/* ----------------------------------------------------------------------
pack values in local atom-based array for exchange with another proc
------------------------------------------------------------------------- */
int FixDrude::pack_exchange(int i, double *buf)
{
int m = 0;
buf[m++] = ubuf(drudeid[i]).d;
return m;
}
/* ----------------------------------------------------------------------
unpack values in local atom-based array from exchange with another proc
------------------------------------------------------------------------- */
int FixDrude::unpack_exchange(int nlocal, double *buf)
{
int m = 0;
drudeid[nlocal] = (tagint) ubuf(buf[m++]).i;
return m;
}
/* ----------------------------------------------------------------------
pack values for border communication at re-neighboring
------------------------------------------------------------------------- */
int FixDrude::pack_border(int n, int *list, double *buf)
{
int m = 0;
for (int i=0; i<n; i++){
int j = list[i];
buf[m++] = ubuf(drudeid[j]).d;
}
return m;
}
/* ----------------------------------------------------------------------
unpack values for border communication at re-neighboring
------------------------------------------------------------------------- */
int FixDrude::unpack_border(int n, int first, double *buf)
{
int m = 0;
for (int i=first; i<first+n; i++){
drudeid[i] = (tagint) ubuf(buf[m++]).i;
}
return m;
}
/* ----------------------------------------------------------------------
Rebuild the list of special neighbors if atom_style is Drude
so that each Drude particle is equivalent to its core atom.
------------------------------------------------------------------------- */
void FixDrude::rebuild_special(){
rebuildflag = 1;
int nlocal = atom->nlocal;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
int *type = atom->type;
// Make sure that drude partners know each other
//build_drudeid();
// Log info
if (comm->me == 0) {
if (screen) fprintf(screen, "Rebuild special list taking Drude particles into account\n");
if (logfile) fprintf(logfile, "Rebuild special list taking Drude particles into account\n");
}
int nspecmax, nspecmax_old, nspecmax_loc;
nspecmax_loc = 0;
for (int i=0; i<nlocal; i++) {
if (nspecmax_loc < nspecial[i][2]) nspecmax_loc = nspecial[i][2];
}
MPI_Allreduce(&nspecmax_loc, &nspecmax_old, 1, MPI_INT, MPI_MAX, world);
if (comm->me == 0) {
if (screen) fprintf(screen, "Old max number of 1-2 to 1-4 neighbors: %d\n", nspecmax_old);
if (logfile) fprintf(logfile, "Old max number of 1-2 to 1-4 neighbors: %d\n", nspecmax_old);
}
// Build lists of drude and core-drude pairs
std::vector<tagint> drude_vec, core_drude_vec, core_special_vec;
for (int i=0; i<nlocal; i++) {
if (drudetype[type[i]] == DRUDE_TYPE) {
drude_vec.push_back(atom->tag[i]);
} else if (drudetype[type[i]] == CORE_TYPE){
core_drude_vec.push_back(atom->tag[i]);
core_drude_vec.push_back(drudeid[i]);
}
}
// Remove Drude particles from the special lists of each proc
comm->ring(drude_vec.size(), sizeof(tagint),
(char *) drude_vec.data(),
9, ring_remove_drude, NULL, 1);
// Add back Drude particles in the lists just after their core
comm->ring(core_drude_vec.size(), sizeof(tagint),
(char *) core_drude_vec.data(),
10, ring_add_drude, NULL, 1);
// Check size of special list
nspecmax_loc = 0;
for (int i=0; i<nlocal; i++) {
if (nspecmax_loc < nspecial[i][2]) nspecmax_loc = nspecial[i][2];
}
MPI_Allreduce(&nspecmax_loc, &nspecmax, 1, MPI_INT, MPI_MAX, world);
if (comm->me == 0) {
if (screen) fprintf(screen, "New max number of 1-2 to 1-4 neighbors: %d (+%d)\n", nspecmax, nspecmax - nspecmax_old);
if (logfile) fprintf(logfile, "New max number of 1-2 to 1-4 neighbors: %d (+%d)\n", nspecmax, nspecmax - nspecmax_old);
}
if (atom->maxspecial < nspecmax) {
char str[1024];
sprintf(str, "Not enough space in special: special_bonds extra should be at least %d", nspecmax - nspecmax_old);
error->all(FLERR, str);
}
// Build list of cores' special lists to communicate to ghost drude particles
for (int i=0; i<nlocal; i++) {
if (drudetype[type[i]] != CORE_TYPE) continue;
core_special_vec.push_back(atom->tag[i]);
core_special_vec.push_back((tagint) nspecial[i][0]);
core_special_vec.push_back((tagint) nspecial[i][1]);
core_special_vec.push_back((tagint) nspecial[i][2]);
for (int j=1; j<nspecial[i][2]; j++)
core_special_vec.push_back(special[i][j]);
}
// Copy core's list into their drude list
comm->ring(core_special_vec.size(), sizeof(tagint),
(char *) core_special_vec.data(),
11, ring_copy_drude, NULL, 1);
}
/* ----------------------------------------------------------------------
* When receive buffer, build a set of drude tags, look into my atoms'
* special list if some tags are drude particles. If so, remove it.
------------------------------------------------------------------------- */
void FixDrude::ring_remove_drude(int size, char *cbuf){
// Remove all drude particles from special list
Atom *atom = sptr->atom;
int nlocal = atom->nlocal;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
int *type = atom->type;
tagint *first = (tagint *) cbuf;
tagint *last = first + size;
std::set<tagint> drude_set(first, last);
int *drudetype = sptr->drudetype;
for (int i=0; i<nlocal; i++) {
if (drudetype[type[i]] == DRUDE_TYPE) continue;
for (int j=0; j<nspecial[i][2]; j++) {
if (drude_set.count(special[i][j]) > 0) { // I identify a drude in my special list, remove it
// left shift
nspecial[i][2]--;
for (int k=j; k<nspecial[i][2]; k++)
special[i][k] = special[i][k+1];
if (j < nspecial[i][1]) {
nspecial[i][1]--;
if (j < nspecial[i][0]) nspecial[i][0]--;
}
j--;
}
}
}
}
/* ----------------------------------------------------------------------
* When receive buffer, build a map core tag -> drude tag.
* Loop on my atoms' special list to find core tags. Insert their Drude
* particle if they have one.
------------------------------------------------------------------------- */
void FixDrude::ring_add_drude(int size, char *cbuf){
// Assume special array size is big enough
// Add all particle just after their core in the special list
Atom *atom = sptr->atom;
int nlocal = atom->nlocal;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
int *type = atom->type;
tagint *drudeid = sptr->drudeid;
int *drudetype = sptr->drudetype;
tagint *first = (tagint *) cbuf;
tagint *last = first + size;
std::map<tagint, tagint> core_drude_map;
tagint *it = first;
while (it < last) {
tagint core_tag = *it;
it++;
core_drude_map[core_tag] = *it;
it++;
}
for (int i=0; i<nlocal; i++) {
if (drudetype[type[i]] == DRUDE_TYPE) continue;
if (core_drude_map.count(atom->tag[i]) > 0) { // I identify myself as a core, add my own drude
// right shift
for (int k=nspecial[i][2]-1; k>=0; k--)
special[i][k+1] = special[i][k];
special[i][0] = drudeid[i];
nspecial[i][0]++;
nspecial[i][1]++;
nspecial[i][2]++;
}
for (int j=0; j<nspecial[i][2]; j++) {
if (core_drude_map.count(special[i][j]) > 0) { // I identify a core in my special list, add his drude
// right shift
for (int k=nspecial[i][2]-1; k>j; k--)
special[i][k+1] = special[i][k];
special[i][j+1] = core_drude_map[special[i][j]];
nspecial[i][2]++;
if (j < nspecial[i][1]) {
nspecial[i][1]++;
if (j < nspecial[i][0]) nspecial[i][0]++;
}
j++;
}
}
}
}
/* ----------------------------------------------------------------------
* When receive buffer, build a map core tag -> pointer to special info
* in the buffer. Loop on my Drude particles and copy their special
* info from that of their core if the latter is found in the map.
------------------------------------------------------------------------- */
void FixDrude::ring_copy_drude(int size, char *cbuf){
// Copy special list of drude from its core (except itself)
Atom *atom = sptr->atom;
int nlocal = atom->nlocal;
int **nspecial = atom->nspecial;
tagint **special = atom->special;
int *type = atom->type;
tagint *drudeid = sptr->drudeid;
int *drudetype = sptr->drudetype;
tagint *first = (tagint *) cbuf;
tagint *last = first + size;
std::map<tagint, tagint*> core_special_map;
tagint *it = first;
while (it < last) {
tagint core_tag = *it;
it++;
core_special_map[core_tag] = it;
it += 2;
it += (int) *it;
}
for (int i=0; i<nlocal; i++) {
if (drudetype[type[i]] != DRUDE_TYPE) continue;
if (core_special_map.count(drudeid[i]) > 0) { // My core is in this list, copy its special info
it = core_special_map[drudeid[i]];
nspecial[i][0] = (int) *it;
it++;
nspecial[i][1] = (int) *it;
it++;
nspecial[i][2] = (int) *it;
it++;
special[i][0] = drudeid[i];
for (int k=1; k<nspecial[i][2]; k++) {
special[i][k] = *it;
it++;
}
}
}
}
/* ----------------------------------------------------------------------
* Set drudeid when a new atom is created,
* special list must be up-to-date
* ----------------------------------------------------------------------*/
void FixDrude::set_arrays(int i){
if (drudetype[atom->type[i]] != NOPOL_TYPE){
if (atom->nspecial[i] ==0) error->all(FLERR, "Polarizable atoms cannot be inserted with special lists info from the molecule template");
drudeid[i] = atom->special[i][0]; // Drude partner should be at first place in the special list
} else {
drudeid[i] = 0;
}
}

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/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
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.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(drude,FixDrude)
#else
#ifndef LMP_FIX_DRUDE_H
#define LMP_FIX_DRUDE_H
#include "fix.h"
#include <set>
#define NOPOL_TYPE 0
#define CORE_TYPE 1
#define DRUDE_TYPE 2
namespace LAMMPS_NS {
class FixDrude : public Fix {
public:
int * drudetype;
tagint * drudeid;
bool is_reduced;
FixDrude(class LAMMPS *, int, char **);
virtual ~FixDrude();
int setmask();
void init();
void grow_arrays(int nmax);
void copy_arrays(int i, int j, int delflag);
void set_arrays(int i);
int pack_exchange(int i, double *buf);
int unpack_exchange(int nlocal, double *buf);
int pack_border(int n, int *list, double *buf);
int unpack_border(int n, int first, double *buf);
private:
int rebuildflag;
static FixDrude *sptr;
std::set<tagint> * partner_set;
void build_drudeid();
static void ring_search_drudeid(int size, char *cbuf);
static void ring_build_partner(int size, char *cbuf);
void rebuild_special();
static void ring_remove_drude(int size, char *cbuf);
static void ring_add_drude(int size, char *cbuf);
static void ring_copy_drude(int size, char *cbuf);
};
}
#endif
#endif

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
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.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/** Fix Drude Transform ******************************************************/
#include "math.h"
#include "fix_drude_transform.h"
#include "atom.h"
#include "domain.h"
#include "comm.h"
#include "error.h"
#include "modify.h"
#include "force.h"
using namespace LAMMPS_NS;
using namespace FixConst;
/* ---------------------------------------------------------------------- */
template <bool inverse>
FixDrudeTransform<inverse>::FixDrudeTransform(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg), mcoeff(NULL)
{
if (narg != 3) error->all(FLERR,"Illegal fix drude/transform command");
comm_forward = 9;
fix_drude = NULL;
}
/* ---------------------------------------------------------------------- */
template <bool inverse>
FixDrudeTransform<inverse>::~FixDrudeTransform()
{
if (mcoeff) delete [] mcoeff;
}
/* ---------------------------------------------------------------------- */
template <bool inverse>
void FixDrudeTransform<inverse>::init()
{
int ifix;
for (ifix = 0; ifix < modify->nfix; ifix++)
if (strcmp(modify->fix[ifix]->style,"drude") == 0) break;
if (ifix == modify->nfix) error->all(FLERR, "fix drude/transform requires fix drude");
fix_drude = (FixDrude *) modify->fix[ifix];
}
/* ---------------------------------------------------------------------- */
template <bool inverse>
int FixDrudeTransform<inverse>::setmask()
{
int mask = 0;
mask |= INITIAL_INTEGRATE;
mask |= FINAL_INTEGRATE;
return mask;
}
/* ---------------------------------------------------------------------- */
template <bool inverse>
void FixDrudeTransform<inverse>::setup(int) {
int nlocal = atom->nlocal;
int ntypes = atom->ntypes;
int * type = atom->type;
double * rmass = atom->rmass, * mass = atom->mass;
tagint * drudeid = fix_drude->drudeid;
int * drudetype = fix_drude->drudetype;
if (!rmass) {
if (!mcoeff) mcoeff = new double[ntypes+1];
double mcoeff_loc[ntypes+1];
for (int itype=0; itype<=ntypes; itype++) mcoeff_loc[itype] = 2.; // an impossible value: mcoeff is at most 1.
for (int i=0; i<nlocal; i++) {
if (drudetype[type[i]] == DRUDE_TYPE) {
int j = atom->map(drudeid[i]);
// i is drude, j is core
if (mcoeff_loc[type[i]] < 1.5) { // already done
if (mcoeff_loc[type[j]] > 1.5){ // not yet done ??
error->all(FLERR,"There must be one Drude type per core type");}
continue;
}
mcoeff_loc[type[i]] = mass[type[i]] / (mass[type[i]] + mass[type[j]]);
mcoeff_loc[type[j]] = -mass[type[i]] / mass[type[j]];
}
}
MPI_Allreduce(mcoeff_loc, mcoeff, ntypes+1, MPI_DOUBLE, MPI_MIN, world);
// mcoeff is 2 for non polarizable
// 0 < mcoeff < 1 for drude
// mcoeff < 0 for core
}
}
/* ---------------------------------------------------------------------- */
namespace LAMMPS_NS { // required for specialization
template <>
void FixDrudeTransform<false>::initial_integrate(int){
comm->forward_comm_fix(this);
real_to_reduced();
//comm->forward_comm_fix(this); // Normally not needed
}
template <>
void FixDrudeTransform<false>::final_integrate(){
comm->forward_comm_fix(this);
real_to_reduced();
//comm->forward_comm_fix(this); // Normally not needed
}
template <>
void FixDrudeTransform<true>::initial_integrate(int){
comm->forward_comm_fix(this);
reduced_to_real();
//comm->forward_comm_fix(this); // Normally not needed
}
template <>
void FixDrudeTransform<true>::final_integrate(){
comm->forward_comm_fix(this);
reduced_to_real();
//comm->forward_comm_fix(this); // Normally not needed
}
} // end of namespace
/* ---------------------------------------------------------------------- */
template <bool inverse>
void FixDrudeTransform<inverse>::real_to_reduced()
{
int nlocal = atom->nlocal;
int ntypes = atom->ntypes;
int dim = domain->dimension;
int * mask = atom->mask, * type = atom->type;
double ** x = atom->x, ** v = atom->v, ** f = atom->f;
double * rmass = atom->rmass, * mass = atom->mass;
double mcore, mdrude, coeff;
int icore, idrude;
tagint * drudeid = fix_drude->drudeid;
int * drudetype = fix_drude->drudetype;
if (!rmass) { // TODO: maybe drudetype can be used instead?
for (int itype=1; itype<=ntypes; itype++)
if (mcoeff[itype] < 1.5) mass[itype] *= 1. - mcoeff[itype];
}
for (int i=0; i<nlocal; i++) {
if (mask[i] & groupbit && drudetype[type[i]] != NOPOL_TYPE) {
drudeid[i] = (tagint) domain->closest_image(i, atom->map(drudeid[i]));
}
}
for (int i=0; i<nlocal; i++) {
if (mask[i] & groupbit && drudetype[type[i]] != NOPOL_TYPE) {
int j = (int) drudeid[i];
if (drudetype[type[i]] == DRUDE_TYPE && j < nlocal) continue;
if (drudetype[type[i]] == DRUDE_TYPE) {
idrude = i;
icore = j;
} else {
icore = i;
idrude = j;
}
if (rmass) {
mcore = rmass[icore];
mdrude = rmass[idrude];
rmass[icore] += mdrude;
rmass[idrude] *= mcore / rmass[icore];
coeff = mdrude / (mcore + mdrude);
} else { // TODO check that all atoms of this types are in the group
coeff = mcoeff[type[idrude]];
}
for (int k=0; k<dim; k++) {
x[idrude][k] -= x[icore][k];
x[icore][k] += coeff * x[idrude][k];
v[idrude][k] -= v[icore][k];
v[icore][k] += coeff * v[idrude][k];
f[icore][k] += f[idrude][k];
f[idrude][k] -= coeff * f[icore][k];
}
}
}
fix_drude->is_reduced = true;
}
/* ---------------------------------------------------------------------- */
template <bool inverse>
void FixDrudeTransform<inverse>::reduced_to_real()
{
int nlocal = atom->nlocal;
int ntypes = atom->ntypes;
int dim = domain->dimension;
int * mask = atom->mask, * type = atom->type;
double ** x = atom->x, ** v = atom->v, ** f = atom->f;
double * rmass = atom->rmass, * mass = atom->mass;
double mcore, mdrude, coeff;
int icore, idrude;
tagint * drudeid = fix_drude->drudeid;
int * drudetype = fix_drude->drudetype;
for (int i=0; i<nlocal; i++) {
if (mask[i] & groupbit && drudetype[type[i]] != NOPOL_TYPE) {
int j = (int) drudeid[i]; // local index of drude partner because drudeid is in reduced form
if (drudetype[type[i]] == DRUDE_TYPE && j < nlocal) continue;
if (drudetype[type[i]] == DRUDE_TYPE) {
idrude = i;
icore = j;
} else {
icore = i;
idrude = j;
}
if (rmass) {
double s = sqrt(1. - rmass[idrude]/rmass[icore]);
rmass[idrude] = 0.5 * rmass[icore] * (1. - s);
mdrude = rmass[idrude];
rmass[icore] -= mdrude;
mcore = rmass[icore];
coeff = mdrude / (mcore + mdrude);
} else {
if (!mcoeff[type[icore]]) { // TODO: should it be > 1.5 ?
double s = sqrt(1. - mass[type[idrude]] / mass[type[icore]]);
mass[type[idrude]] = 0.5 * mass[type[icore]] * (1. - s);
mdrude = mass[type[idrude]];
mass[type[icore]] -= mdrude;
mcore = mass[type[icore]];
mcoeff[type[icore]] = mdrude / (mcore + mdrude);
}
coeff = mcoeff[type[idrude]];
}
for (int k=0; k<dim; k++) {
x[icore][k] -= coeff * x[idrude][k];
x[idrude][k] += x[icore][k];
v[icore][k] -= coeff * v[idrude][k];
v[idrude][k] += v[icore][k];
f[idrude][k] += coeff * f[icore][k];
f[icore][k] -= f[idrude][k];
}
}
}
for (int i=0; i<nlocal; i++) {
if (mask[i] & groupbit && drudetype[type[i]] != NOPOL_TYPE) {
drudeid[i] = atom->tag[(int) drudeid[i]];
}
}
if (!rmass) {
for (int itype=1; itype<=ntypes; itype++)
if (mcoeff[itype] < 1.5) mass[itype] /= 1. - mcoeff[itype];
}
fix_drude->is_reduced = false;
}
/* ---------------------------------------------------------------------- */
template <bool inverse>
int FixDrudeTransform<inverse>::pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc)
{
double ** x = atom->x, ** v = atom->v, ** f = atom->f;
int * type = atom->type, * drudetype = fix_drude->drudetype;
double dx,dy,dz;
int dim = domain->dimension;
int m = 0;
for (int i=0; i<n; i++) {
int j = list[i];
if (pbc_flag == 0 ||
(fix_drude->is_reduced && drudetype[type[j]] == DRUDE_TYPE)) {
for (int k=0; k<dim; k++) buf[m++] = x[j][k];
}
else {
if (domain->triclinic != 0) {
dx = pbc[0]*domain->xprd + pbc[5]*domain->xy;
dy = pbc[1]*domain->yprd;
if (dim == 3) {
dx += + pbc[4]*domain->xz;
dy += pbc[3]*domain->yz;
dz = pbc[2]*domain->zprd;
}
}
else {
dx = pbc[0]*domain->xprd;
dy = pbc[1]*domain->yprd;
if (dim == 3)
dz = pbc[2]*domain->zprd;
}
buf[m++] = x[j][0] + dx;
buf[m++] = x[j][1] + dy;
if (dim == 3)
buf[m++] = x[j][2] + dz;
}
for (int k=0; k<dim; k++) buf[m++] = v[j][k];
for (int k=0; k<dim; k++) buf[m++] = f[j][k];
}
return m;
}
/* ---------------------------------------------------------------------- */
template <bool inverse>
void FixDrudeTransform<inverse>::unpack_forward_comm(int n, int first, double *buf)
{
double ** x = atom->x, ** v = atom->v, ** f = atom->f;
int dim = domain->dimension;
int m = 0;
int last = first + n;
for (int i=first; i<last; i++) {
for (int k=0; k<dim; k++) x[i][k] = buf[m++];
for (int k=0; k<dim; k++) v[i][k] = buf[m++];
for (int k=0; k<dim; k++) f[i][k] = buf[m++];
}
}
/* ---------------------------------------------------------------------- */
template class FixDrudeTransform<false>;
template class FixDrudeTransform<true>;

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/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
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.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(drude/transform/direct,FixDrudeTransform<false>)
FixStyle(drude/transform/inverse,FixDrudeTransform<true>)
#else
#ifndef LMP_FIX_DRUDE_TRANSFORM_H
#define LMP_FIX_DRUDE_TRANSFORM_H
#include "fix.h"
#include "fix_drude.h"
namespace LAMMPS_NS {
template <bool inverse>
class FixDrudeTransform : public Fix {
public:
FixDrudeTransform<inverse>(class LAMMPS *, int, char **);
~FixDrudeTransform<inverse>();
int setmask();
void init();
void setup(int vflag);
void reduced_to_real();
void real_to_reduced();
void initial_integrate(int vflag);
void final_integrate();
int pack_forward_comm(int n, int *list, double *buf, int pbc_flag, int *pbc);
void unpack_forward_comm(int n, int first, double *buf);
protected:
double * mcoeff;
FixDrude * fix_drude;
};
}
#endif
#endif

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
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.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "string.h"
#include "stdlib.h"
#include "math.h"
#include "fix_langevin_drude.h"
#include "atom.h"
#include "force.h"
#include "comm.h"
#include "input.h"
#include "variable.h"
#include "random_mars.h"
#include "group.h"
#include "update.h"
#include "modify.h"
#include "compute.h"
#include "error.h"
#include "domain.h"
using namespace LAMMPS_NS;
using namespace FixConst;
enum{NOBIAS,BIAS};
enum{CONSTANT,EQUAL};
/* ---------------------------------------------------------------------- */
FixLangevinDrude::FixLangevinDrude(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg)
{
if (narg < 9) error->all(FLERR,"Illegal fix langevin/drude command");
// TODO add option for tally
// Langevin thermostat should be applied every step
nevery = 1;
vector_flag = 1;
global_freq = nevery;
extvector = 0;
size_vector = 6;
comm_reverse = 3;
//extscalar = 1;
// core temperature
tstr_core = NULL;
if (strstr(arg[3],"v_") == arg[3]) {
int n = strlen(&arg[3][2]) + 1;
tstr_core = new char[n];
strcpy(tstr_core,&arg[3][2]);
tstyle_core = EQUAL;
} else {
t_start_core = force->numeric(FLERR,arg[3]);
t_target_core = t_start_core;
tstyle_core = CONSTANT;
}
t_period_core = force->numeric(FLERR,arg[4]);
int seed_core = force->inumeric(FLERR,arg[5]);
// drude temperature
tstr_drude = NULL;
if (strstr(arg[7],"v_") == arg[6]) {
int n = strlen(&arg[6][2]) + 1;
tstr_drude = new char[n];
strcpy(tstr_drude,&arg[6][2]);
tstyle_drude = EQUAL;
} else {
t_start_drude = force->numeric(FLERR,arg[6]);
t_target_drude = t_start_drude;
tstyle_drude = CONSTANT;
}
t_period_drude = force->numeric(FLERR,arg[7]);
int seed_drude = force->inumeric(FLERR,arg[8]);
// error checks
if (t_period_core <= 0.0)
error->all(FLERR,"Fix langevin/drude period must be > 0.0");
if (seed_core <= 0) error->all(FLERR,"Illegal langevin/drude seed");
if (t_period_drude <= 0.0)
error->all(FLERR,"Fix langevin/drude period must be > 0.0");
if (seed_drude <= 0) error->all(FLERR,"Illegal langevin/drude seed");
random_core = new RanMars(lmp,seed_core);
random_drude = new RanMars(lmp,seed_drude);
int iarg = 9;
zero = 0;
while (iarg < narg) {
if (strcmp(arg[iarg],"zero") == 0) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix langevin/drude command");
if (strcmp(arg[iarg+1],"no") == 0) zero = 0;
else if (strcmp(arg[iarg+1],"yes") == 0) zero = 1;
else error->all(FLERR,"Illegal fix langevin/drude command");
iarg += 2;
} else error->all(FLERR,"Illegal fix langevin/drude command");
}
tflag = 0; // no external compute/temp is specified yet (for bias)
energy = 0.;
fix_drude = NULL;
temperature = NULL;
id_temp = NULL;
}
/* ---------------------------------------------------------------------- */
FixLangevinDrude::~FixLangevinDrude()
{
delete random_core;
delete [] tstr_core;
delete random_drude;
delete [] tstr_drude;
}
/* ---------------------------------------------------------------------- */
int FixLangevinDrude::setmask()
{
int mask = 0;
mask |= POST_FORCE;
return mask;
}
/* ---------------------------------------------------------------------- */
void FixLangevinDrude::init()
{
// check variable-style target core temperature
if (tstr_core) {
tvar_core = input->variable->find(tstr_core);
if (tvar_core < 0)
error->all(FLERR,"Variable name for fix langevin/drude does not exist");
if (input->variable->equalstyle(tvar_core)) tstyle_core = EQUAL;
else error->all(FLERR,"Variable for fix langevin/drude is invalid style");
}
// check variable-style target drude temperature
if (tstr_drude) {
tvar_drude = input->variable->find(tstr_drude);
if (tvar_drude < 0)
error->all(FLERR,"Variable name for fix langevin/drude does not exist");
if (input->variable->equalstyle(tvar_drude)) tstyle_drude = EQUAL;
else error->all(FLERR,"Variable for fix langevin/drude is invalid style");
}
int ifix;
for (ifix = 0; ifix < modify->nfix; ifix++)
if (strcmp(modify->fix[ifix]->style,"drude") == 0) break;
if (ifix == modify->nfix) error->all(FLERR, "fix langevin/drude requires fix drude");
fix_drude = (FixDrude *) modify->fix[ifix];
}
/* ---------------------------------------------------------------------- */
void FixLangevinDrude::setup(int vflag)
{
if (!strstr(update->integrate_style,"verlet"))
error->all(FLERR,"RESPA style not compatible with fix langevin/drude");
if (!comm->ghost_velocity)
error->all(FLERR,"fix langevin/drude requires ghost velocities. Use comm_modify vel yes");
if (zero) {
int *mask = atom->mask;
int nlocal = atom->nlocal;
int *drudetype = fix_drude->drudetype;
int *type = atom->type;
bigint ncore_loc = 0;
for (int i=0; i<nlocal; i++)
if (mask[i] & groupbit && drudetype[type[i]] != DRUDE_TYPE)
ncore_loc++;
MPI_Allreduce(&ncore_loc, &ncore, 1, MPI_LMP_BIGINT, MPI_SUM, world);
}
}
/* ---------------------------------------------------------------------- */
int FixLangevinDrude::modify_param(int narg, char **arg)
{
if (strcmp(arg[0],"temp") == 0) {
if (narg < 2) error->all(FLERR,"Illegal fix_modify command");
delete [] id_temp;
int n = strlen(arg[1]) + 1;
id_temp = new char[n];
strcpy(id_temp,arg[1]);
int icompute = modify->find_compute(id_temp);
if (icompute < 0)
error->all(FLERR,"Could not find fix_modify temperature ID");
temperature = modify->compute[icompute];
if (temperature->tempflag == 0)
error->all(FLERR,
"Fix_modify temperature ID does not compute temperature");
if (temperature->igroup != igroup && comm->me == 0)
error->warning(FLERR,"Group for fix_modify temp != fix group");
return 2;
}
return 0;
}
/* ---------------------------------------------------------------------- */
void FixLangevinDrude::post_force(int /*vflag*/)
{
// Thermalize by adding the langevin force if thermalize=true.
// Each core-Drude pair is thermalized only once: where the core is local.
double **v = atom->v, **f = atom->f;
int *mask = atom->mask;
int nlocal = atom->nlocal, nall = atom->nlocal + atom->nghost;
int *type = atom->type;
double *mass = atom->mass;
double *rmass = atom->rmass;
double ftm2v = force->ftm2v, mvv2e = force->mvv2e;
double kb = force->boltz, dt = update->dt;
int *drudetype = fix_drude->drudetype;
tagint *drudeid = fix_drude->drudeid;
double vdrude[3], vcore[3]; // velocities in reduced representation
double fdrude[3], fcore[3]; // forces in reduced representation
double Ccore, Cdrude, Gcore, Gdrude;
double fcoresum[3], fcoreloc[3];
int dim = domain->dimension;
// Compute target core temperature
if (tstyle_core == CONSTANT)
t_target_core = t_start_core; // + delta * (t_stop-t_start_core);
else {
modify->clearstep_compute();
t_target_core = input->variable->compute_equal(tvar_core);
if (t_target_core < 0.0)
error->one(FLERR, "Fix langevin/drude variable returned "
"negative core temperature");
modify->addstep_compute(update->ntimestep + nevery);
}
// Compute target drude temperature
if (tstyle_drude == CONSTANT)
t_target_drude = t_start_drude; // + delta * (t_stop-t_start_core);
else {
modify->clearstep_compute();
t_target_drude = input->variable->compute_equal(tvar_drude);
if (t_target_drude < 0.0)
error->one(FLERR, "Fix langevin/drude variable returned "
"negative drude temperature");
modify->addstep_compute(update->ntimestep + nevery);
}
// Clear ghost forces
// They have already been communicated if needed
for (int i = nlocal; i < nall; i++) {
for (int k = 0; k < dim; k++)
f[i][k] = 0.;
}
if (zero) for (int k=0; k<dim; k++) fcoreloc[k] = 0.;
// NB : the masses are the real masses, not the reduced ones
for (int i = 0; i < nlocal; i++) {
if (mask[i] & groupbit) { // only the cores need to be in the group
if (drudetype[type[i]] == NOPOL_TYPE) { // Non-polarizable atom
double mi;
if (rmass)
mi = rmass[i];
else
mi = mass[type[i]];
Gcore = mi / t_period_core / ftm2v;
Ccore = sqrt(2.0 * Gcore * kb * t_target_core / dt / ftm2v / mvv2e);
if (temperature) temperature->remove_bias(i, v[i]);
for(int k = 0; k < dim; k++){
fcore[k] = Ccore * random_core->gaussian() - Gcore * v[i][k];
if (zero) fcoreloc[k] += fcore[k];
f[i][k] += fcore[k];
}
if (temperature) temperature->restore_bias(i, v[i]);
} else {
if (drudetype[type[i]] == DRUDE_TYPE) continue; // do with the core
int j = atom->map(drudeid[i]);
double mi, mj, mtot, mu; // i is core, j is drude
if (rmass) {
mi = rmass[i];
mj = rmass[j];
} else {
mi = mass[type[i]];
mj = mass[type[j]];
}
mtot = mi + mj;
mu = mi * mj / mtot;
mi /= mtot;
mj /= mtot;
Gcore = mtot / t_period_core / ftm2v;
Gdrude = mu / t_period_drude / ftm2v;
Ccore = sqrt(2.0 * Gcore * kb * t_target_core / dt / ftm2v / mvv2e);
Cdrude = sqrt(2.0 * Gdrude * kb * t_target_drude / dt / ftm2v / mvv2e);
if (temperature) {
temperature->remove_bias(i, v[i]);
temperature->remove_bias(j, v[j]);
}
for (int k=0; k<dim; k++) {
// TODO check whether a fix_modify temp can subtract a bias velocity
vcore[k] = mi * v[i][k] + mj * v[j][k];
vdrude[k] = v[j][k] - v[i][k];
fcore[k] = Ccore * random_core->gaussian() - Gcore * vcore[k];
fdrude[k] = Cdrude * random_drude->gaussian() - Gdrude * vdrude[k];
if (zero) fcoreloc[k] += fcore[k];
f[i][k] += mi * fcore[k] - fdrude[k];
f[j][k] += mj * fcore[k] + fdrude[k];
// TODO tally energy if asked
}
if (temperature) {
temperature->restore_bias(i, v[i]);
temperature->restore_bias(j, v[j]);
}
}
}
}
if(zero) { // Remove the drift
MPI_Allreduce(fcoreloc, fcoresum, dim, MPI_DOUBLE, MPI_SUM, world);
for (int k=0; k<dim; k++) fcoresum[k] /= ncore;
for (int i=0; i<nlocal; i++) {
if (mask[i] & groupbit) { // only the cores need to be in the group
if (drudetype[type[i]] == NOPOL_TYPE) {
for (int k=0; k<dim; k++) f[i][k] -= fcoresum[k];
} else {
if (drudetype[type[i]] == DRUDE_TYPE) continue; // do with the core
int j = atom->map(drudeid[i]);
double mi, mj, mtot; // i is core, j is drude
if (rmass) {
mi = rmass[i];
mj = rmass[j];
} else {
mi = mass[type[i]];
mj = mass[type[j]];
}
mtot = mi + mj;
mi /= mtot;
mj /= mtot;
for (int k=0; k<dim; k++) {
f[i][k] -= mi * fcoresum[k];
f[j][k] -= mj * fcoresum[k];
}
}
}
}
}
// Reverse communication of the forces on ghost Drude particles
comm->reverse_comm();
}
/* ---------------------------------------------------------------------- */
void FixLangevinDrude::reset_target(double t_new)
{
t_target_core = t_start_core = t_new;
}
/* ----------------------------------------------------------------------
extract thermostat properties
------------------------------------------------------------------------- */
void *FixLangevinDrude::extract(const char *str, int &dim)
{
dim = 0;
if (strcmp(str,"t_target_core") == 0) {
return &t_target_core;
} else if (strcmp(str,"t_target_drude") == 0) {
return &t_target_drude;
} else error->all(FLERR, "Illegal extract string in fix langevin/drude");
return NULL;
}
/* ---------------------------------------------------------------------- */
int FixLangevinDrude::pack_reverse_comm(int n, int first, double *buf)
{
int i,m,last;
double ** f = atom->f;
m = 0;
last = first + n;
for (i = first; i < last; i++) {
buf[m++] = f[i][0];
buf[m++] = f[i][1];
buf[m++] = f[i][2];
}
return m;
}
/* ---------------------------------------------------------------------- */
void FixLangevinDrude::unpack_reverse_comm(int n, int *list, double *buf)
{
int i,j,m;
double ** f = atom->f;
m = 0;
for (i = 0; i < n; i++) {
j = list[i];
f[j][0] += buf[m++];
f[j][1] += buf[m++];
f[j][2] += buf[m++];
}
}

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/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
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.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
FixStyle(langevin/drude,FixLangevinDrude)
#else
#ifndef LMP_FIX_LANGEVIN_DRUDE_H
#define LMP_FIX_LANGEVIN_DRUDE_H
#include "fix.h"
#include "fix_drude.h"
namespace LAMMPS_NS {
class FixLangevinDrude : public Fix {
public:
FixLangevinDrude(class LAMMPS *, int, char **);
virtual ~FixLangevinDrude();
int setmask();
void init();
void setup(int vflag);
virtual void post_force(int vflag);
void reset_target(double);
virtual void *extract(const char *, int &);
int pack_reverse_comm(int, int, double*);
void unpack_reverse_comm(int, int*, double*);
int modify_param(int, char **);
protected:
double t_start_core,t_period_core,t_target_core;
double t_start_drude,t_period_drude,t_target_drude;
int tstyle_core, tstyle_drude;
int tvar_core, tvar_drude;
char *tstr_core, *tstr_drude;
double energy;
int tflag;
class RanMars *random_core, *random_drude;
int zero;
bigint ncore;
FixDrude * fix_drude;
class Compute *temperature;
char *id_temp;
};
}
#endif
#endif

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
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.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Contributing author: Paul Crozier (SNL)
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_lj_cut_thole_long.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "kspace.h"
#include "update.h"
#include "integrate.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
using namespace MathConst;
#define EWALD_F 1.12837917
#define EWALD_P 9.95473818e-1
#define B0 -0.1335096380159268
#define B1 -2.57839507e-1
#define B2 -1.37203639e-1
#define B3 -8.88822059e-3
#define B4 -5.80844129e-3
#define B5 1.14652755e-1
/* ---------------------------------------------------------------------- */
PairLJCutTholeLong::PairLJCutTholeLong(LAMMPS *lmp) : Pair(lmp)
{
ewaldflag = pppmflag = 1;
writedata = 1;
ftable = NULL;
qdist = 0.0;
fix_drude = NULL;
}
/* ---------------------------------------------------------------------- */
PairLJCutTholeLong::~PairLJCutTholeLong()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(polar);
memory->destroy(thole);
memory->destroy(ascreen);
memory->destroy(cut_lj);
memory->destroy(cut_ljsq);
memory->destroy(scale);
memory->destroy(epsilon);
memory->destroy(sigma);
memory->destroy(lj1);
memory->destroy(lj2);
memory->destroy(lj3);
memory->destroy(lj4);
memory->destroy(offset);
}
if (ftable) free_tables();
}
/* ---------------------------------------------------------------------- */
void PairLJCutTholeLong::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype,itable;
double qi,qj,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair,evdwl;
double r,rsq,r2inv,forcecoul,factor_coul,forcelj,factor_lj,r6inv;
double fraction,table;
double grij,expm2,prefactor,t,erfc,u;
int *ilist,*jlist,*numneigh,**firstneigh;
double factor_f,factor_e;
int di,dj;
double dqi,dqj,dcoul,asr,exp_asr;
int di_closest;
evdwl = ecoul = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
double *special_coul = force->special_coul;
double *special_lj = force->special_lj;
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
int *drudetype = fix_drude->drudetype;
tagint *drudeid = fix_drude->drudeid;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
qi = q[i];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
if (drudetype[type[i]] != NOPOL_TYPE){
di = atom->map(drudeid[i]);
if (di < 0) error->all(FLERR, "Drude partner not found");
di_closest = domain->closest_image(i, di);
if (drudetype[type[i]] == CORE_TYPE)
dqi = -q[di];
else
dqi = qi;
}
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_lj = special_lj[sbmask(j)];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
if (rsq < cut_coulsq) {
qj = q[j];
r = sqrt(rsq);
if (!ncoultablebits || rsq <= tabinnersq) {
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
u = 1. - t;
erfc = t * (1.+u*(B0+u*(B1+u*(B2+u*(B3+u*(B4+u*B5)))))) * expm2;
prefactor = qqrd2e * qi*qj/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else {
union_int_float_t rsq_lookup;
rsq_lookup.f = rsq;
itable = rsq_lookup.i & ncoulmask;
itable >>= ncoulshiftbits;
fraction = (rsq_lookup.f - rtable[itable]) * drtable[itable];
table = ftable[itable] + fraction*dftable[itable];
forcecoul = qi*qj * table;
if (factor_coul < 1.0) {
table = ctable[itable] + fraction*dctable[itable];
prefactor = qi*qj * table;
forcecoul -= (1.0-factor_coul)*prefactor;
}
}
if (drudetype[type[i]] != NOPOL_TYPE &&
drudetype[type[j]] != NOPOL_TYPE){
if (j != di_closest){
if (drudetype[type[j]] == CORE_TYPE){
dj = atom->map(drudeid[j]);
dqj = -q[dj];
} else dqj = qj;
asr = ascreen[type[i]][type[j]] * r;
exp_asr = exp(-asr);
dcoul = qqrd2e * dqi * dqj / r;
factor_f = 0.5*(2. + (exp_asr * (-2. - asr * (2. + asr))))
- factor_coul;
if (eflag) factor_e = 0.5*(2. - (exp_asr * (2. + asr)))
- factor_coul;
forcecoul += factor_f * dcoul;
}
}
} else forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
} else forcelj = 0.0;
fpair = (forcecoul + factor_lj*forcelj) * r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (eflag) {
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq)
ecoul = prefactor*erfc;
else {
table = etable[itable] + fraction*detable[itable];
ecoul = qi*qj * table;
}
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
if (drudetype[type[i]] != NOPOL_TYPE &&
drudetype[type[j]] != NOPOL_TYPE && j != di_closest){
ecoul += factor_e * dcoul;
}
} else ecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
evdwl = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
offset[itype][jtype];
evdwl *= factor_lj;
} else evdwl = 0.0;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,ecoul,fpair,delx,dely,delz);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairLJCutTholeLong::allocate()
{
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(cut_lj,n+1,n+1,"pair:cut_lj");
memory->create(cut_ljsq,n+1,n+1,"pair:cut_ljsq");
memory->create(scale,n+1,n+1,"pair:scale");
memory->create(ascreen,n+1,n+1,"pair:ascreen");
memory->create(thole,n+1,n+1,"pair:thole");
memory->create(polar,n+1,n+1,"pair:polar");
memory->create(epsilon,n+1,n+1,"pair:epsilon");
memory->create(sigma,n+1,n+1,"pair:sigma");
memory->create(lj1,n+1,n+1,"pair:lj1");
memory->create(lj2,n+1,n+1,"pair:lj2");
memory->create(lj3,n+1,n+1,"pair:lj3");
memory->create(lj4,n+1,n+1,"pair:lj4");
memory->create(offset,n+1,n+1,"pair:offset");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairLJCutTholeLong::settings(int narg, char **arg)
{
if (narg < 2 || narg > 3) error->all(FLERR,"Illegal pair_style command");
thole_global = force->numeric(FLERR,arg[0]);
cut_lj_global = force->numeric(FLERR,arg[1]);
if (narg == 2) cut_coul = cut_lj_global;
else cut_coul = force->numeric(FLERR,arg[2]);
// reset cutoffs that have been explicitly set
if (allocated) {
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
if (setflag[i][j]) {
thole[i][j] = thole_global;
cut_lj[i][j] = cut_lj_global;
}
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairLJCutTholeLong::coeff(int narg, char **arg)
{
if (narg < 5 || narg > 7)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
force->bounds(arg[0],atom->ntypes,ilo,ihi);
force->bounds(arg[1],atom->ntypes,jlo,jhi);
double epsilon_one = force->numeric(FLERR,arg[2]);
double sigma_one = force->numeric(FLERR,arg[3]);
double polar_one = force->numeric(FLERR,arg[4]);
double thole_one = thole_global;
if (narg >=6) thole_one = force->numeric(FLERR,arg[5]);
double cut_lj_one = cut_lj_global;
if (narg == 7) cut_lj_one = force->numeric(FLERR,arg[6]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
epsilon[i][j] = epsilon_one;
sigma[i][j] = sigma_one;
polar[i][j] = polar_one;
thole[i][j] = thole_one;
ascreen[i][j] = thole[i][j] / pow(polar[i][j], 1./3.);
cut_lj[i][j] = cut_lj_one;
scale[i][j] = 1.0;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairLJCutTholeLong::init_style()
{
if (!atom->q_flag)
error->all(FLERR,"Pair style lj/cut/thole/long requires atom attribute q");
int ifix;
for (ifix = 0; ifix < modify->nfix; ifix++)
if (strcmp(modify->fix[ifix]->style,"drude") == 0) break;
if (ifix == modify->nfix)
error->all(FLERR, "Pair style lj/cut/thole/long requires fix drude");
fix_drude = (FixDrude *) modify->fix[ifix];
int irequest = neighbor->request(this,instance_me);
cut_coulsq = cut_coul * cut_coul;
// set rRESPA cutoffs
cut_respa = NULL;
// insure use of KSpace long-range solver, set g_ewald
if (force->kspace == NULL)
error->all(FLERR,"Pair style requires a KSpace style");
g_ewald = force->kspace->g_ewald;
// setup force tables
if (ncoultablebits) init_tables(cut_coul,cut_respa);
}
/* ----------------------------------------------------------------------
neighbor callback to inform pair style of neighbor list to use
regular or rRESPA
------------------------------------------------------------------------- */
void PairLJCutTholeLong::init_list(int id, NeighList *ptr)
{
if (id == 0) list = ptr;
else if (id == 1) listinner = ptr;
else if (id == 2) listmiddle = ptr;
else if (id == 3) listouter = ptr;
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairLJCutTholeLong::init_one(int i, int j)
{
if (setflag[i][j] == 0) {
epsilon[i][j] = mix_energy(epsilon[i][i],epsilon[j][j],
sigma[i][i],sigma[j][j]);
sigma[i][j] = mix_distance(sigma[i][i],sigma[j][j]);
cut_lj[i][j] = mix_distance(cut_lj[i][i],cut_lj[j][j]);
polar[i][j] = sqrt(polar[i][i] * polar[j][j]);
thole[i][j] = 0.5 * (thole[i][i] + thole[j][j]);
ascreen[i][j] = thole[i][j] / pow(polar[i][j], 1./3.);
}
// include TIP4P qdist in full cutoff, qdist = 0.0 if not TIP4P
double cut = MAX(cut_lj[i][j],cut_coul+2.0*qdist);
cut_ljsq[i][j] = cut_lj[i][j] * cut_lj[i][j];
lj1[i][j] = 48.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
lj2[i][j] = 24.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
lj3[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],12.0);
lj4[i][j] = 4.0 * epsilon[i][j] * pow(sigma[i][j],6.0);
if (offset_flag) {
double ratio = sigma[i][j] / cut_lj[i][j];
offset[i][j] = 4.0 * epsilon[i][j] * (pow(ratio,12.0) - pow(ratio,6.0));
} else offset[i][j] = 0.0;
cut_ljsq[j][i] = cut_ljsq[i][j];
lj1[j][i] = lj1[i][j];
lj2[j][i] = lj2[i][j];
lj3[j][i] = lj3[i][j];
lj4[j][i] = lj4[i][j];
offset[j][i] = offset[i][j];
polar[j][i] = polar[i][j];
thole[j][i] = thole[i][j];
ascreen[j][i] = ascreen[i][j];
scale[j][i] = scale[i][j];
// check interior rRESPA cutoff
if (cut_respa && MIN(cut_lj[i][j],cut_coul) < cut_respa[3])
error->all(FLERR,"Pair cutoff < Respa interior cutoff");
// compute I,J contribution to long-range tail correction
// count total # of atoms of type I and J via Allreduce
if (tail_flag) {
int *type = atom->type;
int nlocal = atom->nlocal;
double count[2],all[2];
count[0] = count[1] = 0.0;
for (int k = 0; k < nlocal; k++) {
if (type[k] == i) count[0] += 1.0;
if (type[k] == j) count[1] += 1.0;
}
MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
double sig2 = sigma[i][j]*sigma[i][j];
double sig6 = sig2*sig2*sig2;
double rc3 = cut_lj[i][j]*cut_lj[i][j]*cut_lj[i][j];
double rc6 = rc3*rc3;
double rc9 = rc3*rc6;
etail_ij = 8.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
sig6 * (sig6 - 3.0*rc6) / (9.0*rc9);
ptail_ij = 16.0*MY_PI*all[0]*all[1]*epsilon[i][j] *
sig6 * (2.0*sig6 - 3.0*rc6) / (9.0*rc9);
}
return cut;
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJCutTholeLong::write_restart(FILE *fp)
{
write_restart_settings(fp);
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
fwrite(&epsilon[i][j],sizeof(double),1,fp);
fwrite(&sigma[i][j],sizeof(double),1,fp);
fwrite(&polar[i][j],sizeof(double),1,fp);
fwrite(&thole[i][j],sizeof(double),1,fp);
fwrite(&cut_lj[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairLJCutTholeLong::read_restart(FILE *fp)
{
read_restart_settings(fp);
allocate();
int i,j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&epsilon[i][j],sizeof(double),1,fp);
fread(&sigma[i][j],sizeof(double),1,fp);
fread(&polar[i][j],sizeof(double),1,fp);
fread(&thole[i][j],sizeof(double),1,fp);
ascreen[i][j] = thole[i][j] / pow(polar[i][j], 1./3.);
fread(&cut_lj[i][j],sizeof(double),1,fp);
}
MPI_Bcast(&epsilon[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&sigma[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&polar[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&thole[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&ascreen[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_lj[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairLJCutTholeLong::write_restart_settings(FILE *fp)
{
fwrite(&cut_lj_global,sizeof(double),1,fp);
fwrite(&cut_coul,sizeof(double),1,fp);
fwrite(&thole_global,sizeof(double),1,fp);
fwrite(&cut_global,sizeof(double),1,fp);
fwrite(&offset_flag,sizeof(int),1,fp);
fwrite(&mix_flag,sizeof(int),1,fp);
fwrite(&tail_flag,sizeof(int),1,fp);
fwrite(&ncoultablebits,sizeof(int),1,fp);
fwrite(&tabinner,sizeof(double),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairLJCutTholeLong::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&cut_lj_global,sizeof(double),1,fp);
fread(&cut_coul,sizeof(double),1,fp);
fread(&thole_global,sizeof(double),1,fp);
fread(&cut_global,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
fread(&tail_flag,sizeof(int),1,fp);
fread(&ncoultablebits,sizeof(int),1,fp);
fread(&tabinner,sizeof(double),1,fp);
}
MPI_Bcast(&cut_lj_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_coul,1,MPI_DOUBLE,0,world);
MPI_Bcast(&thole_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
MPI_Bcast(&tail_flag,1,MPI_INT,0,world);
MPI_Bcast(&ncoultablebits,1,MPI_INT,0,world);
MPI_Bcast(&tabinner,1,MPI_DOUBLE,0,world);
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void PairLJCutTholeLong::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
fprintf(fp,"%d %g %g\n",i,epsilon[i][i],sigma[i][i]);
}
/* ----------------------------------------------------------------------
proc 0 writes all pairs to data file
------------------------------------------------------------------------- */
void PairLJCutTholeLong::write_data_all(FILE *fp)
{
for (int i = 1; i <= atom->ntypes; i++)
for (int j = i; j <= atom->ntypes; j++)
fprintf(fp,"%d %d %g %g %g\n",i,j,epsilon[i][j],sigma[i][j],cut_lj[i][j]);
}
/* ---------------------------------------------------------------------- */
double PairLJCutTholeLong::single(int i, int j, int itype, int jtype,
double rsq, double factor_coul,
double factor_lj, double &fforce)
{
double r2inv,r6inv,r,grij,expm2,t,erfc,prefactor,u;
double fraction,table,forcecoul,forcelj,phicoul,philj;
int itable;
double factor_f,factor_e;
double dqi,dqj,dcoul,asr,exp_asr;
int di, dj, di_closest;
int *drudetype = fix_drude->drudetype;
tagint *drudeid = fix_drude->drudeid;
int *type = atom->type;
r2inv = 1.0/rsq;
if (rsq < cut_coulsq) {
r = sqrt(rsq);
if (!ncoultablebits || rsq <= tabinnersq) {
grij = g_ewald * r;
expm2 = exp(-grij*grij);
t = 1.0 / (1.0 + EWALD_P*grij);
u = 1. - t;
erfc = t * (1.+u*(B0+u*(B1+u*(B2+u*(B3+u*(B4+u*B5)))))) * expm2;
prefactor = force->qqrd2e * atom->q[i]*atom->q[j]/r;
forcecoul = prefactor * (erfc + EWALD_F*grij*expm2);
if (factor_coul < 1.0) forcecoul -= (1.0-factor_coul)*prefactor;
} else {
union_int_float_t rsq_lookup_single;
rsq_lookup_single.f = rsq;
itable = rsq_lookup_single.i & ncoulmask;
itable >>= ncoulshiftbits;
fraction = (rsq_lookup_single.f - rtable[itable]) * drtable[itable];
table = ftable[itable] + fraction*dftable[itable];
forcecoul = atom->q[i]*atom->q[j] * table;
if (factor_coul < 1.0) {
table = ctable[itable] + fraction*dctable[itable];
prefactor = atom->q[i]*atom->q[j] * table;
forcecoul -= (1.0-factor_coul)*prefactor;
}
}
if (drudetype[type[i]] != NOPOL_TYPE && drudetype[type[j]] != NOPOL_TYPE) {
di = atom->map(drudeid[i]);
di_closest = domain->closest_image(i, di);
if (di_closest != dj){
if (drudetype[i] == CORE_TYPE) dqi = -atom->q[di];
else if (drudetype[i] == DRUDE_TYPE) dqi = atom->q[i];
if (drudetype[j] == CORE_TYPE) {
dj = atom->map(drudeid[j]);
dqj = -atom->q[dj];
} else if (drudetype[j] == DRUDE_TYPE) dqj = atom->q[j];
asr = ascreen[itype][jtype] * r;
exp_asr = exp(-asr);
dcoul = force->qqrd2e * dqi * dqj / r;
factor_f = 0.5*(2. + (exp_asr * (-2. - asr * (2. + asr))))
- factor_coul;
forcecoul += factor_f * dcoul;
factor_e = 0.5*(2. - (exp_asr * (2. + asr))) - factor_coul;
}
}
} else forcecoul = 0.0;
if (rsq < cut_ljsq[itype][jtype]) {
r6inv = r2inv*r2inv*r2inv;
forcelj = r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]);
} else forcelj = 0.0;
fforce = (forcecoul + factor_lj*forcelj) * r2inv;
double eng = 0.0;
if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq)
phicoul = prefactor*erfc;
else {
table = etable[itable] + fraction*detable[itable];
phicoul = atom->q[i]*atom->q[j] * table;
}
if (factor_coul < 1.0) phicoul -= (1.0-factor_coul)*prefactor;
if (drudetype[type[i]] != NOPOL_TYPE && drudetype[type[j]] != NOPOL_TYPE &&
di_closest != dj)
phicoul += factor_e * dcoul;
eng += phicoul;
}
if (rsq < cut_ljsq[itype][jtype]) {
philj = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]) -
offset[itype][jtype];
eng += factor_lj*philj;
}
return eng;
}
/* ---------------------------------------------------------------------- */
void *PairLJCutTholeLong::extract(const char *str, int &dim)
{
dim = 0;
if (strcmp(str,"cut_coul") == 0) return (void *) &cut_coul;
dim = 6;
if (strcmp(str,"epsilon") == 0) return (void *) epsilon;
if (strcmp(str,"sigma") == 0) return (void *) sigma;
if (strcmp(str,"scale") == 0) return (void *) scale;
if (strcmp(str,"polar") == 0) return (void *) polar;
if (strcmp(str,"thole") == 0) return (void *) thole;
if (strcmp(str,"ascreen") == 0) return (void *) ascreen;
return NULL;
}

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/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
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.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle(lj/cut/thole/long,PairLJCutTholeLong)
#else
#ifndef LMP_PAIR_LJ_CUT_THOLE_LONG_H
#define LMP_PAIR_LJ_CUT_THOLE_LONG_H
#include "pair.h"
#include "fix_drude.h"
namespace LAMMPS_NS {
class PairLJCutTholeLong : public Pair {
public:
PairLJCutTholeLong(class LAMMPS *);
virtual ~PairLJCutTholeLong();
virtual void compute(int, int);
virtual void settings(int, char **);
void coeff(int, char **);
virtual void init_style();
void init_list(int, class NeighList *);
virtual double init_one(int, int);
void write_restart(FILE *);
void read_restart(FILE *);
virtual void write_restart_settings(FILE *);
virtual void read_restart_settings(FILE *);
void write_data(FILE *);
void write_data_all(FILE *);
virtual double single(int, int, int, int, double, double, double, double &);
virtual void *extract(const char *, int &);
protected:
double cut_lj_global;
double **cut_lj,**cut_ljsq;
double cut_coul,cut_coulsq;
double **epsilon,**sigma;
double **lj1,**lj2,**lj3,**lj4,**offset;
double *cut_respa;
double qdist; // TIP4P distance from O site to negative charge
double g_ewald;
double thole_global;
double cut_global;
double **cut,**scale;
double **polar,**thole,**ascreen;
FixDrude *fix_drude;
virtual void allocate();
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Incorrect args for pair coefficients
Self-explanatory. Check the input script or data file.
E: Pair style lj/cut/coul/long requires atom attribute q
The atom style defined does not have this attribute.
E: Pair style requires a KSpace style
No kspace style is defined.
E: Pair cutoff < Respa interior cutoff
One or more pairwise cutoffs are too short to use with the specified
rRESPA cutoffs.
*/

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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
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.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_thole.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
#include "fix.h"
#include "fix_store.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairThole::PairThole(LAMMPS *lmp) : Pair(lmp) {
fix_drude = NULL;
}
/* ---------------------------------------------------------------------- */
PairThole::~PairThole()
{
if (allocated) {
memory->destroy(setflag);
memory->destroy(cutsq);
memory->destroy(polar);
memory->destroy(thole);
memory->destroy(ascreen);
memory->destroy(cut);
memory->destroy(scale);
}
}
/* ---------------------------------------------------------------------- */
void PairThole::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itype,jtype;
double qi,qj,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair;
double r,rsq,r2inv,rinv,forcecoul,factor_coul;
int *ilist,*jlist,*numneigh,**firstneigh;
double factor_f,factor_e;
int di,dj;
double dcoul,asr,exp_asr;
ecoul = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
double **x = atom->x;
double **f = atom->f;
double *q = atom->q;
int *type = atom->type;
int nlocal = atom->nlocal;
double *special_coul = force->special_coul;
int newton_pair = force->newton_pair;
double qqrd2e = force->qqrd2e;
int *drudetype = fix_drude->drudetype;
tagint *drudeid = fix_drude->drudeid;
inum = list->inum;
ilist = list->ilist;
numneigh = list->numneigh;
firstneigh = list->firstneigh;
// loop over neighbors of my atoms
for (ii = 0; ii < inum; ii++) {
i = ilist[ii];
// only on core-drude pair
if (drudetype[type[i]] == NOPOL_TYPE)
continue;
di = domain->closest_image(i, atom->map(drudeid[i]));
// get dq of the core via the drude charge
if (drudetype[type[i]] == DRUDE_TYPE)
qi = q[i];
else
qi = -q[di];
xtmp = x[i][0];
ytmp = x[i][1];
ztmp = x[i][2];
itype = type[i];
jlist = firstneigh[i];
jnum = numneigh[i];
for (jj = 0; jj < jnum; jj++) {
j = jlist[jj];
factor_coul = special_coul[sbmask(j)];
j &= NEIGHMASK;
// only on core-drude pair, but not into the same pair
if (drudetype[type[j]] == NOPOL_TYPE || j == di)
continue;
// get dq of the core via the drude charge
if (drudetype[type[j]] == DRUDE_TYPE)
qj = q[j];
else {
dj = domain->closest_image(j, atom->map(drudeid[j]));
qj = -q[dj];
}
delx = xtmp - x[j][0];
dely = ytmp - x[j][1];
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
rinv = sqrt(r2inv);
r = sqrt(rsq);
asr = ascreen[itype][jtype] * r;
exp_asr = exp(-asr);
dcoul = qqrd2e * qi * qj *scale[itype][jtype] * rinv;
factor_f = 0.5*(2. + (exp_asr * (-2. - asr * (2. + asr)))) - factor_coul;
if(eflag) factor_e = 0.5*(2. - (exp_asr * (2. + asr))) - factor_coul;
fpair = factor_f * dcoul * r2inv;
f[i][0] += delx*fpair;
f[i][1] += dely*fpair;
f[i][2] += delz*fpair;
if (newton_pair || j < nlocal) {
f[j][0] -= delx*fpair;
f[j][1] -= dely*fpair;
f[j][2] -= delz*fpair;
}
if (eflag)
ecoul = factor_e * dcoul;
if (evflag) ev_tally(i,j,nlocal,newton_pair,
0.0,ecoul,fpair,delx,dely,delz);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}
/* ----------------------------------------------------------------------
allocate all arrays
------------------------------------------------------------------------- */
void PairThole::allocate()
{
allocated = 1;
int n = atom->ntypes;
memory->create(setflag,n+1,n+1,"pair:setflag");
for (int i = 1; i <= n; i++)
for (int j = i; j <= n; j++)
setflag[i][j] = 0;
memory->create(cutsq,n+1,n+1,"pair:cutsq");
memory->create(cut,n+1,n+1,"pair:cut");
memory->create(scale,n+1,n+1,"pair:scale");
memory->create(ascreen,n+1,n+1,"pair:ascreen");
memory->create(thole,n+1,n+1,"pair:thole");
memory->create(polar,n+1,n+1,"pair:polar");
}
/* ----------------------------------------------------------------------
global settings
------------------------------------------------------------------------- */
void PairThole::settings(int narg, char **arg)
{
if (narg != 2) error->all(FLERR,"Illegal pair_style command");
thole_global = force->numeric(FLERR,arg[0]);
cut_global = force->numeric(FLERR,arg[1]);
// reset cutoffs that have been explicitly set
if (allocated) {
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i+1; j <= atom->ntypes; j++)
if (setflag[i][j]) {
thole[i][j] = thole_global;
cut[i][j] = cut_global;
}
}
}
/* ----------------------------------------------------------------------
set coeffs for one or more type pairs
------------------------------------------------------------------------- */
void PairThole::coeff(int narg, char **arg)
{
if (narg < 3 || narg > 5)
error->all(FLERR,"Incorrect args for pair coefficients");
if (!allocated) allocate();
int ilo,ihi,jlo,jhi;
force->bounds(arg[0],atom->ntypes,ilo,ihi);
force->bounds(arg[1],atom->ntypes,jlo,jhi);
double polar_one = force->numeric(FLERR,arg[2]);
double thole_one = thole_global;
double cut_one = cut_global;
if (narg >=4) thole_one = force->numeric(FLERR,arg[3]);
if (narg == 5) cut_one = force->numeric(FLERR,arg[4]);
int count = 0;
for (int i = ilo; i <= ihi; i++) {
for (int j = MAX(jlo,i); j <= jhi; j++) {
polar[i][j] = polar_one;
thole[i][j] = thole_one;
ascreen[i][j] = thole[i][j] / pow(polar[i][j], 1./3.);
cut[i][j] = cut_one;
scale[i][j] = 1.0;
setflag[i][j] = 1;
count++;
}
}
if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}
/* ----------------------------------------------------------------------
init specific to this pair style
------------------------------------------------------------------------- */
void PairThole::init_style()
{
if (!atom->q_flag)
error->all(FLERR,"Pair style thole requires atom attribute q");
int ifix;
for (ifix = 0; ifix < modify->nfix; ifix++)
if (strcmp(modify->fix[ifix]->style,"drude") == 0) break;
if (ifix == modify->nfix) error->all(FLERR, "Pair thole requires fix drude");
fix_drude = (FixDrude *) modify->fix[ifix];
neighbor->request(this,instance_me);
}
/* ----------------------------------------------------------------------
init for one type pair i,j and corresponding j,i
------------------------------------------------------------------------- */
double PairThole::init_one(int i, int j)
{
if (setflag[i][j] == 0)
cut[i][j] = mix_distance(cut[i][i],cut[j][j]);
polar[j][i] = polar[i][j];
thole[j][i] = thole[i][j];
ascreen[j][i] = ascreen[i][j];
scale[j][i] = scale[i][j];
return cut[i][j];
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairThole::write_restart(FILE *fp)
{
write_restart_settings(fp);
int i,j;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
fwrite(&setflag[i][j],sizeof(int),1,fp);
if (setflag[i][j]) {
fwrite(&polar[i][j],sizeof(double),1,fp);
fwrite(&thole[i][j],sizeof(double),1,fp);
fwrite(&cut[i][j],sizeof(double),1,fp);
}
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairThole::read_restart(FILE *fp)
{
read_restart_settings(fp);
allocate();
int i,j;
int me = comm->me;
for (i = 1; i <= atom->ntypes; i++)
for (j = i; j <= atom->ntypes; j++) {
if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
if (setflag[i][j]) {
if (me == 0) {
fread(&polar[i][j],sizeof(double),1,fp);
fread(&thole[i][j],sizeof(double),1,fp);
fread(&cut[i][j],sizeof(double),1,fp);
ascreen[i][j] = thole[i][j] / pow(polar[i][j], 1./3.);
}
MPI_Bcast(&polar[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&thole[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&ascreen[i][j],1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut[i][j],1,MPI_DOUBLE,0,world);
}
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void PairThole::write_restart_settings(FILE *fp)
{
fwrite(&thole_global,sizeof(double),1,fp);
fwrite(&cut_global,sizeof(double),1,fp);
fwrite(&offset_flag,sizeof(int),1,fp);
fwrite(&mix_flag,sizeof(int),1,fp);
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void PairThole::read_restart_settings(FILE *fp)
{
if (comm->me == 0) {
fread(&thole_global,sizeof(double),1,fp);
fread(&cut_global,sizeof(double),1,fp);
fread(&offset_flag,sizeof(int),1,fp);
fread(&mix_flag,sizeof(int),1,fp);
}
MPI_Bcast(&thole_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&cut_global,1,MPI_DOUBLE,0,world);
MPI_Bcast(&offset_flag,1,MPI_INT,0,world);
MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
}
/* ---------------------------------------------------------------------- */
double PairThole::single(int i, int j, int itype, int jtype,
double rsq, double factor_coul, double factor_lj,
double &fforce)
{
double r2inv,rinv,r,forcecoul,phicoul;
double qi,qj,factor_f,factor_e,dcoul,asr,exp_asr;
int di, dj;
int *drudetype = fix_drude->drudetype;
tagint *drudeid = fix_drude->drudeid;
int *type = atom->type;
// only on core-drude pair, but not on the same pair
if (drudetype[type[i]] == NOPOL_TYPE || drudetype[type[j]] == NOPOL_TYPE ||
j == i)
return 0.0;
// get dq of the core via the drude charge
if (drudetype[type[i]] == DRUDE_TYPE)
qi = atom->q[i];
else {
di = domain->closest_image(i, atom->map(drudeid[i]));
qi = -atom->q[di];
}
if (drudetype[type[j]] == DRUDE_TYPE)
qj = atom->q[j];
else {
dj = domain->closest_image(j, atom->map(drudeid[j]));
qj = -atom->q[dj];
}
r2inv = 1.0/rsq;
if (rsq < cutsq[itype][jtype]) {
rinv = sqrt(r2inv);
r = sqrt(rsq);
asr = ascreen[itype][jtype] * r;
exp_asr = exp(-asr);
dcoul = force->qqrd2e * qi * qj * rinv;
factor_f = 0.5*(2. + (exp_asr * (-2. - asr * (2. + asr)))) - factor_coul;
forcecoul += factor_f * dcoul;
factor_e = 0.5*(2. - (exp_asr * (2. + asr))) - factor_coul;
} else forcecoul= 0.0;
fforce = factor_f*forcecoul * r2inv;
if (rsq < cutsq[itype][jtype]) {
phicoul = factor_e * dcoul;
} else phicoul = 0.0;
return phicoul;
}
/* ---------------------------------------------------------------------- */
void *PairThole::extract(const char *str, int &dim)
{
dim = 4;
if (strcmp(str,"scale") == 0) return (void *) scale;
if (strcmp(str,"polar") == 0) return (void *) polar;
if (strcmp(str,"thole") == 0) return (void *) thole;
if (strcmp(str,"ascreen") == 0) return (void *) ascreen;
return NULL;
}

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/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
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.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifdef PAIR_CLASS
PairStyle(thole,PairThole)
#else
#ifndef LMP_PAIR_THOLE_H
#define LMP_PAIR_THOLE_H
#include "pair.h"
#include "fix_drude.h"
namespace LAMMPS_NS {
class PairThole : public Pair {
public:
PairThole(class LAMMPS *);
virtual ~PairThole();
virtual void compute(int, int);
virtual void settings(int, char **);
void coeff(int, char **);
void init_style();
double init_one(int, int);
void write_restart(FILE *);
void read_restart(FILE *);
virtual void write_restart_settings(FILE *);
virtual void read_restart_settings(FILE *);
virtual double single(int, int, int, int, double, double, double, double &);
void *extract(const char *, int &);
protected:
double thole_global;
double cut_global;
double **cut,**scale;
double **polar,**thole,**ascreen;
FixDrude * fix_drude;
virtual void allocate();
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
E: Incorrect args for pair coefficients
Self-explanatory. Check the input script or data file.
E: Pair style thole requires atom attribute q
The atom style defined does not have these attributes.
*/