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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13708 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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sjplimp
2015-07-24 15:50:34 +00:00
parent 303d9b9f54
commit e91bd244af
10 changed files with 254 additions and 5 deletions
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2
src/CORESHELL/Install.sh
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@ -30,3 +30,5 @@ action pair_born_coul_long_cs.cpp pair_born_coul_long.cpp
action pair_buck_coul_long_cs.cpp pair_buck_coul_long.cpp
action pair_born_coul_long_cs.h pair_born_coul_long.h
action pair_buck_coul_long_cs.h pair_buck_coul_long.h
action pair_coul_long_cs.cpp pair_coul_long.cpp
action pair_coul_long_cs.h pair_coul_long.h

159
src/CORESHELL/pair_coul_long_cs.cpp Normal file
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@ -0,0 +1,159 @@
/* ----------------------------------------------------------------------
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.
------------------------------------------------------------------------- */
/* ----------------------------------------------------------------------
Added epsilon for use with CORESHELL and USER-DRUDE
------------------------------------------------------------------------- */
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_coul_long_cs.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "kspace.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "update.h"
#include "integrate.h"
#include "respa.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#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
/* ---------------------------------------------------------------------- */
PairCoulLongCS::PairCoulLongCS(LAMMPS *lmp) : PairCoulLong(lmp) {}
/* ---------------------------------------------------------------------- */
void PairCoulLongCS::compute(int eflag, int vflag)
{
int i,j,ii,jj,inum,jnum,itable,itype,jtype;
double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair;
double fraction,table;
double r,r2inv,forcecoul,factor_coul;
double grij,expm2,prefactor,t,erfc,u;
int *ilist,*jlist,*numneigh,**firstneigh;
double rsq;
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;
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];
qtmp = q[i];
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;
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 < cut_coulsq) {
r2inv = 1.0/rsq;
r = sqrt(rsq);
if (!ncoultablebits || rsq <= tabinnersq) {
prefactor = qqrd2e * scale[itype][jtype] * qtmp*q[j];
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 /= 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 = scale[itype][jtype] * qtmp*q[j] * table;
if (factor_coul < 1.0) {
table = ctable[itable] + fraction*dctable[itable];
prefactor = scale[itype][jtype] * qtmp*q[j] * table;
forcecoul -= (1.0-factor_coul)*prefactor;
}
}
fpair = forcecoul * 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 (!ncoultablebits || rsq <= tabinnersq)
ecoul = prefactor*erfc;
else {
table = etable[itable] + fraction*detable[itable];
ecoul = scale[itype][jtype] * qtmp*q[j] * table;
}
if (factor_coul < 1.0) ecoul -= (1.0-factor_coul)*prefactor;
}
if (evflag) ev_tally(i,j,nlocal,newton_pair,
0.0,ecoul,fpair,delx,dely,delz);
}
}
}
if (vflag_fdotr) virial_fdotr_compute();
}

58
src/CORESHELL/pair_coul_long_cs.h Normal file
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@ -0,0 +1,58 @@
/* -*- 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(coul/long/cs,PairCoulLongCS)
#else
#ifndef LMP_PAIR_COUL_LONG_CS_H
#define LMP_PAIR_COUL_LONG_CS_H
#include "pair_coul_long.h"
namespace LAMMPS_NS {
class PairCoulLongCS : public PairCoulLong {
public:
PairCoulLongCS(class LAMMPS *);
virtual void compute(int, int);
};
}
#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/drude 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.
*/

6
src/Makefile
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@ -46,9 +46,9 @@ 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-misc \
user-molfile user-omp user-phonon user-qmmm user-qtb user-quip \
user-reaxc user-sph
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
PACKLIB = gpu kim kokkos meam poems python reax voronoi \
user-atc user-awpmd user-colvars user-cuda user-molfile \

5
src/compute_chunk_atom.cpp
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@ -722,12 +722,17 @@ int ComputeChunkAtom::setup_chunks()
// assign chunk IDs to atoms
// will exclude atoms not in group or in optional region
// for binning styles, need to setup bins and their volume first
// else chunk_volume_scalar = box volume
// IDs are needed to scan for max ID and for compress()
if (binflag) {
nchunk = setup_bins();
bin_volumes();
} else {
chunk_volume_scalar = domain->xprd * domain->yprd;
if (domain->dimension == 3) chunk_volume_scalar *= domain->zprd;
}
assign_chunk_ids();
// set nchunk for chunk styles other than binning

1
src/fix.cpp
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@ -66,6 +66,7 @@ Fix::Fix(LAMMPS *lmp, int narg, char **arg) : Pointers(lmp)
wd_header = wd_section = 0;
dynamic_group_allow = 0;
dof_flag = 0;
special_alter_flag = 0;
cudable_comm = 0;
scalar_flag = vector_flag = array_flag = 0;

3
src/fix.h
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@ -50,6 +50,7 @@ class Fix : protected Pointers {
int wd_section; // # of sections fix writes to data file
int dynamic_group_allow; // 1 if can be used with dynamic group, else 0
int dof_flag; // 1 if has dof() method (not min_dof())
int special_alter_flag; // 1 if has special_alter() meth for spec lists
int cudable_comm; // 1 if fix has CUDA-enabled communication
int scalar_flag; // 0/1 if compute_scalar() function exists
@ -194,6 +195,8 @@ class Fix : protected Pointers {
virtual void zero_momentum() {}
virtual void zero_rotation() {}
virtual void rebuild_special() {}
virtual int modify_param(int, char **) {return 0;}
virtual void *extract(const char *, int &) {return NULL;}

5
src/neighbor.cpp
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@ -310,6 +310,7 @@ void Neighbor::init()
// flag = 1 if both LJ/Coulomb special values are 1.0
// flag = 2 otherwise or if KSpace solver is enabled
// pairwise portion of KSpace solver uses all 1-2,1-3,1-4 neighbors
// or selected Coulomb-approixmation pair styles require it
if (force->special_lj[1] == 0.0 && force->special_coul[1] == 0.0)
special_flag[1] = 0;
@ -329,8 +330,8 @@ void Neighbor::init()
special_flag[3] = 1;
else special_flag[3] = 2;
if (force->kspace || force->pair_match("coul/wolf",0)
|| force->pair_match("coul/dsf",0))
if (force->kspace || force->pair_match("coul/wolf",0) ||
force->pair_match("coul/dsf",0) || force->pair_match("thole",0))
special_flag[1] = special_flag[2] = special_flag[3] = 2;
// maxwt = max multiplicative factor on atom indices stored in neigh list

19
src/special.cpp
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@ -18,6 +18,8 @@
#include "atom_vec.h"
#include "force.h"
#include "comm.h"
#include "modify.h"
#include "fix.h"
#include "accelerator_kokkos.h"
#include "memory.h"
#include "error.h"
@ -191,6 +193,7 @@ void Special::build()
force->special_lj[3] == 1.0 && force->special_coul[3] == 1.0) {
dedup();
combine();
fix_alteration();
return;
}
@ -307,6 +310,7 @@ void Special::build()
dedup();
if (force->special_angle) angle_trim();
combine();
fix_alteration();
return;
}
@ -419,6 +423,7 @@ void Special::build()
if (force->special_angle) angle_trim();
if (force->special_dihedral) dihedral_trim();
combine();
fix_alteration();
}
/* ----------------------------------------------------------------------
@ -1127,3 +1132,17 @@ void Special::ring_eight(int ndatum, char *cbuf)
i += 2;
}
}
/* ----------------------------------------------------------------------
allow fixes to alter special list
currently, only fix drude does this
so that both the Drude core and electron are same level of neighbor
------------------------------------------------------------------------- */
void Special::fix_alteration()
{
for (int ifix = 0; ifix < modify->nfix; ifix++)
if (modify->fix[ifix]->special_alter_flag)
modify->fix[ifix]->rebuild_special();
}

1
src/special.h
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@ -37,6 +37,7 @@ class Special : protected Pointers {
void angle_trim();
void dihedral_trim();
void combine();
void fix_alteration();
// static variable for ring communication callback to access class data
// callback functions for ring communication