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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14756 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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This commit is contained in:
sjplimp
2016-03-21 16:01:21 +00:00
parent 784d8cc2f8
commit 36776f425b
9 changed files with 132 additions and 30 deletions
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9
src/GRANULAR/fix_pour.cpp
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@ -42,6 +42,7 @@ enum{ONE,RANGE,POLY};
enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED}; // several files
#define EPSILON 0.001
#define SMALL 1.0e-10
/* ---------------------------------------------------------------------- */
@ -900,13 +901,13 @@ void FixPour::options(int narg, char **arg)
molfrac[nmol-1] = 1.0;
iarg += 2;
} else if (strcmp(arg[iarg],"molfrac") == 0) {
if (mode != MOLECULE) error->all(FLERR,"Illegal fix deposit command");
if (iarg+nmol+1 > narg) error->all(FLERR,"Illegal fix deposit command");
if (mode != MOLECULE) error->all(FLERR,"Illegal fix pour command");
if (iarg+nmol+1 > narg) error->all(FLERR,"Illegal fix pour command");
molfrac[0] = force->numeric(FLERR,arg[iarg+1]);
for (int i = 1; i < nmol; i++)
molfrac[i] = molfrac[i-1] + force->numeric(FLERR,arg[iarg+i+1]);
if (molfrac[nmol-1] < 1.0-EPSILON || molfrac[nmol-1] > 1.0+EPSILON)
error->all(FLERR,"Illegal fix deposit command");
error->all(FLERR,"Illegal fix pour command");
molfrac[nmol-1] = 1.0;
iarg += nmol+1;
@ -976,7 +977,7 @@ void FixPour::options(int narg, char **arg)
}
double sum = 0.0;
for (int i = 0; i < npoly; i++) sum += frac_poly[i];
if (sum != 1.0)
if (fabs(sum - 1.0) > SMALL)
error->all(FLERR,"Fix pour polydisperse fractions do not sum to 1.0");
} else error->all(FLERR,"Illegal fix pour command");

101
src/MANYBODY/pair_airebo.cpp
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@ -15,6 +15,8 @@
Contributing author: Ase Henry (MIT)
Bugfixes and optimizations:
Marcel Fallet & Steve Stuart (Clemson), Axel Kohlmeyer (Temple U)
AIREBO-M modification to optionally replace LJ with Morse potentials.
Thomas C. O'Connor (JHU) 2014
------------------------------------------------------------------------- */
#include <math.h>
@ -51,6 +53,8 @@ PairAIREBO::PairAIREBO(LAMMPS *lmp) : Pair(lmp)
single_enable = 0;
one_coeff = 1;
ghostneigh = 1;
ljflag = torflag = 1;
morseflag = 0;
maxlocal = 0;
REBO_numneigh = NULL;
@ -142,7 +146,6 @@ void PairAIREBO::settings(int narg, char **arg)
cutlj = force->numeric(FLERR,arg[0]);
ljflag = torflag = 1;
if (narg == 3) {
ljflag = force->inumeric(FLERR,arg[1]);
torflag = force->inumeric(FLERR,arg[2]);
@ -290,10 +293,23 @@ double PairAIREBO::init_one(int i, int j)
cutghost[i][j] = rcmax[ii][jj];
cutljsq[ii][jj] = cutlj*sigma[ii][jj] * cutlj*sigma[ii][jj];
lj1[ii][jj] = 48.0 * epsilon[ii][jj] * pow(sigma[ii][jj],12.0);
lj2[ii][jj] = 24.0 * epsilon[ii][jj] * pow(sigma[ii][jj],6.0);
lj3[ii][jj] = 4.0 * epsilon[ii][jj] * pow(sigma[ii][jj],12.0);
lj4[ii][jj] = 4.0 * epsilon[ii][jj] * pow(sigma[ii][jj],6.0);
if (morseflag) {
// using LJ precomputed parameter arrays to store values for Morse potential
lj1[ii][jj] = epsilonM[ii][jj] * exp(alphaM[ii][jj]*reqM[ii][jj]);
lj2[ii][jj] = exp(alphaM[ii][jj]*reqM[ii][jj]);
lj3[ii][jj] = 2*epsilonM[ii][jj]*alphaM[ii][jj]*exp(alphaM[ii][jj]*reqM[ii][jj]);
lj4[ii][jj] = alphaM[ii][jj];
} else {
lj1[ii][jj] = 48.0 * epsilon[ii][jj] * pow(sigma[ii][jj],12.0);
lj2[ii][jj] = 24.0 * epsilon[ii][jj] * pow(sigma[ii][jj],6.0);
lj3[ii][jj] = 4.0 * epsilon[ii][jj] * pow(sigma[ii][jj],12.0);
lj4[ii][jj] = 4.0 * epsilon[ii][jj] * pow(sigma[ii][jj],6.0);
}
cutghost[j][i] = cutghost[i][j];
cutljsq[jj][ii] = cutljsq[ii][jj];
@ -732,11 +748,20 @@ void PairAIREBO::FLJ(int eflag, int vflag)
dslw = 0.0;
}
r2inv = 1.0/rijsq;
r6inv = r2inv*r2inv*r2inv;
if (morseflag) {
vdw = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
dvdw = -r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]) / rij;
const double exr = exp(-rij*lj4[itype][jtype]);
vdw = lj1[itype][jtype]*exr*(lj2[itype][jtype]*exr - 2);
dvdw = lj3[itype][jtype]*exr*(1-lj2[itype][jtype]*exr);
} else {
r2inv = 1.0/rijsq;
r6inv = r2inv*r2inv*r2inv;
vdw = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
dvdw = -r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]) / rij;
}
// VLJ now becomes vdw * slw, derivaties, etc.
@ -3322,6 +3347,10 @@ void PairAIREBO::read_file(char *filename)
epsilon_CC,epsilon_CH,epsilon_HH;
double sigma_CC,sigma_CH,sigma_HH,epsilonT_CCCC,epsilonT_CCCH,epsilonT_HCCH;
// additional parameters for Morse potential.
double epsilonM_CC,epsilonM_CH,epsilonM_HH,alphaM_CC,alphaM_CH,alphaM_HH;
double reqM_CC,reqM_CH,reqM_HH;
MPI_Comm_rank(world,&me);
// read file on proc 0
@ -3330,7 +3359,10 @@ void PairAIREBO::read_file(char *filename)
FILE *fp = force->open_potential(filename);
if (fp == NULL) {
char str[128];
sprintf(str,"Cannot open AIREBO potential file %s",filename);
if (morseflag)
sprintf(str,"Cannot open AIREBO-M potential file %s",filename);
else
sprintf(str,"Cannot open AIREBO potential file %s",filename);
error->one(FLERR,str);
}
@ -3477,6 +3509,29 @@ void PairAIREBO::read_file(char *filename)
fgets(s,MAXLINE,fp);
sscanf(s,"%lg",&epsilonT_HCCH);
if (morseflag) {
// lines for reading in MORSE parameters from CH.airebo_m file
fgets(s,MAXLINE,fp);
sscanf(s,"%lg",&epsilonM_CC);
fgets(s,MAXLINE,fp);
sscanf(s,"%lg",&epsilonM_CH);
fgets(s,MAXLINE,fp);
sscanf(s,"%lg",&epsilonM_HH);
fgets(s,MAXLINE,fp);
sscanf(s,"%lg",&alphaM_CC);
fgets(s,MAXLINE,fp);
sscanf(s,"%lg",&alphaM_CH);
fgets(s,MAXLINE,fp);
sscanf(s,"%lg",&alphaM_HH);
fgets(s,MAXLINE,fp);
sscanf(s,"%lg",&reqM_CC);
fgets(s,MAXLINE,fp);
sscanf(s,"%lg",&reqM_CH);
fgets(s,MAXLINE,fp);
sscanf(s,"%lg",&reqM_HH);
}
// gC spline
fgets(s,MAXLINE,fp);
@ -3805,6 +3860,25 @@ void PairAIREBO::read_file(char *filename)
sigma[1][0] = sigma[0][1];
sigma[1][1] = sigma_HH;
if (morseflag) {
// Morse parameter assignments
epsilonM[0][0] = epsilonM_CC;
epsilonM[0][1] = epsilonM_CH;
epsilonM[1][0] = epsilonM[0][1];
epsilonM[1][1] = epsilonM_HH;
alphaM[0][0] = alphaM_CC;
alphaM[0][1] = alphaM_CH;
alphaM[1][0] = alphaM[0][1];
alphaM[1][1] = alphaM_HH;
reqM[0][0] = reqM_CC;
reqM[0][1] = reqM_CH;
reqM[1][0] = reqM[0][1];
reqM[1][1] = reqM_HH;
}
// torsional
thmin = -1.0;
@ -3854,6 +3928,13 @@ void PairAIREBO::read_file(char *filename)
MPI_Bcast(&sigma[0][0],4,MPI_DOUBLE,0,world);
MPI_Bcast(&epsilonT[0][0],4,MPI_DOUBLE,0,world);
if (morseflag) {
// Morse parameter broadcast
MPI_Bcast(&epsilonM[0][0],4,MPI_DOUBLE,0,world);
MPI_Bcast(&alphaM[0][0],4,MPI_DOUBLE,0,world);
MPI_Bcast(&reqM[0][0],4,MPI_DOUBLE,0,world);
}
MPI_Bcast(&gCdom[0],5,MPI_DOUBLE,0,world);
MPI_Bcast(&gC1[0][0],24,MPI_DOUBLE,0,world);
MPI_Bcast(&gC2[0][0],24,MPI_DOUBLE,0,world);

6
src/MANYBODY/pair_airebo.h
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@ -42,7 +42,8 @@ class PairAIREBO : public Pair {
int *map; // 0 (C), 1 (H), or -1 (NULL) for each type
int me;
int ljflag,torflag; // 0/1 if LJ,torsion terms included
int ljflag,torflag; // 0/1 if LJ/Morse,torsion terms included
int morseflag; // 1 if Morse instead of LJ for non-bonded
double cutlj; // user-specified LJ cutoff
double cutljrebosq; // cut for when to compute
@ -68,6 +69,9 @@ class PairAIREBO : public Pair {
double rcLJmin[2][2],rcLJmax[2][2],rcLJmaxsq[2][2],bLJmin[2][2],bLJmax[2][2];
double epsilon[2][2],sigma[2][2],epsilonT[2][2];
// parameters for Morse variant
double epsilonM[2][2],alphaM[2][2],reqM[2][2];
// spline coefficients
double gCdom[5],gC1[4][6],gC2[4][6],gHdom[4],gH[3][6];

1
src/MANYBODY/pair_rebo.cpp
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@ -12,7 +12,6 @@
------------------------------------------------------------------------- */
#include "pair_rebo.h"
#include "force.h"
#include "error.h"
using namespace LAMMPS_NS;

17
src/USER-OMP/pair_airebo_omp.cpp
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@ -2178,11 +2178,20 @@ void PairAIREBOOMP::FLJ_thr(int ifrom, int ito, int evflag, int eflag,
dslw = 0.0;
}
r2inv = 1.0/rijsq;
r6inv = r2inv*r2inv*r2inv;
if (morseflag) {
vdw = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
dvdw = -r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]) / rij;
const double exr = exp(-rij*lj4[itype][jtype]);
vdw = lj1[itype][jtype]*exr*(lj2[itype][jtype]*exr - 2);
dvdw = lj3[itype][jtype]*exr*(1-lj2[itype][jtype]*exr);
} else {
r2inv = 1.0/rijsq;
r6inv = r2inv*r2inv*r2inv;
vdw = r6inv*(lj3[itype][jtype]*r6inv-lj4[itype][jtype]);
dvdw = -r6inv * (lj1[itype][jtype]*r6inv - lj2[itype][jtype]) / rij;
}
// VLJ now becomes vdw * slw, derivaties, etc.

3
src/USER-REAXC/fix_qeq_reax.cpp
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@ -367,7 +367,8 @@ void FixQEqReax::init_shielding()
int ntypes;
ntypes = atom->ntypes;
memory->create(shld,ntypes+1,ntypes+1,"qeq:shileding");
if (shld == NULL)
memory->create(shld,ntypes+1,ntypes+1,"qeq:shileding");
for( i = 1; i <= ntypes; ++i )
for( j = 1; j <= ntypes; ++j )

10
src/USER-REAXC/fix_reaxc_species.cpp
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@ -58,6 +58,8 @@ FixReaxCSpecies::FixReaxCSpecies(LAMMPS *lmp, int narg, char **arg) :
size_peratom_cols = 0;
peratom_freq = 1;
nvalid = -1;
MPI_Comm_rank(world,&me);
MPI_Comm_size(world,&nprocs);
ntypes = atom->ntypes;
@ -269,7 +271,8 @@ int FixReaxCSpecies::setmask()
void FixReaxCSpecies::setup(int vflag)
{
ntotal = static_cast<int> (atom->natoms);
memory->create(Name,ntypes,"reax/c/species:Name");
if (Name == NULL)
memory->create(Name,ntypes,"reax/c/species:Name");
post_integrate();
}
@ -286,7 +289,10 @@ void FixReaxCSpecies::init()
"pair_style reax/c");
reaxc->fixspecies_flag = 1;
nvalid = update->ntimestep+nfreq;
// reset next output timestep if not yet set or timestep has been reset
if (nvalid != update->ntimestep)
nvalid = update->ntimestep+nfreq;
// check if this fix has been called twice
int count = 0;

2
src/VORONOI/README
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@ -1,7 +1,7 @@
The VORONOI package adds a compute voronoi/atom command which
calculates a Voronoi tesselation of the system.
It uses the Voro++ library, available at http://math.lbl.gov/voro++ to
It uses the Voro++ library, available at http://math.lbl.gov/voro++/ to
compute the tesselation locally on each processor. Voro++ was
developed by Chris H. Rycroft while at UC Berkeley / Lawrence Berkeley
Laboratory.

13
src/domain.cpp
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@ -503,12 +503,13 @@ void Domain::pbc()
double *coord;
int n3 = 3*nlocal;
if (x) coord = &x[0][0];
int flag = 0;
for (i = 0; i < n3; i++)
if (!ISFINITE(*coord++)) flag = 1;
if (flag) error->one(FLERR,"Non-numeric atom coords - simulation unstable");
if (x) {
coord = &x[0][0];
int flag = 0;
for (i = 0; i < n3; i++)
if (!ISFINITE(*coord++)) flag = 1;
if (flag) error->one(FLERR,"Non-numeric atom coords - simulation unstable");
}
// setup for PBC checks
if (triclinic == 0) {