git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5103 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2010-10-22 21:26:02 +00:00
parent 49f49a85e3
commit 8889d8dfb9
8 changed files with 299 additions and 25 deletions

180
src/compute_ti.cpp Normal file
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@ -0,0 +1,180 @@
/* ----------------------------------------------------------------------
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: Sai Jayaraman (University of Notre Dame)
------------------------------------------------------------------------- */
#include "mpi.h"
#include "string.h"
#include "compute_ti.h"
#include "update.h"
#include "modify.h"
#include "domain.h"
#include "force.h"
#include "pair.h"
#include "kspace.h"
#include "input.h"
#include "variable.h"
#include "error.h"
using namespace LAMMPS_NS;
enum{PAIR,TAIL,KSPACE};
#define INVOKED_SCALAR 1
/* ---------------------------------------------------------------------- */
ComputeTI::ComputeTI(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg)
{
if (narg < 4) error->all("Illegal compute ti command");
peflag = 1;
scalar_flag = 1;
extscalar = 1;
timeflag = 1;
// terms come in triplets
nterms = (narg-3) / 3;
if (narg != 3*nterms + 3) error->all("Illegal compute ti command");
which = new int[nterms];
ivar1 = new int[nterms];
ivar2 = new int[nterms];
var1 = new char*[nterms];
var2 = new char*[nterms];
pptr = new Pair*[nterms];
pstyle = new char*[nterms];
for (int m = 0; m < nterms; m++) pstyle[m] = NULL;
// parse keywords
nterms = 0;
int iarg = 3;
while (iarg < narg) {
if (iarg+3 > narg) error->all("Illegal fix adapt command");
if (strcmp(arg[iarg],"kspace") == 0) which[nterms] = KSPACE;
else if (strcmp(arg[iarg],"tail") == 0) which[nterms] = TAIL;
else {
which[nterms] = PAIR;
int n = strlen(&arg[iarg+1][2]) + 1;
pstyle[nterms] = new char[n];
strcpy(pstyle[nterms],&arg[iarg+1][2]);
}
if (strstr(arg[iarg+2],"v_") == arg[iarg+2]) {
int n = strlen(&arg[iarg+2][2]) + 1;
var1[nterms] = new char[n];
strcpy(var1[nterms],&arg[iarg+2][2]);
} else error->all("Illegal compute ti command");
if (strstr(arg[iarg+3],"v_") == arg[iarg+3]) {
int n = strlen(&arg[iarg+3][2]) + 1;
var2[nterms] = new char[n];
strcpy(var2[nterms],&arg[iarg+3][2]);
} else error->all("Illegal compute ti command");
nterms++;
iarg += 3;
}
}
/* --------------------------------------------------------------------- */
ComputeTI::~ComputeTI()
{
for (int m = 0; m < nterms; m++) {
delete [] var1[m];
delete [] var2[m];
delete [] pstyle[m];
}
delete [] which;
delete [] ivar1;
delete [] ivar2;
delete [] var1;
delete [] var2;
delete [] pptr;
delete [] pstyle;
}
/* --------------------------------------------------------------------- */
void ComputeTI::init()
{
// setup and error checks
for (int m = 0; m < nterms; m++) {
ivar1[m] = input->variable->find(var1[m]);
ivar2[m] = input->variable->find(var2[m]);
if (ivar1[m] < 0 || ivar2 < 0)
error->all("Variable name for compute ti does not exist");
if (!input->variable->equalstyle(ivar1[m]) ||
!input->variable->equalstyle(ivar2[m]))
error->all("Variable for compute ti is invalid style");
if (which[m] == PAIR) {
pptr[m] = force->pair_match(pstyle[m],1);
if (pptr[m] == NULL) error->all("Compute ti pair style does not exist");
} else if (which[m] == TAIL) {
if (force->pair == NULL || force->pair->tail_flag == 0)
error->all("Compute ti tail when pair style does not "
"compute tail corrections");
} else if (which[m] == KSPACE) {
if (force->kspace == NULL)
error->all("Compute ti is incompatible with KSpace style");
}
}
}
/* --------------------------------------------------------------------- */
double ComputeTI::compute_scalar()
{
double eng,engall,value1,value2;
invoked_scalar |= INVOKED_SCALAR;
if (update->eflag_global != invoked_scalar)
error->all("Energy was not tallied on needed timestep");
double dUdl = 0.0;
for (int m = 0; m < nterms; m++) {
value1 = input->variable->compute_equal(ivar1[m]);
value2 = input->variable->compute_equal(ivar2[m]);
if (value1 == 0.0) continue;
if (which[m] == PAIR) {
eng = pptr[m]->eng_vdwl + pptr[m]->eng_coul;
MPI_Allreduce(&eng,&engall,1,MPI_DOUBLE,MPI_SUM,world);
dUdl += engall/value1 * value2;
} else if (which[m] == TAIL) {
double vol = domain->xprd*domain->yprd*domain->zprd;
eng = force->pair->etail / vol;
dUdl += eng/value1 * value2;
} else if (which[m] == KSPACE) {
eng = force->kspace->energy;
dUdl += eng/value1 * value2;
}
}
scalar = dUdl;
return scalar;
}

46
src/compute_ti.h Normal file
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@ -0,0 +1,46 @@
/* ----------------------------------------------------------------------
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(ti,ComputeTI)
#else
#ifndef COMPUTE_TI_H
#define COMPUTE_TI_H
#include "compute.h"
namespace LAMMPS_NS {
class ComputeTI : public Compute {
public:
ComputeTI(class LAMMPS *, int, char **);
~ComputeTI();
void init();
double compute_scalar();
private:
int nterms;
int *which;
int *ivar1,*ivar2;
char **var1,**var2;
class Pair **pptr;
char **pstyle;
};
}
#endif
#endif

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@ -403,3 +403,14 @@ double PairBorn::single(int i, int j, int itype, int jtype,
d[itype][jtype]*r2inv*r6inv - offset[itype][jtype];
return factor_lj*phiborn;
}
/* ---------------------------------------------------------------------- */
void *PairBorn::extract(char *str, int &dim)
{
dim = 2;
if (strcmp(str,"a") == 0) return (void *) a;
if (strcmp(str,"c") == 0) return (void *) c;
if (strcmp(str,"d") == 0) return (void *) d;
return NULL;
}

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@ -37,6 +37,7 @@ class PairBorn : public Pair {
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
double single(int, int, int, int, double, double, double, double &);
void *extract(char *, int &);
private:
double cut_global;

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@ -14,6 +14,7 @@
#include "math.h"
#include "stdio.h"
#include "stdlib.h"
#include "string.h"
#include "pair_buck.h"
#include "atom.h"
#include "comm.h"
@ -342,3 +343,13 @@ double PairBuck::single(int i, int j, int itype, int jtype,
offset[itype][jtype];
return factor_lj*phibuck;
}
/* ---------------------------------------------------------------------- */
void *PairBuck::extract(char *str, int &dim)
{
dim = 2;
if (strcmp(str,"a") == 0) return (void *) a;
if (strcmp(str,"c") == 0) return (void *) c;
return NULL;
}

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@ -37,6 +37,7 @@ class PairBuck : public Pair {
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
double single(int, int, int, int, double, double, double, double &);
void *extract(char *, int &);
private:
double cut_global;

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@ -37,12 +37,18 @@ using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
PairGauss::PairGauss(LAMMPS *lmp) :Pair(lmp) {}
PairGauss::PairGauss(LAMMPS *lmp) :Pair(lmp)
{
nextra = 1;
pvector = new double[1];
}
/* ---------------------------------------------------------------------- */
PairGauss::~PairGauss()
{
delete [] pvector;
if (allocated) {
memory->destroy_2d_int_array(setflag);
memory->destroy_2d_double_array(cutsq);
@ -66,7 +72,8 @@ void PairGauss::compute(int eflag, int vflag)
evdwl = 0.0;
if (eflag || vflag) ev_setup(eflag,vflag);
else evflag = vflag_fdotr = 0;
int occ = 0;
double **x = atom->x;
double **f = atom->f;
int *type = atom->type;
@ -98,7 +105,12 @@ void PairGauss::compute(int eflag, int vflag)
delz = ztmp - x[j][2];
rsq = delx*delx + dely*dely + delz*delz;
jtype = type[j];
// define a Gaussian well to be occupied if
// the site it interacts with is within the force maximum
if (eflag_global && rsq < 0.5/b[itype][jtype]) occ++;
if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0/rsq;
r = sqrt(rsq);
@ -120,11 +132,12 @@ void PairGauss::compute(int eflag, int vflag)
offset[itype][jtype]);
if (evflag) ev_tally(i,j,nlocal,newton_pair,
evdwl,0.0,fpair,delx,dely,delz);
evdwl,0.0,fpair,delx,dely,delz);
}
}
}
if (eflag_global) pvector[0] = occ;
if (vflag_fdotr) virial_compute();
}
@ -314,3 +327,12 @@ double PairGauss::single(int i, int j, int itype, int jtype, double rsq,
fforce = forcelj*r2inv;
return philj;
}
/* ---------------------------------------------------------------------- */
void *PairGauss::extract(char *str, int &dim)
{
dim = 2;
if (strcmp(str,"a") == 0) return (void *) a;
return NULL;
}

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@ -24,28 +24,30 @@ PairStyle(gauss,PairGauss)
namespace LAMMPS_NS {
class PairGauss : public Pair {
public:
PairGauss(class LAMMPS *);
~PairGauss();
void compute(int,int);
void settings(int, char **);
void coeff(int, char **);
double init_one(int, int);
void write_restart(FILE *);
void read_restart(FILE *);
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
double single(int, int, int, int, double, double, double, double &);
class PairGauss : public Pair {
public:
PairGauss(class LAMMPS *);
~PairGauss();
void compute(int,int);
void settings(int, char **);
void coeff(int, char **);
double init_one(int, int);
void write_restart(FILE *);
void read_restart(FILE *);
void write_restart_settings(FILE *);
void read_restart_settings(FILE *);
double single(int, int, int, int, double, double, double, double &);
void *extract(char *, int &);
private:
double cut_global;
double **cut;
double **a,**b;
double **offset;
private:
double cut_global;
double **cut;
double **a,**b;
double **offset;
void allocate();
};
void allocate();
};
}
#endif