From 801111a7abfa5aa59495b515d62a2879a8dbbf71 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 10 Nov 2016 15:00:36 -0500
Subject: [PATCH] dummy framework implementation for AGNI pair style
---
src/.gitignore | 2 +
src/USER-MISC/pair_agni.cpp | 480 ++++++++++++++++++++++++++++++++++++
src/USER-MISC/pair_agni.h | 83 +++++++
3 files changed, 565 insertions(+)
create mode 100644 src/USER-MISC/pair_agni.cpp
create mode 100644 src/USER-MISC/pair_agni.h
diff --git a/src/.gitignore b/src/.gitignore
index 02b05b364b..cb96561845 100644
--- a/src/.gitignore
+++ b/src/.gitignore
@@ -539,6 +539,8 @@
/pair_adp.cpp
/pair_adp.h
+/pair_agni.cpp
+/pair_agni.h
/pair_airebo.cpp
/pair_airebo.h
/pair_airebo_morse.cpp
diff --git a/src/USER-MISC/pair_agni.cpp b/src/USER-MISC/pair_agni.cpp
new file mode 100644
index 0000000000..1b56570b07
--- /dev/null
+++ b/src/USER-MISC/pair_agni.cpp
@@ -0,0 +1,480 @@
+/* ----------------------------------------------------------------------
+ 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: Axel Kohlmeyer (Temple U)
+------------------------------------------------------------------------- */
+
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "pair_agni.h"
+#include "atom.h"
+#include "neighbor.h"
+#include "neigh_request.h"
+#include "force.h"
+#include "comm.h"
+#include "memory.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "memory.h"
+#include "error.h"
+#include "citeme.h"
+
+using namespace LAMMPS_NS;
+
+static const char cite_pair_agni[] =
+ "pair agni command:\n\n"
+ "@article{botu2015adaptive,\n"
+ " author = {Botu, Venkatesh and Ramprasad, Rampi},\n"
+ " title = {Adaptive machine learning framework to"
+ " accelerate ab initio molecular dynamics},\n"
+ " journal = {International Journal of Quantum Chemistry},\n"
+ " volume = {115},\n"
+ " number = {16},\n"
+ " pages = {1074--1083},\n"
+ " year = {2015},\n"
+ " publisher = {Wiley Online Library}\n"
+ "}\n\n"
+ "@article{botu2015learning,\n"
+ " author = {Botu, Venkatesh and Ramprasad, Rampi},\n"
+ " title = {Learning scheme to predict atomic forces"
+ " and accelerate materials simulations},\n"
+ " journal = {Physical Review B},\n"
+ " volume = {92},\n"
+ " number = {9},\n"
+ " pages = {094306},\n"
+ " year = {2015},\n"
+ " publisher = {APS}\n"
+ "}\n\n";
+
+
+#define MAXLINE 1024
+#define DELTA 4
+
+/* ---------------------------------------------------------------------- */
+
+PairAGNI::PairAGNI(LAMMPS *lmp) : Pair(lmp)
+{
+ if (lmp->citeme) lmp->citeme->add(cite_pair_agni);
+
+ single_enable = 0;
+ restartinfo = 0;
+ one_coeff = 1;
+ manybody_flag = 1;
+
+ nelements = 0;
+ elements = NULL;
+ nparams = 0;
+ params = NULL;
+ map = NULL;
+}
+
+/* ----------------------------------------------------------------------
+ check if allocated, since class can be destructed when incomplete
+------------------------------------------------------------------------- */
+
+PairAGNI::~PairAGNI()
+{
+ if (elements)
+ for (int i = 0; i < nelements; i++) delete [] elements[i];
+ delete [] elements;
+ memory->destroy(params);
+
+ if (allocated) {
+ memory->destroy(setflag);
+ memory->destroy(cutsq);
+ delete [] map;
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairAGNI::compute(int eflag, int vflag)
+{
+ int i,j,k,ii,jj,kk,inum,jnum,jnumm1;
+ int itype,jtype,ktype,ijparam,ikparam,ijkparam;
+ tagint itag,jtag;
+ double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
+ double rsq,rsq1,rsq2;
+ double delr1[3],delr2[3],fj[3],fk[3];
+ int *ilist,*jlist,*numneigh,**firstneigh;
+
+ evdwl = 0.0;
+ if (eflag || vflag) ev_setup(eflag,vflag);
+ else evflag = vflag_fdotr = 0;
+
+ double **x = atom->x;
+ double **f = atom->f;
+ tagint *tag = atom->tag;
+ int *type = atom->type;
+ int nlocal = atom->nlocal;
+ int newton_pair = force->newton_pair;
+
+ inum = list->inum;
+ ilist = list->ilist;
+ numneigh = list->numneigh;
+ firstneigh = list->firstneigh;
+
+ double fxtmp,fytmp,fztmp;
+
+ // loop over full neighbor list of my atoms
+
+ for (ii = 0; ii < inum; ii++) {
+ i = ilist[ii];
+ itag = tag[i];
+ itype = map[type[i]];
+ xtmp = x[i][0];
+ ytmp = x[i][1];
+ ztmp = x[i][2];
+ fxtmp = fytmp = fztmp = 0.0;
+
+ jlist = firstneigh[i];
+ jnum = numneigh[i];
+
+ for (jj = 0; jj < jnum; jj++) {
+ j = jlist[jj];
+ 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 = map[type[j]];
+ // ijparam = elem2param[itype][jtype];
+ if (rsq < params[ijparam].cutsq) {
+
+ // XXX compute force
+
+ fxtmp += delx*fpair;
+ fytmp += dely*fpair;
+ fztmp += delz*fpair;
+
+ if (evflag) ev_tally(i,j,nlocal,newton_pair,
+ 0,0.0,fpair,delx,dely,delz);
+ }
+ }
+ f[i][0] += fxtmp;
+ f[i][1] += fytmp;
+ f[i][2] += fztmp;
+ }
+
+ if (vflag_fdotr) virial_fdotr_compute();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairAGNI::allocate()
+{
+ allocated = 1;
+ int n = atom->ntypes;
+
+ memory->create(setflag,n+1,n+1,"pair:setflag");
+ memory->create(cutsq,n+1,n+1,"pair:cutsq");
+ map = new int[n+1];
+}
+
+/* ----------------------------------------------------------------------
+ global settings
+------------------------------------------------------------------------- */
+
+void PairAGNI::settings(int narg, char **arg)
+{
+ if (narg != 0) error->all(FLERR,"Illegal pair_style command");
+}
+
+/* ----------------------------------------------------------------------
+ set coeffs for one or more type pairs
+------------------------------------------------------------------------- */
+
+void PairAGNI::coeff(int narg, char **arg)
+{
+ int i,j,n;
+
+ if (!allocated) allocate();
+
+ if (narg != 3 + atom->ntypes)
+ error->all(FLERR,"Incorrect args for pair coefficients");
+
+ // insure I,J args are * *
+
+ if (strcmp(arg[0],"*") != 0 || strcmp(arg[1],"*") != 0)
+ error->all(FLERR,"Incorrect args for pair coefficients");
+
+ // read args that map atom types to elements in potential file
+ // map[i] = which element the Ith atom type is, -1 if NULL
+ // nelements = # of unique elements
+ // elements = list of element names
+
+ if (elements) {
+ for (i = 0; i < nelements; i++) delete [] elements[i];
+ delete [] elements;
+ }
+ elements = new char*[atom->ntypes];
+ for (i = 0; i < atom->ntypes; i++) elements[i] = NULL;
+
+ nelements = 0;
+ for (i = 3; i < narg; i++) {
+ if (strcmp(arg[i],"NULL") == 0) {
+ map[i-2] = -1;
+ continue;
+ }
+ for (j = 0; j < nelements; j++)
+ if (strcmp(arg[i],elements[j]) == 0) break;
+ map[i-2] = j;
+ if (j == nelements) {
+ n = strlen(arg[i]) + 1;
+ elements[j] = new char[n];
+ strcpy(elements[j],arg[i]);
+ nelements++;
+ }
+ }
+
+ // read potential file and initialize potential parameters
+
+ read_file(arg[2]);
+ setup_params();
+
+ // clear setflag since coeff() called once with I,J = * *
+
+ n = atom->ntypes;
+ for (int i = 1; i <= n; i++)
+ for (int j = i; j <= n; j++)
+ setflag[i][j] = 0;
+
+ // set setflag i,j for type pairs where both are mapped to elements
+
+ int count = 0;
+ for (int i = 1; i <= n; i++)
+ for (int j = i; j <= n; j++)
+ if (map[i] >= 0 && map[j] >= 0) {
+ setflag[i][j] = 1;
+ count++;
+ }
+
+ if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
+}
+
+/* ----------------------------------------------------------------------
+ init specific to this pair style
+------------------------------------------------------------------------- */
+
+void PairAGNI::init_style()
+{
+ // need a full neighbor list
+
+ int irequest = neighbor->request(this,instance_me);
+ neighbor->requests[irequest]->half = 0;
+ neighbor->requests[irequest]->full = 1;
+}
+
+/* ----------------------------------------------------------------------
+ init for one type pair i,j and corresponding j,i
+------------------------------------------------------------------------- */
+
+double PairAGNI::init_one(int i, int j)
+{
+ if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");
+
+ return cutmax;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairAGNI::read_file(char *file)
+{
+ int params_per_line = 14;
+ char **words = new char*[params_per_line+1];
+
+ memory->sfree(params);
+ params = NULL;
+ nparams = 0;
+
+ // open file on proc 0
+
+ FILE *fp;
+ if (comm->me == 0) {
+ fp = force->open_potential(file);
+ if (fp == NULL) {
+ char str[128];
+ sprintf(str,"Cannot open AGNI potential file %s",file);
+ error->one(FLERR,str);
+ }
+ }
+
+ // read each set of params from potential file
+ // one set of params can span multiple lines
+ // store params if all 3 element tags are in element list
+
+ int n,nwords,ielement,jelement,kelement;
+ char line[MAXLINE],*ptr;
+ int eof = 0;
+
+ while (1) {
+ if (comm->me == 0) {
+ ptr = fgets(line,MAXLINE,fp);
+ if (ptr == NULL) {
+ eof = 1;
+ fclose(fp);
+ } else n = strlen(line) + 1;
+ }
+ MPI_Bcast(&eof,1,MPI_INT,0,world);
+ if (eof) break;
+ MPI_Bcast(&n,1,MPI_INT,0,world);
+ MPI_Bcast(line,n,MPI_CHAR,0,world);
+
+ // strip comment, skip line if blank
+
+ if ((ptr = strchr(line,'#'))) *ptr = '\0';
+ nwords = atom->count_words(line);
+ if (nwords == 0) continue;
+
+ // concatenate additional lines until have params_per_line words
+
+ while (nwords < params_per_line) {
+ n = strlen(line);
+ if (comm->me == 0) {
+ ptr = fgets(&line[n],MAXLINE-n,fp);
+ if (ptr == NULL) {
+ eof = 1;
+ fclose(fp);
+ } else n = strlen(line) + 1;
+ }
+ MPI_Bcast(&eof,1,MPI_INT,0,world);
+ if (eof) break;
+ MPI_Bcast(&n,1,MPI_INT,0,world);
+ MPI_Bcast(line,n,MPI_CHAR,0,world);
+ if ((ptr = strchr(line,'#'))) *ptr = '\0';
+ nwords = atom->count_words(line);
+ }
+
+ if (nwords != params_per_line)
+ error->all(FLERR,"Incorrect format in Stillinger-Weber potential file");
+
+ // words = ptrs to all words in line
+
+ nwords = 0;
+ words[nwords++] = strtok(line," \t\n\r\f");
+ while ((words[nwords++] = strtok(NULL," \t\n\r\f"))) continue;
+
+ // ielement,jelement,kelement = 1st args
+ // if all 3 args are in element list, then parse this line
+ // else skip to next entry in file
+
+ for (ielement = 0; ielement < nelements; ielement++)
+ if (strcmp(words[0],elements[ielement]) == 0) break;
+ if (ielement == nelements) continue;
+ for (jelement = 0; jelement < nelements; jelement++)
+ if (strcmp(words[1],elements[jelement]) == 0) break;
+ if (jelement == nelements) continue;
+ for (kelement = 0; kelement < nelements; kelement++)
+ if (strcmp(words[2],elements[kelement]) == 0) break;
+ if (kelement == nelements) continue;
+
+ // load up parameter settings and error check their values
+
+ params[nparams].ielement = ielement;
+ params[nparams].jelement = jelement;
+ params[nparams].epsilon = atof(words[3]);
+ params[nparams].sigma = atof(words[4]);
+
+ if (params[nparams].epsilon < 0.0 || params[nparams].sigma < 0.0)
+ error->all(FLERR,"Illegal AGNI parameter");
+
+ nparams++;
+ }
+
+ delete [] words;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairAGNI::setup_params()
+{
+ int i,j,k,m,n;
+ double rtmp;
+
+#if 0
+ // set elem2param for all triplet combinations
+ // must be a single exact match to lines read from file
+ // do not allow for ACB in place of ABC
+
+ memory->destroy(elem2param);
+ memory->create(elem2param,nelements,nelements,nelements,"pair:elem2param");
+
+ for (i = 0; i < nelements; i++)
+ for (j = 0; j < nelements; j++)
+ for (k = 0; k < nelements; k++) {
+ n = -1;
+ for (m = 0; m < nparams; m++) {
+ if (i == params[m].ielement && j == params[m].jelement &&
+ k == params[m].kelement) {
+ if (n >= 0) error->all(FLERR,"Potential file has duplicate entry");
+ n = m;
+ }
+ }
+ if (n < 0) error->all(FLERR,"Potential file is missing an entry");
+ elem2param[i][j][k] = n;
+ }
+
+
+ // compute parameter values derived from inputs
+
+ // set cutsq using shortcut to reduce neighbor list for accelerated
+ // calculations. cut must remain unchanged as it is a potential parameter
+ // (cut = a*sigma)
+
+ for (m = 0; m < nparams; m++) {
+ params[m].cut = params[m].sigma*params[m].littlea;
+
+ rtmp = params[m].cut;
+ if (params[m].tol > 0.0) {
+ if (params[m].tol > 0.01) params[m].tol = 0.01;
+ if (params[m].gamma < 1.0)
+ rtmp = rtmp +
+ params[m].gamma * params[m].sigma / log(params[m].tol);
+ else rtmp = rtmp +
+ params[m].sigma / log(params[m].tol);
+ }
+ params[m].cutsq = rtmp * rtmp;
+
+ params[m].sigma_gamma = params[m].sigma*params[m].gamma;
+ params[m].lambda_epsilon = params[m].lambda*params[m].epsilon;
+ params[m].lambda_epsilon2 = 2.0*params[m].lambda*params[m].epsilon;
+ params[m].c1 = params[m].biga*params[m].epsilon *
+ params[m].powerp*params[m].bigb *
+ pow(params[m].sigma,params[m].powerp);
+ params[m].c2 = params[m].biga*params[m].epsilon*params[m].powerq *
+ pow(params[m].sigma,params[m].powerq);
+ params[m].c3 = params[m].biga*params[m].epsilon*params[m].bigb *
+ pow(params[m].sigma,params[m].powerp+1.0);
+ params[m].c4 = params[m].biga*params[m].epsilon *
+ pow(params[m].sigma,params[m].powerq+1.0);
+ params[m].c5 = params[m].biga*params[m].epsilon*params[m].bigb *
+ pow(params[m].sigma,params[m].powerp);
+ params[m].c6 = params[m].biga*params[m].epsilon *
+ pow(params[m].sigma,params[m].powerq);
+ }
+
+ // set cutmax to max of all params
+
+ cutmax = 0.0;
+ for (m = 0; m < nparams; m++) {
+ rtmp = sqrt(params[m].cutsq);
+ if (rtmp > cutmax) cutmax = rtmp;
+ }
+#endif
+}
+
diff --git a/src/USER-MISC/pair_agni.h b/src/USER-MISC/pair_agni.h
new file mode 100644
index 0000000000..9b3631f1b0
--- /dev/null
+++ b/src/USER-MISC/pair_agni.h
@@ -0,0 +1,83 @@
+/* -*- 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(agni,PairAGNI)
+
+#else
+
+#ifndef LMP_PAIR_AGNI_H
+#define LMP_PAIR_AGNI_H
+
+#include "pair.h"
+
+namespace LAMMPS_NS {
+
+class PairAGNI : public Pair {
+ public:
+ PairAGNI(class LAMMPS *);
+ virtual ~PairAGNI();
+ virtual void compute(int, int);
+ void settings(int, char **);
+ virtual void coeff(int, char **);
+ virtual double init_one(int, int);
+ virtual void init_style();
+
+ struct Param {
+ double epsilon,sigma;
+ double cut,cutsq;
+ int ielement,jelement;
+ };
+
+ protected:
+ double cutmax; // max cutoff for all elements
+ int nelements; // # of unique atom type labels
+ char **elements; // names of unique elements
+ int *map; // mapping from atom types to elements
+ int nparams; // # of stored parameter sets
+ Param *params; // parameter set for an I-J interaction
+
+ virtual void allocate();
+ void read_file(char *);
+ virtual void setup_params();
+};
+
+}
+
+#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: Cannot open AGNI potential file %s
+
+The specified AGNI potential file cannot be opened. Check that the path
+and name are correct.
+
+E: Incorrect format in AGNI potential file
+
+The potential file is not compatible with the AGNI pair style
+implementation in this LAMMPS version.
+
+*/
--
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