add gao-weber potentials (regular and with ZBL core) with SiC potential files

NOTE: documentation is missing

potentials/SiC.gw

+# DATE: 2016-05-06 CONTRIBUTOR: German Samolyuk, samolyuk@gmail.com CITATION: ???
+# Gao-Weber parameters for various elements and mixtures
+# multiple entries can be added to this file, LAMMPS reads the ones it needs
+# these entries are in LAMMPS "metal" units:
+
+# format of a single entry (one or more lines):
+#   element 1, element 2, element 3, 
+#        m,  gamma, lambda3, c,     d,       h,          n,        beta,   lambda2, X_ij*B,  R,   D, lambda1, A
+
+#E1 E2 E3 m gamma lambda3 c d h n beta lambda2 B R D lambda1 A
+
+Si Si Si 1 0.013318 0 14 2.1 -1 0.78000 1 1.80821400248640 632.658058300867 2.35 0.15 2.38684248328205 1708.79738703139
+Si Si C  1 0.013318 0 14 2.1 -1 0.78000 1 1.80821400248640 632.658058300867 2.35 0.15 2.38684248328205 1708.79738703139
+Si C  Si 1 0.013318 0 14 2.1 -1 0.78000 1 1.96859970919818 428.946015420752 2.35 0.15 3.03361215187440 1820.05673775234
+C  Si Si 1 0.011304 0 19 2.5 -1 0.80468 1 1.96859970919818 428.946015420752 2.35 0.15 3.03361215187440 1820.05673775234
+C  C  Si 1 0.011304 0 19 2.5 -1 0.80469 1 1.76776695296637 203.208547714849 2.35 0.15 2.54558441227157 458.510465798439
+C  Si C  1 0.011304 0 19 2.5 -1 0.80469 1 1.96859970919818 428.946015420752 2.35 0.15 3.03361215187440 1820.05673775234
+Si C  C  1 0.013318 0 14 2.1 -1 0.78000 1 1.96859970919818 428.946015420752 2.35 0.15 3.03361215187440 1820.05673775234
+C  C  C  1 0.011304 0 19 2.5 -1 0.80469 1 1.76776695296637 203.208547714849 2.35 0.15 2.54558441227157 458.510465798439

potentials/SiC.gw.zbl

+# DATE: 2016-05-06 CONTRIBUTOR: German Samolyuk, samolyuk@gmail.com CITATION: ???
+# Gao-Weber parameters for various elements and mixtures
+# multiple entries can be added to this file, LAMMPS reads the ones it needs
+# these entries are in LAMMPS "metal" units:
+
+# format of a single entry (one or more lines):
+#   element 1, element 2, element 3, 
+#        m,  gamma, lambda3, c,     d,       h,          n,        beta,   lambda2, X_ij*B,  R,   D, lambda1, A
+
+#E1 E2 E3 m gamma lambda3 c d h n beta lambda2 B R D lambda1 A Z_i, Z_j, ZBLcut, ZBLexpscale
+
+Si Si Si 1 0.013318 0 14 2.1 -1 0.78000 1 1.80821400248640 632.658058300867 2.35 0.15 2.38684248328205 1708.79738703139 14 14 .95   14
+Si Si C  1 0.013318 0 14 2.1 -1 0.78000 1 1.80821400248640 632.658058300867 2.35 0.15 2.38684248328205 1708.79738703139 14 14 .95   14
+Si C  Si 1 0.013318 0 14 2.1 -1 0.78000 1 1.96859970919818 428.946015420752 2.35 0.15 3.03361215187440 1820.05673775234 14 6  .95   14
+C  Si Si 1 0.011304 0 19 2.5 -1 0.80468 1 1.96859970919818 428.946015420752 2.35 0.15 3.03361215187440 1820.05673775234 6  14 .95   14
+C  C  Si 1 0.011304 0 19 2.5 -1 0.80469 1 1.76776695296637 203.208547714849 2.35 0.15 2.54558441227157 458.510465798439 6  6  .95   14
+C  Si C  1 0.011304 0 19 2.5 -1 0.80469 1 1.96859970919818 428.946015420752 2.35 0.15 3.03361215187440 1820.05673775234 6  14 .95   14
+Si C  C  1 0.013318 0 14 2.1 -1 0.78000 1 1.96859970919818 428.946015420752 2.35 0.15 3.03361215187440 1820.05673775234 14 6  .95   14
+C  C  C  1 0.011304 0 19 2.5 -1 0.80469 1 1.76776695296637 203.208547714849 2.35 0.15 2.54558441227157 458.510465798439 6  6  .95   14

src/MANYBODY/pair_gw.h

+/* -*- 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(gw,PairGW)
+
+#else
+
+#ifndef LMP_PAIR_GW_H
+#define LMP_PAIR_GW_H
+
+#include "pair.h"
+
+namespace LAMMPS_NS {
+
+class PairGW : public Pair {
+ public:
+  PairGW(class LAMMPS *);
+  virtual ~PairGW();
+  virtual void compute(int, int);
+  void settings(int, char **);
+  void coeff(int, char **);
+  void init_style();
+  double init_one(int, int);
+
+ protected:
+  struct Param {
+    double lam1,lam2,lam3;
+    double c,d,h;
+    double gamma,powerm;
+    double powern,beta;
+    double biga,bigb,bigd,bigr;
+    double cut,cutsq;
+    double c1,c2,c3,c4;
+    int ielement,jelement,kelement;
+    int powermint;
+    double Z_i,Z_j;
+    double ZBLcut,ZBLexpscale;
+  };
+
+  Param *params;                // parameter set for an I-J-K interaction
+  char **elements;              // names of unique elements
+  int ***elem2param;            // mapping from element triplets to paramegw
+  int *map;                     // mapping from atom types to elements
+  double cutmax;                // max cutoff for all elements
+  int nelements;                // # of unique elements
+  int nparams;                  // # of stored parameter sets
+  int maxparam;                 // max # of parameter sets
+
+  int **pages;                     // neighbor list pages
+  int maxlocal;                    // size of numneigh, firstneigh arrays
+  int maxpage;                     // # of pages currently allocated
+  int pgsize;                      // size of neighbor page
+  int oneatom;                     // max # of neighbors for one atom
+
+
+  int *GW_numneigh;             // # of pair neighbors for each atom
+  int **GW_firstneigh;          // ptr to 1st neighbor of each atom
+
+  void GW_neigh();
+  void add_pages(int howmany = 1);
+
+  void allocate();
+  virtual void read_file(char *);
+  void setup_params();
+  virtual void repulsive(Param *, double, double &, int, double &);
+  double zeta(Param *, double, double, double *, double *);
+  virtual void force_zeta(Param *, double, double, double &,
+                          double &, int, double &);
+  void attractive(Param *, double, double, double, double *, double *,
+                  double *, double *, double *);
+
+  double gw_fc(double, Param *);
+  double gw_fc_d(double, Param *);
+  virtual double gw_fa(double, Param *);
+  virtual double gw_fa_d(double, Param *);
+  double gw_bij(double, Param *);
+  double gw_bij_d(double, Param *);
+
+  void gw_zetaterm_d(double, double *, double, double *, double,
+                               double *, double *, double *, Param *);
+  void costheta_d(double *, double, double *, double,
+                  double *, double *, double *);
+
+  // inlined functions for efficiency
+
+  inline double gw_gijk(const double costheta,
+                          const Param * const param) const {
+    const double gw_c = param->c * param->c;
+    const double gw_d = param->d * param->d;
+    const double hcth = param->h - costheta;
+
+	  //printf("gw_gijk: gw_c=%f gw_d=%f hcth=%f=%f-%f\n", gw_c, gw_d, hcth, param->h, costheta);
+
+    return param->gamma*(1.0 + gw_c/gw_d - gw_c / (gw_d + hcth*hcth));
+  }
+
+  inline double gw_gijk_d(const double costheta,
+                            const Param * const param) const {
+    const double gw_c = param->c * param->c;
+    const double gw_d = param->d * param->d;
+    const double hcth = param->h - costheta;
+    const double numerator = -2.0 * gw_c * hcth;
+    const double denominator = 1.0/(gw_d + hcth*hcth);
+    return param->gamma*numerator*denominator*denominator;
+  }
+
+  inline double vec3_dot(const double x[3], const double y[3]) const {
+    return x[0]*y[0] + x[1]*y[1] + x[2]*y[2];
+  }
+
+  inline void vec3_add(const double x[3], const double y[3],
+                       double * const z) const {
+    z[0] = x[0]+y[0];  z[1] = x[1]+y[1];  z[2] = x[2]+y[2];
+  }
+
+  inline void vec3_scale(const double k, const double x[3],
+                         double y[3]) const {
+    y[0] = k*x[0];  y[1] = k*x[1];  y[2] = k*x[2];
+  }
+
+  inline void vec3_scaleadd(const double k, const double x[3],
+                            const double y[3], double * const z) const {
+    z[0] = k*x[0]+y[0];
+    z[1] = k*x[1]+y[1];
+    z[2] = k*x[2]+y[2];
+  }
+};
+
+}
+
+#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 GW requires atom IDs
+
+This is a requirement to use the GW potential.
+
+E: Pair style GW requires newton pair on
+
+See the newton command.  This is a restriction to use the GW
+potential.
+
+E: All pair coeffs are not set
+
+All pair coefficients must be set in the data file or by the
+pair_coeff command before running a simulation.
+
+E: Cannot open GW potential file %s
+
+The specified GW potential file cannot be opened.  Check that the
+path and name are correct.
+
+E: Incorrect format in GW potential file
+
+Incorrect number of words per line in the potential file.
+
+E: Illegal GW parameter
+
+One or more of the coefficients defined in the potential file is
+invalid.
+
+E: Potential file has duplicate entry
+
+The potential file for a SW or GW potential has more than
+one entry for the same 3 ordered elements.
+
+E: Potential file is missing an entry
+
+The potential file for a SW or GW potential does not have a
+needed entry.
+
+*/

src/MANYBODY/pair_gw_zbl.cpp

+/* ----------------------------------------------------------------------
+   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: German Samolyuk (ORNL)
+   Based on PairTersoffZBL by Aidan Thompson (SNL) and David Farrell (NWU)
+------------------------------------------------------------------------- */
+
+#include <math.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include "pair_gw_zbl.h"
+#include "atom.h"
+#include "update.h"
+#include "neighbor.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "force.h"
+#include "comm.h"
+#include "memory.h"
+#include "error.h"
+
+#include "math_const.h"
+using namespace LAMMPS_NS;
+using namespace MathConst;
+
+#define MAXLINE 1024
+#define DELTA 4
+
+/* ---------------------------------------------------------------------- */
+
+PairGWZBL::PairGWZBL(LAMMPS *lmp) : PairGW(lmp)
+{
+  // hard-wired constants in metal or real units
+  // a0 = Bohr radius
+  // epsilon0 = permittivity of vacuum = q / energy-distance units
+  // e = unit charge
+  // 1 Kcal/mole = 0.043365121 eV
+
+  if (strcmp(update->unit_style,"metal") == 0) {
+    global_a_0 = 0.529;
+    global_epsilon_0 = 0.00552635;
+    global_e = 1.0;
+  } else if (strcmp(update->unit_style,"real") == 0) {
+    global_a_0 = 0.529;
+    global_epsilon_0 = 0.00552635 * 0.043365121;
+    global_e = 1.0;
+  } else error->all(FLERR,"Pair gw/zbl requires metal or real units");
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairGWZBL::read_file(char *file)
+{
+  int params_per_line = 21;
+  char **words = new char*[params_per_line+1];
+
+  memory->sfree(params);
+  params = NULL;
+  nparams = maxparam = 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 GW potential file %s",file);
+      error->one(FLERR,str);
+    }
+  }
+
+  // read each line out of file, skipping blank lines or leading '#'
+  // store line of 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 GW 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 line
+
+    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
+
+    if (nparams == maxparam) {
+      maxparam += DELTA;
+      params = (Param *) memory->srealloc(params,maxparam*sizeof(Param),
+                                          "pair:params");
+    }
+
+    params[nparams].ielement = ielement;
+    params[nparams].jelement = jelement;
+    params[nparams].kelement = kelement;
+    params[nparams].powerm = atof(words[3]);
+    params[nparams].gamma = atof(words[4]);
+    params[nparams].lam3 = atof(words[5]);
+    params[nparams].c = atof(words[6]);
+    params[nparams].d = atof(words[7]);
+    params[nparams].h = atof(words[8]);
+    params[nparams].powern = atof(words[9]);
+    params[nparams].beta = atof(words[10]);
+    params[nparams].lam2 = atof(words[11]);
+    params[nparams].bigb = atof(words[12]);
+    params[nparams].bigr = atof(words[13]);
+    params[nparams].bigd = atof(words[14]);
+    params[nparams].lam1 = atof(words[15]);
+    params[nparams].biga = atof(words[16]);
+    params[nparams].Z_i = atof(words[17]);
+    params[nparams].Z_j = atof(words[18]);
+    params[nparams].ZBLcut = atof(words[19]);
+    params[nparams].ZBLexpscale = atof(words[20]);
+
+    // currently only allow m exponent of 1 or 3
+
+    params[nparams].powermint = int(params[nparams].powerm);
+
+    if (
+        params[nparams].lam3 < 0.0 || params[nparams].c < 0.0 ||
+        params[nparams].d < 0.0 || params[nparams].powern < 0.0 ||
+        params[nparams].beta < 0.0 || params[nparams].lam2 < 0.0 ||
+        params[nparams].bigb < 0.0 || params[nparams].bigr < 0.0 ||
+        params[nparams].bigd < 0.0 ||
+        params[nparams].bigd > params[nparams].bigr ||
+        params[nparams].lam3 < 0.0 || params[nparams].biga < 0.0 ||
+        params[nparams].powerm - params[nparams].powermint != 0.0 ||
+        (params[nparams].powermint != 3 && params[nparams].powermint != 1) ||
+        params[nparams].gamma < 0.0 ||
+        params[nparams].Z_i < 1.0 || params[nparams].Z_j < 1.0 ||
+        params[nparams].ZBLcut < 0.0 || params[nparams].ZBLexpscale < 0.0)
+      error->all(FLERR,"Illegal GW parameter");
+
+    nparams++;
+  }
+
+  delete [] words;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void PairGWZBL::repulsive(Param *param, double rsq, double &fforce,
+                               int eflag, double &eng)
+{
+  double r,tmp_fc,tmp_fc_d,tmp_exp;
+
+  // GW repulsive portion
+
+  r = sqrt(rsq);
+  tmp_fc = gw_fc(r,param);
+  tmp_fc_d = gw_fc_d(r,param);
+  tmp_exp = exp(-param->lam1 * r);
+  double fforce_gw = param->biga * tmp_exp * (tmp_fc_d - tmp_fc*param->lam1);
+  double eng_gw = tmp_fc * param->biga * tmp_exp;
+
+  // ZBL repulsive portion
+
+  double esq = pow(global_e,2.0);
+  double a_ij = (0.8854*global_a_0) /
+    (pow(param->Z_i,0.23) + pow(param->Z_j,0.23));
+  double premult = (param->Z_i * param->Z_j * esq)/(4.0*MY_PI*global_epsilon_0);
+  double r_ov_a = r/a_ij;
+  double phi = 0.1818*exp(-3.2*r_ov_a) + 0.5099*exp(-0.9423*r_ov_a) +
+    0.2802*exp(-0.4029*r_ov_a) + 0.02817*exp(-0.2016*r_ov_a);
+  double dphi = (1.0/a_ij) * (-3.2*0.1818*exp(-3.2*r_ov_a) -
+                              0.9423*0.5099*exp(-0.9423*r_ov_a) -
+                              0.4029*0.2802*exp(-0.4029*r_ov_a) -
+                              0.2016*0.02817*exp(-0.2016*r_ov_a));
+  double fforce_ZBL = premult*-phi/rsq + premult*dphi/r;
+  double eng_ZBL = premult*(1.0/r)*phi;
+
+  // combine two parts with smoothing by Fermi-like function
+
+  fforce = -(-F_fermi_d(r,param) * eng_ZBL +
+             (1.0 - F_fermi(r,param))*fforce_ZBL +
+             F_fermi_d(r,param)*eng_gw + F_fermi(r,param)*fforce_gw) / r;
+
+  if (eflag)
+    eng = (1.0 - F_fermi(r,param))*eng_ZBL + F_fermi(r,param)*eng_gw;
+}
+
+/* ---------------------------------------------------------------------- */
+
+double PairGWZBL::gw_fa(double r, Param *param)
+{
+  if (r > param->bigr + param->bigd) return 0.0;
+  return -param->bigb * exp(-param->lam2 * r) * gw_fc(r,param) *
+    F_fermi(r,param);
+}
+
+/* ---------------------------------------------------------------------- */
+
+double PairGWZBL::gw_fa_d(double r, Param *param)
+{
+  if (r > param->bigr + param->bigd) return 0.0;
+  return param->bigb * exp(-param->lam2 * r) *
+    (param->lam2 * gw_fc(r,param) * F_fermi(r,param) -
+     gw_fc_d(r,param) * F_fermi(r,param) - gw_fc(r,param) *
+     F_fermi_d(r,param));
+}
+
+/* ----------------------------------------------------------------------
+   Fermi-like smoothing function
+------------------------------------------------------------------------- */
+
+double PairGWZBL::F_fermi(double r, Param *param)
+{
+  return 1.0 / (1.0 + exp(-param->ZBLexpscale*(r-param->ZBLcut)));
+}
+
+/* ----------------------------------------------------------------------
+   Fermi-like smoothing function derivative with respect to r
+------------------------------------------------------------------------- */
+
+double PairGWZBL::F_fermi_d(double r, Param *param)
+{
+  return param->ZBLexpscale*exp(-param->ZBLexpscale*(r-param->ZBLcut)) /
+    pow(1.0 + exp(-param->ZBLexpscale*(r-param->ZBLcut)),2.0);
+}

src/MANYBODY/pair_gw_zbl.h

+/* -*- 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(gw/zbl,PairGWZBL)
+
+#else
+
+#ifndef LMP_PAIR_GW_ZBL_H
+#define LMP_PAIR_GW_ZBL_H
+
+#include "pair_gw.h"
+
+namespace LAMMPS_NS {
+
+class PairGWZBL : public PairGW {
+ public:
+  PairGWZBL(class LAMMPS *);
+  ~PairGWZBL() {}
+
+ private:
+  double global_a_0;                // Bohr radius for Coulomb repulsion
+  double global_epsilon_0;        // permittivity of vacuum for Coulomb repulsion
+  double global_e;                // proton charge (negative of electron charge)
+
+  void read_file(char *);
+  void repulsive(Param *, double, double &, int, double &);
+
+  double gw_fa(double, Param *);
+  double gw_fa_d(double, Param *);
+
+  double F_fermi(double, Param *);
+  double F_fermi_d(double, Param *);
+};
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Pair GW/zbl requires metal or real units
+
+This is a current restriction of this pair potential.
+
+E: Cannot open GW potential file %s
+
+The specified GW potential file cannot be opened.  Check that the
+path and name are correct.
+
+E: Incorrect format in GW potential file
+
+Incorrect number of words per line in the potential file.
+
+E: Illegal GW parameter
+
+One or more of the coefficients defined in the potential file is
+invalid.
+
+*/