LAMMPS_NS::PairHDNNPExternal Class Reference

#include <pair_hdnnp_external.h>

Inheritance diagram for LAMMPS_NS::PairHDNNPExternal:

Collaboration diagram for LAMMPS_NS::PairHDNNPExternal:

Public Member Functions
	PairHDNNPExternal (class LAMMPS *)
	~PairHDNNPExternal () override
void	compute (int, int) override
void	settings (int, char **) override
void	coeff (int, char **) override
void	init_style () override
double	init_one (int, int) override

Protected Member Functions
virtual void	allocate ()

Protected Attributes
double	cflength
double	cfenergy
double	maxCutoffRadius
char *	directory
char *	elements
char *	command
nnp::ElementMap	em
nnp::Structure	structure

Detailed Description

Definition at line 32 of file pair_hdnnp_external.h.

Constructor & Destructor Documentation

PairHDNNPExternal()

PairHDNNPExternal::PairHDNNPExternal

(

class LAMMPS *

lmp

)

Definition at line 38 of file pair_hdnnp_external.cpp.

                                                : Pair(lmp)
{
}

~PairHDNNPExternal()

PairHDNNPExternal::~PairHDNNPExternal ( )

override

Definition at line 46 of file pair_hdnnp_external.cpp.

{
}

Member Function Documentation

compute()

void PairHDNNPExternal::compute ( int  eflag, int  vflag  )

override

Definition at line 52 of file pair_hdnnp_external.cpp.

{
  if(eflag || vflag) ev_setup(eflag,vflag);
  else evflag = vflag_fdotr = eflag_global = eflag_atom = 0;
 
  // Clear structure completely.
  structure.reset();
 
  // Set simulation box.
  if (domain->nonperiodic < 2) structure.isPeriodic = true;
  else structure.isPeriodic = false;
  if (structure.isPeriodic) structure.isTriclinic = (bool)domain->triclinic;
  structure.box[0][0] = domain->h[0] * cflength;
  structure.box[0][1] = 0.0;
  structure.box[0][2] = 0.0;
  structure.box[1][0] = domain->h[5] * cflength;
  structure.box[1][1] = domain->h[1] * cflength;
  structure.box[1][2] = 0.0;
  structure.box[2][0] = domain->h[4] * cflength;
  structure.box[2][1] = domain->h[3] * cflength;
  structure.box[2][2] = domain->h[2] * cflength;
 
  // Fill structure with atoms.
  for (int i = 0; i < atom->nlocal; ++i)
  {
    structure.atoms.push_back(nnp::Atom());
    nnp::Atom& a = structure.atoms.back();
    a.r[0] = atom->x[i][0] * cflength;
    a.r[1] = atom->x[i][1] * cflength;
    a.r[2] = atom->x[i][2] * cflength;
    a.element = atom->type[i] - 1;
    structure.numAtoms++;
  }
 
  // Write "input.data" file to disk.
  structure.writeToFile(string(directory) + "input.data");
 
  // Run external command and throw away stdout output.
  string com = "cd " + string(directory) + "; " + string(command) + " > external.out";
  system(com.c_str());
 
  // Read back in total potential energy.
  ifstream f;
  f.open(string(directory) + "energy.out");
  if (!f.is_open()) error->all(FLERR,"Could not open energy output file");
  string line;
  double energy = 0.0;
  getline(f, line); // Ignore first line, RuNNer and n2p2 have header here.
  while (getline(f, line))
  {
    if ((line.size() > 0) && (line.at(0) != '#')) // Ignore n2p2 header.
    {
      // 4th columns contains NNP energy.
      sscanf(line.c_str(), "%*s %*s %*s %lf", &energy);
    }
  }
  f.close();
  energy /= cfenergy;
 
  // Add energy contribution to total energy.
  if (eflag_global)
     ev_tally(0,0,atom->nlocal,1,energy,0.0,0.0,0.0,0.0,0.0);
 
  // Read back in forces.
  f.open(string(directory) + "nnforces.out");
  if (!f.is_open()) error->all(FLERR,"Could not open force output file");
  int c = 0;
  double const cfforce = cfenergy / cflength;
  getline(f, line); // Ignore first line, RuNNer and n2p2 have header here.
  while (getline(f, line))
  {
    if ((line.size() > 0) && (line.at(0) != '#')) // Ignore n2p2 header.
    {
      if (c > atom->nlocal - 1) error->all(FLERR,"Too many atoms in force file.");
      double fx;
      double fy;
      double fz;
      sscanf(line.c_str(), "%*s %*s %*s %*s %*s %lf %lf %lf", &fx, &fy, &fz);
      atom->f[c][0] = fx / cfforce;
      atom->f[c][1] = fy / cfforce;
      atom->f[c][2] = fz / cfforce;
      c++;
    }
  }
 
  f.close();
 
  // If virial needed calculate via F dot r.
  // TODO: Pressure calculation is probably wrong anyway, tell user only to use
  // in NVE, NVT ensemble.
  if (vflag_fdotr) virial_fdotr_compute();
}

References nnp::Structure::atoms, nnp::Structure::box, cfenergy, cflength, command, directory, nnp::Atom::element, nnp::Structure::isPeriodic, nnp::Structure::isTriclinic, nnp::Structure::numAtoms, nnp::Atom::r, nnp::Structure::reset(), structure, and nnp::Structure::writeToFile().

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settings()

void PairHDNNPExternal::settings ( int  narg, char **  arg  )

override

Definition at line 149 of file pair_hdnnp_external.cpp.

{
  int iarg = 0;
 
  // elements list is mandatory
  if (narg < 1) error->all(FLERR,"Illegal pair_style command");
 
  // element list, mandatory
  int len = strlen(arg[iarg]) + 1;
  elements = new char[len];
  sprintf(elements, "%s", arg[iarg]);
  iarg++;
  em.registerElements(elements);
  vector<FILE*> fp;
  if (screen) fp.push_back(screen);
  if (logfile) fp.push_back(logfile);
  structure.setElementMap(em);
 
  // default settings
  len = strlen("hdnnp/") + 1;
  directory = new char[len];
  strcpy(directory,"hdnnp/");
  len = strlen("nnp-predict 0") + 1;
  command = new char[len];
  strcpy(command,"nnp-predict 0");
  cflength = 1.0;
  cfenergy = 1.0;
 
  while(iarg < narg) {
    // set NNP directory
    if (strcmp(arg[iarg],"dir") == 0) {
      if (iarg+2 > narg)
        error->all(FLERR,"Illegal pair_style command");
      delete[] directory;
      len = strlen(arg[iarg+1]) + 2;
      directory = new char[len];
      sprintf(directory, "%s/", arg[iarg+1]);
      iarg += 2;
    // set external prediction command
    } else if (strcmp(arg[iarg],"command") == 0) {
      if (iarg+2 > narg)
        error->all(FLERR,"Illegal pair_style command");
      delete[] command;
      len = strlen(arg[iarg+1]) + 1;
      command = new char[len];
      sprintf(command, "%s", arg[iarg+1]);
      iarg += 2;
    // length unit conversion factor
    } else if (strcmp(arg[iarg],"cflength") == 0) {
      if (iarg+2 > narg)
        error->all(FLERR,"Illegal pair_style command");
      cflength = utils::numeric(FLERR,arg[iarg+1],false,lmp);
      iarg += 2;
    // energy unit conversion factor
    } else if (strcmp(arg[iarg],"cfenergy") == 0) {
      if (iarg+2 > narg)
        error->all(FLERR,"Illegal pair_style command");
      cfenergy = utils::numeric(FLERR,arg[iarg+1],false,lmp);
      iarg += 2;
    } else error->all(FLERR,"Illegal pair_style command");
  }
 
  for (auto f : fp)
  {
      fprintf(f, "*****************************************"
                 "**************************************\n");
      fprintf(f, "pair_style hdnnp/external settings:\n");
      fprintf(f, "-----------------------------------\n");
      fprintf(f, "elements = %s\n", elements);
      fprintf(f, "dir      = %s\n", directory);
      fprintf(f, "command  = %s\n", command);
      fprintf(f, "cflength = %16.8E\n", cflength);
      fprintf(f, "cfenergy = %16.8E\n", cfenergy);
      fprintf(f, "*****************************************"
                 "**************************************\n");
      fprintf(f, "CAUTION: Explicit element mapping is not available for hdnnp/external,\n");
      fprintf(f, "         please carefully check whether this map between LAMMPS\n");
      fprintf(f, "         atom types and element strings is correct:\n");
      fprintf(f, "---------------------------\n");
      fprintf(f, "LAMMPS type  |  NNP element\n");
      fprintf(f, "---------------------------\n");
      int lammpsNtypes = em.size();
      for (int i = 0; i < lammpsNtypes; ++i)
      {
          fprintf(f, "%11d <-> %2s (%3zu)\n",
                  i, em[i].c_str(), em.atomicNumber(i));
      }
      fprintf(f, "*****************************************"
                 "**************************************\n");
  }
}

References nnp::ElementMap::atomicNumber(), cfenergy, cflength, command, directory, elements, em, nnp::ElementMap::registerElements(), nnp::Structure::setElementMap(), nnp::ElementMap::size(), and structure.

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coeff()

void PairHDNNPExternal::coeff ( int  narg, char **  arg  )

override

Definition at line 245 of file pair_hdnnp_external.cpp.

{
  if (!allocated) allocate();
 
  if (narg != 3) error->all(FLERR,"Incorrect args for pair coefficients");
 
  int ilo,ihi,jlo,jhi;
  utils::bounds(FLERR,arg[0],1,atom->ntypes,ilo,ihi,error);
  utils::bounds(FLERR,arg[1],1,atom->ntypes,jlo,jhi,error);
 
  maxCutoffRadius = utils::numeric(FLERR,arg[2],false,lmp);
 
  // TODO: Check how this flag is set.
  int count = 0;
  for(int i=ilo; i<=ihi; i++) {
    for(int j=MAX(jlo,i); j<=jhi; j++) {
      setflag[i][j] = 1;
      count++;
    }
  }
 
  if (count == 0) error->all(FLERR,"Incorrect args for pair coefficients");
}

References allocate(), and maxCutoffRadius.

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init_style()

void PairHDNNPExternal::init_style ( )

override

Definition at line 273 of file pair_hdnnp_external.cpp.

{
  if (comm->nprocs > 1)
  {
    error->all(FLERR,"MPI is not supported for this pair_style");
  }
}

init_one()

double PairHDNNPExternal::init_one ( int  i, int  j  )

override

Definition at line 285 of file pair_hdnnp_external.cpp.

{
  // TODO: Check how this actually works for different cutoffs.
  return maxCutoffRadius;
}

References maxCutoffRadius.

allocate()

void PairHDNNPExternal::allocate ( )

protectedvirtual

Definition at line 295 of file pair_hdnnp_external.cpp.

{
  allocated = 1;
  int n = atom->ntypes;
 
  memory->create(setflag,n+1,n+1,"pair:setflag");
  for (int i = 1; i <= n; i++)
    for (int j = i; j <= n; j++)
      setflag[i][j] = 0;
 
  memory->create(cutsq,n+1,n+1,"pair:cutsq");
}

Referenced by coeff().

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Member Data Documentation

cflength

double LAMMPS_NS::PairHDNNPExternal::cflength

protected

Definition at line 46 of file pair_hdnnp_external.h.

Referenced by compute(), and settings().

cfenergy

double LAMMPS_NS::PairHDNNPExternal::cfenergy

protected

Definition at line 47 of file pair_hdnnp_external.h.

Referenced by compute(), and settings().

maxCutoffRadius

double LAMMPS_NS::PairHDNNPExternal::maxCutoffRadius

protected

Definition at line 48 of file pair_hdnnp_external.h.

Referenced by coeff(), and init_one().

directory

char* LAMMPS_NS::PairHDNNPExternal::directory

protected

Definition at line 49 of file pair_hdnnp_external.h.

Referenced by compute(), and settings().

elements

char* LAMMPS_NS::PairHDNNPExternal::elements

protected

Definition at line 50 of file pair_hdnnp_external.h.

Referenced by settings().

command

char* LAMMPS_NS::PairHDNNPExternal::command

protected

Definition at line 51 of file pair_hdnnp_external.h.

Referenced by compute(), and settings().

em

nnp::ElementMap LAMMPS_NS::PairHDNNPExternal::em

protected

Definition at line 52 of file pair_hdnnp_external.h.

Referenced by settings().

structure

nnp::Structure LAMMPS_NS::PairHDNNPExternal::structure

protected

Definition at line 53 of file pair_hdnnp_external.h.

Referenced by compute(), and settings().

---

The documentation for this class was generated from the following files:

• /home/runner/work/n2p2/n2p2/src/interface/LAMMPS/src/ML-HDNNP/pair_hdnnp_external.h
• /home/runner/work/n2p2/n2p2/src/interface/LAMMPS/src/ML-HDNNP/pair_hdnnp_external.cpp