Initial commit for pair style srp-react files
This commit is contained in:
Vaibhav Palkar
239
src/MISC/pair_srp_react.cpp
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239
src/MISC/pair_srp_react.cpp
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// clang-format off
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/* ----------------------------------------------------------------------
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LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
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https://www.lammps.org/, Sandia National Laboratories
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Steve Plimpton, sjplimp@sandia.gov
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Copyright (2003) Sandia Corporation. Under the terms of Contract
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DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
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certain rights in this software. This software is distributed under
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the GNU General Public License.
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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/* ----------------------------------------------------------------------
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Contributing author: Vaibhav Palkar (Kuksenok Lab, Clemson University)
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based on the pair srp code by Timothy Sirk (ARL)
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This pair style interfaces the pair style srp with the stochastic reaction
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fixes bond/break and bond/create by updating pseudo beads corresponding to
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bonds as bond breaking and formation takes place. This is useful in
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simulation of reactions in polymers with soft potentials such as DPD.
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See the doc page for pair_style srp/react command for usage instructions.
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There is an example script for this package in examples/PACKAGES/srp_react/.
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------------------------------------------------------------------------- */
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#include "pair_srp_react.h"
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#include "atom.h"
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#include "citeme.h"
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#include "comm.h"
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#include "domain.h"
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#include "error.h"
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#include "fix.h"
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#include "fix_srp_react.h"
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#include "force.h"
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#include "memory.h"
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#include "modify.h"
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#include "neigh_list.h"
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#include "neighbor.h"
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#include "output.h"
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#include "thermo.h"
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#include <cmath>
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#include <cstring>
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using namespace LAMMPS_NS;
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static const char cite_srpreact[] =
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"@Article{palkar2022\n"
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" author = {Palkar, Vaibhav and Kuksenok, Olga},\n"
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" title = {Controlling Degradation and Erosion of Polymer Networks: Insights from Mesoscale Modeling},\n"
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" journal = {J. Phys. Chem. B},\n"
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" year = {2022},\n"
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" volume = {126},\n"
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" pages = {336-346}\n"
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"}\n\n";
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static int srp_instance = 0;
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/* ----------------------------------------------------------------------
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constructor
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---------------------------------------------------------------------- */
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PairSRPREACT::PairSRPREACT(LAMMPS *lmp) : PairSRP(lmp)
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{
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if (lmp->citeme) lmp->citeme->add(cite_srpreact);
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// pair srp/react has its own fix, hence delete fix srp instance
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// created in the constructor of pair srp
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for( int ifix = 0; ifix<modify->nfix; ifix++)
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if( strcmp(modify->get_fix_by_index(ifix)->style, "SRP") == 0)
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modify->delete_fix(ifix);
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// similar to fix SRP, create fix SRP REACT instance here with unique fix id
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f_srp = (FixSRPREACT *) modify->add_fix(fmt::format("{:02d}_FIX_SRP_REACT all SRPREACT",srp_instance));
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++srp_instance;
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}
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/* ----------------------------------------------------------------------
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global settings
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------------------------------------------------------------------------- */
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void PairSRPREACT::settings(int narg, char **arg)
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{
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if (narg < 3 || narg > 8)
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error->all(FLERR,"Illegal pair_style command");
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if (atom->tag_enable == 0)
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error->all(FLERR,"Pair_style srp requires atom IDs");
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cut_global = utils::numeric(FLERR,arg[0],false,lmp);
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// wildcard
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if (strcmp(arg[1],"*") == 0) {
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btype = 0;
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} else {
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btype = utils::inumeric(FLERR,arg[1],false,lmp);
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if ((btype > atom->nbondtypes) || (btype <= 0))
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error->all(FLERR,"Illegal pair_style command");
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}
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// settings
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midpoint = false;
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min = false;
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if (strcmp(arg[2],"min") == 0) min = true;
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else if (strcmp(arg[2],"mid") == 0) midpoint = true;
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else
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error->all(FLERR,"Illegal pair_style command");
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// default for bond/break and bond/create settings
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bond_create=false;
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bond_break=false;
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idbreak = nullptr;
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idcreate= nullptr;
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// find whether id is of bond/break or bond/create
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const char* reactid = arg[3];
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if(strcmp(modify->get_fix_by_id(reactid)->style,"bond/break") == 0)
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{
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bond_break = true;
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int n = strlen(reactid) + 1;
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idbreak = new char[n];
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strcpy(idbreak,reactid);
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}
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else if(strcmp(modify->get_fix_by_id(reactid)->style,"bond/create") == 0)
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{
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bond_create = true;
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int n = strlen(reactid) + 1;
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idcreate = new char[n];
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strcpy(idcreate,reactid);
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}
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else
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error->all(FLERR,"Illegal pair_style command");
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int iarg = 4;
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// default exclude 1-2
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// scaling for 1-2, etc not supported
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exclude = 1;
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// use last atom type by default for bond particles
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bptype = atom->ntypes;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"exclude") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal pair srp command");
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exclude = utils::logical(FLERR, arg[iarg+1], false, lmp);
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if (min && !exclude) error->all(FLERR,"Illegal exclude option in pair srp command");
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iarg += 2;
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} else if (strcmp(arg[iarg],"bptype") == 0) {
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if (iarg+2 > narg) error->all(FLERR,"Illegal pair srp command");
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bptype = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
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if ((bptype < 1) || (bptype > atom->ntypes))
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error->all(FLERR,"Illegal bond particle type for srp");
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iarg += 2;
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} else error->all(FLERR,"Illegal pair srp command");
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}
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// reset cutoffs if explicitly set
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if (allocated) {
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int i,j;
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for (i = 1; i <= bptype; i++)
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for (j = i; j <= bptype; j++)
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if (setflag[i][j]) cut[i][j] = cut_global;
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}
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}
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/* ----------------------------------------------------------------------
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init specific to this pair style
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------------------------------------------------------------------------- */
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void PairSRPREACT::init_style()
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{
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if (!force->newton_pair)
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error->all(FLERR,"PairSRPREACT: Pair srp requires newton pair on");
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// verify that fix SRP is still defined and has not been changed.
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if (strcmp(f_srp->style,"SRPREACT") != 0)
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error->all(FLERR,"Fix SRP has been changed unexpectedly");
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if (comm->me == 0)
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utils::logmesg(lmp,"Using type {} for bond particles\n",bptype);
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// set bond and bond particle types in fix srp
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// bonds of this type will be represented by bond particles
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// if bond type is 0, then all bonds have bond particles
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// btype = bond type
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char c0[20];
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char* arg0[2];
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sprintf(c0, "%d", btype);
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arg0[0] = (char *) "btype";
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arg0[1] = c0;
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f_srp->modify_params(2, arg0);
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// bptype = bond particle type
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sprintf(c0, "%d", bptype);
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arg0[0] = (char *) "bptype";
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arg0[1] = c0;
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f_srp->modify_params(2, arg0);
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// if using fix bond/break, set id of fix bond/break in fix srp
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// idbreak = id of fix bond break
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if( bond_break )
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{
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sprintf(c0, "%s", idbreak);
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arg0[0] = (char *) "bond/break";
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arg0[1] = c0;
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f_srp->modify_params(2, arg0);
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delete [] idbreak;
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}
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// if using fix bond/create, set id of fix bond/create in fix srp
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// idcreate = id of fix bond break
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if( bond_create )
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{
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sprintf(c0, "%s", idcreate);
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arg0[0] = (char *) "bond/create";
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arg0[1] = c0;
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f_srp->modify_params(2, arg0);
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delete [] idcreate;
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}
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// bond particles do not contribute to energy or virial
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// bond particles do not belong to group all
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// but thermo normalization is by nall
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// therefore should turn off normalization
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char *arg1[2];
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arg1[0] = (char *) "norm";
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arg1[1] = (char *) "no";
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output->thermo->modify_params(2, arg1);
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if (comm->me == 0) error->message(FLERR,"Thermo normalization turned off by pair srp");
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neighbor->request(this,instance_me);
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}
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