Removing residual files
This commit is contained in:
Joel Thomas Clemmer
@ -1,254 +0,0 @@
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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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#include "atom_vec_sphere_bpm.h"
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#include "atom.h"
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#include "error.h"
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#include "fix.h"
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#include "fix_adapt.h"
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#include "math_const.h"
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#include "modify.h"
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#include "utils.h"
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#include <cstring>
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using namespace LAMMPS_NS;
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using namespace MathConst;
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/* ---------------------------------------------------------------------- */
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AtomVecSphereBPM::AtomVecSphereBPM(LAMMPS *lmp) : AtomVec(lmp)
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{
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mass_type = PER_ATOM;
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molecular = Atom::MOLECULAR;
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bonds_allow = 1;
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atom->molecule_flag = 1;
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atom->sphere_flag = 1;
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atom->radius_flag = atom->rmass_flag = atom->omega_flag =
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atom->torque_flag = atom->quat_flag = 1;
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// strings with peratom variables to include in each AtomVec method
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// strings cannot contain fields in corresponding AtomVec default strings
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// order of fields in a string does not matter
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// except: fields_data_atom & fields_data_vel must match data file
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fields_grow = (char *)
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"molecule num_bond bond_type bond_atom nspecial special radius rmass omega torque quat";
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fields_copy = (char *)
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"molecule num_bond bond_type bond_atom nspecial special radius rmass omega quat";
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fields_comm = (char *) "";
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fields_comm_vel = (char *) "omega quat";
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fields_reverse = (char *) "torque";
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fields_border = (char *) "molecule radius rmass";
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fields_border_vel = (char *) "molecule radius rmass omega quat";
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fields_exchange = (char *)
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"molecule num_bond bond_type bond_atom nspecial special radius rmass omega quat";
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fields_restart = (char *)
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"molecule num_bond bond_type bond_atom radius rmass omega quat";
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fields_create = (char *)
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"molecule num_bond nspecial radius rmass omega quat";
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fields_data_atom = (char *) "id molecule type radius rmass x";
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fields_data_vel = (char *) "id v omega";
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bond_per_atom = 0;
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bond_negative = NULL;
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}
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/* ----------------------------------------------------------------------
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process sub-style args
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optional arg = 0/1 for static/dynamic particle radii
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------------------------------------------------------------------------- */
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void AtomVecSphereBPM::process_args(int narg, char **arg)
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{
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if (narg != 0 && narg != 1)
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error->all(FLERR,"Illegal atom_style sphere/bpm command");
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radvary = 0;
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if (narg == 1) {
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radvary = utils::numeric(FLERR,arg[0],true,lmp);
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if (radvary < 0 || radvary > 1)
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error->all(FLERR,"Illegal atom_style sphere/bpm command");
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}
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// dynamic particle radius and mass must be communicated every step
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if (radvary) {
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fields_comm = (char *) "radius rmass";
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fields_comm_vel = (char *) "radius rmass omega";
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}
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// delay setting up of fields until now
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setup_fields();
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}
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/* ---------------------------------------------------------------------- */
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void AtomVecSphereBPM::init()
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{
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AtomVec::init();
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// check if optional radvary setting should have been set to 1
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for (int i = 0; i < modify->nfix; i++)
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if (strcmp(modify->fix[i]->style,"adapt") == 0) {
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FixAdapt *fix = (FixAdapt *) modify->fix[i];
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if (fix->diamflag && radvary == 0)
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error->all(FLERR,"Fix adapt changes particle radii "
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"but atom_style sphere is not dynamic");
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}
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}
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/* ----------------------------------------------------------------------
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set local copies of all grow ptrs used by this class, except defaults
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needed in replicate when 2 atom classes exist and it calls pack_restart()
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------------------------------------------------------------------------- */
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void AtomVecSphereBPM::grow_pointers()
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{
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radius = atom->radius;
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rmass = atom->rmass;
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omega = atom->omega;
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quat = atom->quat;
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num_bond = atom->num_bond;
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bond_type = atom->bond_type;
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nspecial = atom->nspecial;
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}
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/* ----------------------------------------------------------------------
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initialize non-zero atom quantities
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------------------------------------------------------------------------- */
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void AtomVecSphereBPM::create_atom_post(int ilocal)
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{
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radius[ilocal] = 0.5;
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rmass[ilocal] = 4.0*MY_PI/3.0 * 0.5*0.5*0.5;
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quat[ilocal][0] = 1.0;
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quat[ilocal][1] = 0.0;
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quat[ilocal][2] = 0.0;
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quat[ilocal][3] = 0.0;
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}
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/* ----------------------------------------------------------------------
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modify values for AtomVec::pack_restart() to pack
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------------------------------------------------------------------------- */
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void AtomVecSphereBPM::pack_restart_pre(int ilocal)
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{
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// insure bond_negative vector is needed length
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if (bond_per_atom < atom->bond_per_atom) {
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delete [] bond_negative;
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bond_per_atom = atom->bond_per_atom;
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bond_negative = new int[bond_per_atom];
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}
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// flip any negative types to positive and flag which ones
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any_bond_negative = 0;
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for (int m = 0; m < num_bond[ilocal]; m++) {
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if (bond_type[ilocal][m] < 0) {
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bond_negative[m] = 1;
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bond_type[ilocal][m] = -bond_type[ilocal][m];
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any_bond_negative = 1;
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} else bond_negative[m] = 0;
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}
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}
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/* ----------------------------------------------------------------------
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unmodify values packed by AtomVec::pack_restart()
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------------------------------------------------------------------------- */
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void AtomVecSphereBPM::pack_restart_post(int ilocal)
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{
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// restore the flagged types to their negative values
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if (any_bond_negative) {
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for (int m = 0; m < num_bond[ilocal]; m++)
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if (bond_negative[m]) bond_type[ilocal][m] = -bond_type[ilocal][m];
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}
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}
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/* ----------------------------------------------------------------------
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initialize other atom quantities after AtomVec::unpack_restart()
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------------------------------------------------------------------------- */
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void AtomVecSphereBPM::unpack_restart_init(int ilocal)
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{
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nspecial[ilocal][0] = 0;
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nspecial[ilocal][1] = 0;
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nspecial[ilocal][2] = 0;
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}
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/* ----------------------------------------------------------------------
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modify what AtomVec::data_atom() just unpacked
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or initialize other atom quantities
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------------------------------------------------------------------------- */
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void AtomVecSphereBPM::data_atom_post(int ilocal)
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{
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radius_one = 0.5 * atom->radius[ilocal];
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radius[ilocal] = radius_one;
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if (radius_one > 0.0)
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rmass[ilocal] *= 4.0*MY_PI/3.0 * radius_one*radius_one*radius_one;
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if (rmass[ilocal] <= 0.0)
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error->one(FLERR,"Invalid density in Atoms section of data file");
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omega[ilocal][0] = 0.0;
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omega[ilocal][1] = 0.0;
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omega[ilocal][2] = 0.0;
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quat[ilocal][0] = 1.0;
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quat[ilocal][1] = 0.0;
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quat[ilocal][2] = 0.0;
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quat[ilocal][3] = 0.0;
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num_bond[ilocal] = 0;
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nspecial[ilocal][0] = 0;
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nspecial[ilocal][1] = 0;
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nspecial[ilocal][2] = 0;
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}
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/* ----------------------------------------------------------------------
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modify values for AtomVec::pack_data() to pack
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------------------------------------------------------------------------- */
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void AtomVecSphereBPM::pack_data_pre(int ilocal)
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{
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radius_one = radius[ilocal];
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rmass_one = rmass[ilocal];
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radius[ilocal] *= 2.0;
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if (radius_one!= 0.0)
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rmass[ilocal] =
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rmass_one / (4.0*MY_PI/3.0 * radius_one*radius_one*radius_one);
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}
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/* ----------------------------------------------------------------------
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unmodify values packed by AtomVec::pack_data()
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------------------------------------------------------------------------- */
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void AtomVecSphereBPM::pack_data_post(int ilocal)
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{
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radius[ilocal] = radius_one;
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rmass[ilocal] = rmass_one;
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}
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@ -1,83 +0,0 @@
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/* -*- c++ -*- ----------------------------------------------------------
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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
|
||||
the GNU General Public License.
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||||
|
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See the README file in the top-level LAMMPS directory.
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------------------------------------------------------------------------- */
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#ifdef ATOM_CLASS
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// clang-format off
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AtomStyle(sphere/bpm,AtomVecSphereBPM)
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// clang-format on
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#else
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#ifndef LMP_ATOM_VEC_SPHERE_BPM_H
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#define LMP_ATOM_VEC_SPHERE_BPM_H
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#include "atom_vec.h"
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namespace LAMMPS_NS {
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class AtomVecSphereBPM : public AtomVec {
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public:
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AtomVecSphereBPM(class LAMMPS *);
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void process_args(int, char **) override;
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void init() override;
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void grow_pointers() override;
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void create_atom_post(int) override;
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void pack_restart_pre(int) override;
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void pack_restart_post(int) override;
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void unpack_restart_init(int) override;
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void data_atom_post(int) override;
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void pack_data_pre(int) override;
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void pack_data_post(int) override;
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private:
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int *num_bond;
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int **bond_type;
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int **nspecial;
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double *radius,*rmass;
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double **omega, **torque, **quat;
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int any_bond_negative;
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int bond_per_atom;
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int *bond_negative;
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int radvary;
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double radius_one,rmass_one;
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};
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} // namespace LAMMPS_NS
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#endif
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#endif
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/* ERROR/WARNING messages:
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E: Per-processor system is too big
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The number of owned atoms plus ghost atoms on a single
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processor must fit in 32-bit integer.
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E: Invalid atom type in Atoms section of data file
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Atom types must range from 1 to specified # of types.
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E: Invalid radius in Atoms section of data file
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Radius must be >= 0.0.
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E: Invalid density in Atoms section of data file
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Density value cannot be <= 0.0.
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*/
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@ -1,161 +0,0 @@
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// clang-format off
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/* ----------------------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, 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.
|
||||
------------------------------------------------------------------------- */
|
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#include "fix_nve_sphere_bpm.h"
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#include "atom.h"
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#include "atom_vec.h"
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#include "domain.h"
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#include "error.h"
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#include "force.h"
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#include "math_extra.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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using namespace FixConst;
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using namespace MathExtra;
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/* ---------------------------------------------------------------------- */
|
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FixNVESphereBPM::FixNVESphereBPM(LAMMPS *lmp, int narg, char **arg) :
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FixNVE(lmp, narg, arg)
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{
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if (narg < 3) error->all(FLERR,"Illegal fix nve/sphere/bpm command");
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|
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time_integrate = 1;
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// process extra keywords
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// inertia = moment of inertia prefactor for sphere or disc
|
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inertia = 0.4;
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|
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int iarg = 3;
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while (iarg < narg) {
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if (strcmp(arg[iarg],"disc")==0) {
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inertia = 0.5;
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if (domain->dimension != 2)
|
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error->all(FLERR,"Fix nve/sphere/bpm disc requires 2d simulation");
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iarg++;
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}
|
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else error->all(FLERR,"Illegal fix nve/sphere/bpm command");
|
||||
}
|
||||
|
||||
inv_inertia = 1.0/inertia;
|
||||
|
||||
// error checks
|
||||
|
||||
if (!atom->quat_flag || !atom->sphere_flag)
|
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error->all(FLERR,"Fix nve/sphere/bpm requires atom style sphere/bpm");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixNVESphereBPM::init()
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{
|
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FixNVE::init();
|
||||
|
||||
// check that all particles are finite-size spheres
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||||
// no point particles allowed
|
||||
|
||||
double *radius = atom->radius;
|
||||
int *mask = atom->mask;
|
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int nlocal = atom->nlocal;
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit)
|
||||
if (radius[i] == 0.0)
|
||||
error->one(FLERR,"Fix nve/sphere/bpm requires extended particles");
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixNVESphereBPM::initial_integrate(int /*vflag*/)
|
||||
{
|
||||
double dtq,dtfm,dtirotate,particle_inertia;
|
||||
|
||||
double **x = atom->x;
|
||||
double **v = atom->v;
|
||||
double **f = atom->f;
|
||||
double **omega = atom->omega;
|
||||
double **torque = atom->torque;
|
||||
double **quat = atom->quat;
|
||||
double *radius = atom->radius;
|
||||
double *rmass = atom->rmass;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
|
||||
|
||||
// set timestep here since dt may have changed or come via rRESPA
|
||||
dtq = 0.5 * dtv;
|
||||
|
||||
// update v,x,omega,quat for all particles
|
||||
// d_omega/dt = torque / inertia
|
||||
|
||||
for (int i = 0; i < nlocal; i++) {
|
||||
if (mask[i] & groupbit) {
|
||||
dtfm = dtf / rmass[i];
|
||||
v[i][0] += dtfm * f[i][0];
|
||||
v[i][1] += dtfm * f[i][1];
|
||||
v[i][2] += dtfm * f[i][2];
|
||||
x[i][0] += dtv * v[i][0];
|
||||
x[i][1] += dtv * v[i][1];
|
||||
x[i][2] += dtv * v[i][2];
|
||||
|
||||
particle_inertia = inertia*(radius[i]*radius[i]*rmass[i]);
|
||||
dtirotate = dtf / particle_inertia;
|
||||
omega[i][0] += dtirotate * torque[i][0];
|
||||
omega[i][1] += dtirotate * torque[i][1];
|
||||
omega[i][2] += dtirotate * torque[i][2];
|
||||
|
||||
MathExtra::richardson_sphere(quat[i],omega[i],dtq);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
/* ---------------------------------------------------------------------- */
|
||||
|
||||
void FixNVESphereBPM::final_integrate()
|
||||
{
|
||||
double dtfm,dtirotate,particle_inertia;
|
||||
|
||||
double **v = atom->v;
|
||||
double **f = atom->f;
|
||||
double **omega = atom->omega;
|
||||
double **torque = atom->torque;
|
||||
double *rmass = atom->rmass;
|
||||
double *radius = atom->radius;
|
||||
int *mask = atom->mask;
|
||||
int nlocal = atom->nlocal;
|
||||
if (igroup == atom->firstgroup) nlocal = atom->nfirst;
|
||||
|
||||
// update v,omega for all particles
|
||||
// d_omega/dt = torque / inertia
|
||||
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
if (mask[i] & groupbit) {
|
||||
dtfm = dtf / rmass[i];
|
||||
v[i][0] += dtfm * f[i][0];
|
||||
v[i][1] += dtfm * f[i][1];
|
||||
v[i][2] += dtfm * f[i][2];
|
||||
|
||||
particle_inertia = inertia*(radius[i]*radius[i]*rmass[i]);
|
||||
dtirotate = dtf / particle_inertia;
|
||||
omega[i][0] += dtirotate * torque[i][0];
|
||||
omega[i][1] += dtirotate * torque[i][1];
|
||||
omega[i][2] += dtirotate * torque[i][2];
|
||||
}
|
||||
}
|
||||
@ -1,71 +0,0 @@
|
||||
/* -*- c++ -*- ----------------------------------------------------------
|
||||
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||
https://www.lammps.org/, 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 FIX_CLASS
|
||||
// clang-format off
|
||||
FixStyle(nve/sphere/bpm,FixNVESphereBPM)
|
||||
// clang-format on
|
||||
#else
|
||||
|
||||
#ifndef LMP_FIX_NVE_SPHERE_BPM_H
|
||||
#define LMP_FIX_NVE_SPHERE_BPM_H
|
||||
|
||||
#include "fix_nve.h"
|
||||
|
||||
namespace LAMMPS_NS {
|
||||
|
||||
class FixNVESphereBPM : public FixNVE {
|
||||
public:
|
||||
FixNVESphereBPM(class LAMMPS *, int, char **);
|
||||
|
||||
void init() override;
|
||||
void initial_integrate(int) override;
|
||||
void final_integrate() override;
|
||||
|
||||
protected:
|
||||
double inertia, inv_inertia;
|
||||
int extra;
|
||||
int dlm;
|
||||
};
|
||||
|
||||
} // namespace LAMMPS_NS
|
||||
|
||||
#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: Fix nve/sphere/bpm disc requires 2d simulation
|
||||
|
||||
UNDOCUMENTED
|
||||
|
||||
E: Fix nve/sphere/bpm requires atom style sphere/bpm
|
||||
|
||||
Self-explanatory.
|
||||
|
||||
E: Fix nve/sphere/bpm update dipole requires atom attribute mu
|
||||
|
||||
An atom style with this attribute is needed.
|
||||
|
||||
E: Fix nve/sphere/bpm requires extended particles
|
||||
|
||||
This fix can only be used for particles of a finite size.
|
||||
|
||||
|
||||
*/
|
||||
Reference in New Issue
Block a user