enable and apply clang-format
This commit is contained in:
Axel Kohlmeyer
@ -1,4 +1,3 @@
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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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@ -18,22 +17,23 @@
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#include "fix_numdiff_virial.h"
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#include <cstring>
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#include "atom.h"
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#include "domain.h"
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#include "update.h"
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#include "modify.h"
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#include "compute.h"
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#include "respa.h"
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#include "force.h"
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#include "pair.h"
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#include "bond.h"
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#include "angle.h"
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#include "atom.h"
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#include "bond.h"
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#include "compute.h"
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#include "dihedral.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 "improper.h"
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#include "kspace.h"
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#include "memory.h"
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#include "error.h"
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#include "modify.h"
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#include "pair.h"
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#include "respa.h"
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#include "update.h"
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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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@ -41,28 +41,24 @@ using namespace FixConst;
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/* ---------------------------------------------------------------------- */
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FixNumDiffVirial::FixNumDiffVirial(LAMMPS *lmp, int narg, char **arg) :
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Fix(lmp, narg, arg), id_pe(nullptr),
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temp_x(nullptr), temp_f(nullptr)
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Fix(lmp, narg, arg), id_pe(nullptr), temp_x(nullptr), temp_f(nullptr)
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{
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if (narg < 5) error->all(FLERR,"Illegal fix numdiff/virial command");
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if (igroup) error->all(FLERR,"Compute numdiff/virial must use group all");
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if (narg < 5) error->all(FLERR, "Illegal fix numdiff/virial command");
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if (igroup) error->all(FLERR, "Compute numdiff/virial must use group all");
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peratom_freq = nevery;
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respa_level_support = 1;
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vector_flag = 1;
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size_vector = NDIR_VIRIAL;
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extvector = 0;
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maxatom = 0;
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nevery = utils::inumeric(FLERR,arg[3],false,lmp);
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delta = utils::numeric(FLERR,arg[4],false,lmp);
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if (nevery <= 0 || delta <= 0.0)
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error->all(FLERR,"Illegal fix numdiff command");
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nevery = utils::inumeric(FLERR, arg[3], false, lmp);
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delta = utils::numeric(FLERR, arg[4], false, lmp);
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if (nevery <= 0 || delta <= 0.0) error->all(FLERR, "Illegal fix numdiff command");
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std::string cmd = id + std::string("_pe");
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id_pe = utils::strdup(cmd);
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cmd += " all pe";
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modify->add_compute(cmd);
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@ -74,9 +70,9 @@ FixNumDiffVirial::FixNumDiffVirial(LAMMPS *lmp, int narg, char **arg) :
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// set fixed-point to default = center of cell
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fixedpoint[0] = 0.5*(domain->boxlo[0]+domain->boxhi[0]);
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fixedpoint[1] = 0.5*(domain->boxlo[1]+domain->boxhi[1]);
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fixedpoint[2] = 0.5*(domain->boxlo[2]+domain->boxhi[2]);
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fixedpoint[0] = 0.5 * (domain->boxlo[0] + domain->boxhi[0]);
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fixedpoint[1] = 0.5 * (domain->boxlo[1] + domain->boxhi[1]);
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fixedpoint[2] = 0.5 * (domain->boxlo[2] + domain->boxhi[2]);
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// define the cartesian indices for each strain (Voigt order)
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@ -86,7 +82,7 @@ FixNumDiffVirial::FixNumDiffVirial(LAMMPS *lmp, int narg, char **arg) :
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dirlist[1][1] = 1;
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dirlist[2][0] = 2;
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dirlist[2][1] = 2;
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dirlist[3][0] = 1;
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dirlist[3][1] = 2;
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dirlist[4][0] = 0;
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@ -126,17 +122,21 @@ void FixNumDiffVirial::init()
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// check for PE compute
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int icompute = modify->find_compute(id_pe);
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if (icompute < 0) error->all(FLERR,"Compute ID for fix numdiff does not exist");
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if (icompute < 0) error->all(FLERR, "Compute ID for fix numdiff does not exist");
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pe = modify->compute[icompute];
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if (force->pair && force->pair->compute_flag) pair_compute_flag = 1;
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else pair_compute_flag = 0;
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if (force->kspace && force->kspace->compute_flag) kspace_compute_flag = 1;
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else kspace_compute_flag = 0;
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if (force->pair && force->pair->compute_flag)
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pair_compute_flag = 1;
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else
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pair_compute_flag = 0;
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if (force->kspace && force->kspace->compute_flag)
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kspace_compute_flag = 1;
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else
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kspace_compute_flag = 0;
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if (utils::strmatch(update->integrate_style,"^respa")) {
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ilevel_respa = ((Respa *) update->integrate)->nlevels-1;
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if (respa_level >= 0) ilevel_respa = MIN(respa_level,ilevel_respa);
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if (utils::strmatch(update->integrate_style, "^respa")) {
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ilevel_respa = ((Respa *) update->integrate)->nlevels - 1;
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if (respa_level >= 0) ilevel_respa = MIN(respa_level, ilevel_respa);
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}
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}
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@ -144,11 +144,11 @@ void FixNumDiffVirial::init()
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void FixNumDiffVirial::setup(int vflag)
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{
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if (utils::strmatch(update->integrate_style,"^verlet"))
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if (utils::strmatch(update->integrate_style, "^verlet"))
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post_force(vflag);
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else {
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((Respa *) update->integrate)->copy_flevel_f(ilevel_respa);
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post_force_respa(vflag,ilevel_respa,0);
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post_force_respa(vflag, ilevel_respa, 0);
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((Respa *) update->integrate)->copy_f_flevel(ilevel_respa);
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}
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}
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@ -206,11 +206,11 @@ void FixNumDiffVirial::calculate_virial()
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temp_x[i][k] = x[i][k];
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temp_f[i][k] = f[i][k];
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}
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// loop over 6 strain directions
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// compute a finite difference force in each dimension
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int flag,allflag;
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int flag, allflag;
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double nktv2p = force->nktv2p;
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double inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd);
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@ -228,16 +228,14 @@ void FixNumDiffVirial::calculate_virial()
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restore_atoms(nall, idir);
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}
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// recompute energy so all contributions are as before
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// recompute energy so all contributions are as before
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energy = update_energy();
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// restore original forces for owned and ghost atoms
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for (int i = 0; i < nall; i++)
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for (int k = 0; k < 3; k++)
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f[i][k] = temp_f[i][k];
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for (int k = 0; k < 3; k++) f[i][k] = temp_f[i][k];
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}
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/* ----------------------------------------------------------------------
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@ -247,11 +245,10 @@ void FixNumDiffVirial::calculate_virial()
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void FixNumDiffVirial::displace_atoms(int nall, int idir, double magnitude)
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{
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double **x = atom->x;
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int k = dirlist[idir][0];
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int l = dirlist[idir][1];
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int k = dirlist[idir][0];
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int l = dirlist[idir][1];
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for (int i = 0; i < nall; i++)
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x[i][k] = temp_x[i][k] + delta*magnitude*
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(temp_x[i][l]-fixedpoint[l]);
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x[i][k] = temp_x[i][k] + delta * magnitude * (temp_x[i][l] - fixedpoint[l]);
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}
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/* ----------------------------------------------------------------------
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@ -261,10 +258,8 @@ void FixNumDiffVirial::displace_atoms(int nall, int idir, double magnitude)
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void FixNumDiffVirial::restore_atoms(int nall, int idir)
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{
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double **x = atom->x;
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int k = dirlist[idir][0];
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for (int i = 0; i < nall; i++) {
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x[i][k] = temp_x[i][k];
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}
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int k = dirlist[idir][0];
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for (int i = 0; i < nall; i++) { x[i][k] = temp_x[i][k]; }
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}
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/* ----------------------------------------------------------------------
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@ -276,16 +271,16 @@ double FixNumDiffVirial::update_energy()
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{
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int eflag = 1;
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if (pair_compute_flag) force->pair->compute(eflag,0);
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if (pair_compute_flag) force->pair->compute(eflag, 0);
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if (atom->molecular != Atom::ATOMIC) {
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if (force->bond) force->bond->compute(eflag,0);
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if (force->angle) force->angle->compute(eflag,0);
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if (force->dihedral) force->dihedral->compute(eflag,0);
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if (force->improper) force->improper->compute(eflag,0);
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if (force->bond) force->bond->compute(eflag, 0);
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if (force->angle) force->angle->compute(eflag, 0);
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if (force->dihedral) force->dihedral->compute(eflag, 0);
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if (force->improper) force->improper->compute(eflag, 0);
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}
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if (kspace_compute_flag) force->kspace->compute(eflag,0);
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if (kspace_compute_flag) force->kspace->compute(eflag, 0);
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double energy = pe->compute_scalar();
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return energy;
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@ -309,8 +304,8 @@ void FixNumDiffVirial::reallocate()
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memory->destroy(temp_x);
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memory->destroy(temp_f);
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maxatom = atom->nmax;
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memory->create(temp_x,maxatom,3,"numdiff/virial:temp_x");
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memory->create(temp_f,maxatom,3,"numdiff/virial:temp_f");
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memory->create(temp_x, maxatom, 3, "numdiff/virial:temp_x");
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memory->create(temp_f, maxatom, 3, "numdiff/virial:temp_f");
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}
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/* ----------------------------------------------------------------------
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@ -320,6 +315,6 @@ void FixNumDiffVirial::reallocate()
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double FixNumDiffVirial::memory_usage()
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{
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double bytes = 0.0;
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bytes += (double)2 * maxatom*3 * sizeof(double);
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bytes += (double) 2 * maxatom * 3 * sizeof(double);
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return bytes;
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}
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@ -38,30 +38,30 @@ class FixNumDiffVirial : public Fix {
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double memory_usage() override;
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private:
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static const int NDIR_VIRIAL = 6; // dimension of virial and strain vectors
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double delta; // strain magnitude
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int maxatom; // allocated size of atom arrays
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static const int NDIR_VIRIAL = 6; // dimension of virial and strain vectors
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double delta; // strain magnitude
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int maxatom; // allocated size of atom arrays
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int ilevel_respa;
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int pair_compute_flag; // 0 if pair->compute is skipped
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int kspace_compute_flag; // 0 if kspace->compute is skipped
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char *id_pe; // name of energy compute
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class Compute *pe; // pointer to energy compute
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char *id_pe; // name of energy compute
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class Compute *pe; // pointer to energy compute
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double virial[NDIR_VIRIAL]; // finite diff virial components (Voigt order)
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double **temp_x; // original coords
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double **temp_f; // original forces
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double fixedpoint[3]; // define displacement field origin
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int dirlist[NDIR_VIRIAL][2];// strain cartesian indices (Voigt order)
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double compute_vector(int) override; // access function for virial
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void calculate_virial(); // virial calculation
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void displace_atoms(int, int, double);// apply displacement field
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void restore_atoms(int, int); // restore original positions
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double update_energy(); // calculate new energy
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void virial_clear(); // set virial to zero
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void reallocate(); // grow the atom arrays
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double virial[NDIR_VIRIAL]; // finite diff virial components (Voigt order)
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double **temp_x; // original coords
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double **temp_f; // original forces
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double fixedpoint[3]; // define displacement field origin
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int dirlist[NDIR_VIRIAL][2]; // strain cartesian indices (Voigt order)
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double compute_vector(int) override; // access function for virial
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void calculate_virial(); // virial calculation
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void displace_atoms(int, int, double); // apply displacement field
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void restore_atoms(int, int); // restore original positions
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double update_energy(); // calculate new energy
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void virial_clear(); // set virial to zero
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void reallocate(); // grow the atom arrays
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};
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} // namespace LAMMPS_NS
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