include updates for commonly used packages

This commit is contained in:
Axel Kohlmeyer
2020-09-03 01:45:05 -04:00
parent c7c4297cfc
commit 55704368d0
42 changed files with 234 additions and 307 deletions

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@ -12,16 +12,15 @@
------------------------------------------------------------------------- */
#include "body_nparticle.h"
#include <cstring>
#include <cstdlib>
#include "my_pool_chunk.h"
#include "math_extra.h"
#include "atom_vec_body.h"
#include "atom.h"
#include "force.h"
#include "memory.h"
#include "atom_vec_body.h"
#include "error.h"
#include "fmt/format.h"
#include "math_extra.h"
#include "memory.h"
#include "my_pool_chunk.h"
#include <cstring>
using namespace LAMMPS_NS;

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@ -16,17 +16,17 @@
------------------------------------------------------------------------- */
#include "body_rounded_polygon.h"
#include <cmath>
#include <cstring>
#include "my_pool_chunk.h"
#include "atom_vec_body.h"
#include "atom.h"
#include "force.h"
#include "atom_vec_body.h"
#include "domain.h"
#include "error.h"
#include "math_extra.h"
#include "memory.h"
#include "error.h"
#include "fmt/format.h"
#include "my_pool_chunk.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;

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@ -16,17 +16,16 @@
------------------------------------------------------------------------- */
#include "body_rounded_polyhedron.h"
#include <cmath>
#include <cstring>
#include <cstdlib>
#include "my_pool_chunk.h"
#include "atom_vec_body.h"
#include "atom.h"
#include "force.h"
#include "atom_vec_body.h"
#include "error.h"
#include "math_extra.h"
#include "memory.h"
#include "error.h"
#include "fmt/format.h"
#include "my_pool_chunk.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;

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@ -13,14 +13,14 @@
#include "compute_body_local.h"
#include <cstring>
#include "atom.h"
#include "atom_vec_body.h"
#include "body.h"
#include "update.h"
#include "force.h"
#include "memory.h"
#include "error.h"
#include "memory.h"
#include "update.h"
#include <cstring>
using namespace LAMMPS_NS;

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@ -19,7 +19,6 @@
#include <cmath>
#include "atom.h"
#include "atom_vec.h"
#include "error.h"
using namespace LAMMPS_NS;

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@ -17,12 +17,12 @@
#ifdef LAMMPS_ZSTD
#include "dump_atom_zstd.h"
#include "domain.h"
#include "dump_atom_zstd.h"
#include "error.h"
#include "file_writer.h"
#include "update.h"
#include <cstring>

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@ -16,16 +16,16 @@
------------------------------------------------------------------------- */
#ifdef LAMMPS_ZSTD
#include "dump_cfg_zstd.h"
#include "atom.h"
#include "domain.h"
#include "dump_cfg_zstd.h"
#include "error.h"
#include "file_writer.h"
#include "update.h"
#include <cstring>
using namespace LAMMPS_NS;
#define UNWRAPEXPAND 10.0

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@ -17,12 +17,12 @@
#ifdef LAMMPS_ZSTD
#include "dump_custom_zstd.h"
#include "domain.h"
#include "dump_custom_zstd.h"
#include "error.h"
#include "file_writer.h"
#include "update.h"
#include <cstring>

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@ -19,12 +19,11 @@
#include "dump_xyz_zstd.h"
#include "error.h"
#include "file_writer.h"
#include "update.h"
#include <cstring>
using namespace LAMMPS_NS;
DumpXYZZstd::DumpXYZZstd(LAMMPS *lmp, int narg, char **arg) :

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@ -12,15 +12,10 @@
------------------------------------------------------------------------- */
#include "atom_vec_dipole.h"
#include <cmath>
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "memory.h"
#include "error.h"
#include "atom.h"
#include <cmath>
using namespace LAMMPS_NS;

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@ -19,19 +19,17 @@
------------------------------------------------------------------------- */
#include "ewald.h"
#include <mpi.h>
#include <cmath>
#include <string>
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "pair.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
#include "fmt/format.h"
#include "pair.h"
#include <cmath>
using namespace LAMMPS_NS;
using namespace MathConst;

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@ -16,22 +16,20 @@
------------------------------------------------------------------------- */
#include "ewald_dipole.h"
#include <mpi.h>
#include <cstring>
#include <string>
#include <cmath>
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "pair.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "math_const.h"
#include "math_special.h"
#include "memory.h"
#include "error.h"
#include "pair.h"
#include "update.h"
#include "utils.h"
#include "fmt/format.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;

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@ -16,21 +16,19 @@
------------------------------------------------------------------------- */
#include "ewald_dipole_spin.h"
#include <mpi.h>
#include <cstring>
#include <string>
#include <cmath>
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "pair.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "pair.h"
#include "update.h"
#include "utils.h"
#include "fmt/format.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;

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@ -16,23 +16,21 @@
------------------------------------------------------------------------- */
#include "ewald_disp.h"
#include <mpi.h>
#include <cstring>
#include <string>
#include <cmath>
#include "math_vector.h"
#include "math_const.h"
#include "math_special.h"
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "pair.h"
#include "domain.h"
#include "memory.h"
#include "error.h"
#include "force.h"
#include "math_const.h"
#include "math_special.h"
#include "math_vector.h"
#include "memory.h"
#include "pair.h"
#include "update.h"
#include "utils.h"
#include "fmt/format.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;

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@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
#include "fft3d_wrap.h"
#include <mpi.h>
#include "error.h"
using namespace LAMMPS_NS;

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@ -16,24 +16,22 @@
------------------------------------------------------------------------- */
#include "fix_tune_kspace.h"
#include <cmath>
#include <cstring>
#include <limits>
#include "comm.h"
#include "update.h"
#include "compute.h"
#include "error.h"
#include "force.h"
#include "info.h"
#include "kspace.h"
#include "pair.h"
#include "error.h"
#include "memory.h"
#include "timer.h"
#include "neighbor.h"
#include "modify.h"
#include "compute.h"
#include "neighbor.h"
#include "pair.h"
#include "timer.h"
#include "update.h"
#include <cmath>
#include <cstring>
#include <limits>
#define SWAP(a,b) {temp=(a);(a)=(b);(b)=temp;}
#define SIGN(a,b) ((b) >= 0.0 ? fabs(a) : -fabs(a))

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@ -12,12 +12,12 @@
------------------------------------------------------------------------- */
#include "gridcomm.h"
#include <mpi.h>
#include "comm.h"
#include "kspace.h"
#include "irregular.h"
#include "memory.h"
#include "error.h"
#include "irregular.h"
#include "kspace.h"
#include "memory.h"
using namespace LAMMPS_NS;

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@ -16,22 +16,20 @@
------------------------------------------------------------------------- */
#include "msm.h"
#include <mpi.h>
#include <cstring>
#include <cmath>
#include "atom.h"
#include "comm.h"
#include "gridcomm.h"
#include "neighbor.h"
#include "force.h"
#include "pair.h"
#include "domain.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
#include "fmt/format.h"
#include "force.h"
#include "gridcomm.h"
#include "math_const.h"
#include "memory.h"
#include "neighbor.h"
#include "pair.h"
#include <cstring>
#include <cmath>
using namespace LAMMPS_NS;
using namespace MathConst;

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@ -19,28 +19,25 @@
------------------------------------------------------------------------- */
#include "pppm.h"
#include <mpi.h>
#include <cstring>
#include <string>
#include <cmath>
#include "atom.h"
#include "comm.h"
#include "gridcomm.h"
#include "neighbor.h"
#include "force.h"
#include "pair.h"
#include "bond.h"
#include "angle.h"
#include "domain.h"
#include "fft3d_wrap.h"
#include "remap_wrap.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
#include "fmt/format.h"
#include "angle.h"
#include "atom.h"
#include "bond.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "fft3d_wrap.h"
#include "force.h"
#include "gridcomm.h"
#include "math_const.h"
#include "math_special.h"
#include "memory.h"
#include "neighbor.h"
#include "pair.h"
#include "remap_wrap.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;

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@ -16,20 +16,18 @@
------------------------------------------------------------------------- */
#include "pppm_cg.h"
#include <mpi.h>
#include <cmath>
#include <cstring>
#include "atom.h"
#include "gridcomm.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "neighbor.h"
#include "memory.h"
#include "gridcomm.h"
#include "math_const.h"
#include "memory.h"
#include "neighbor.h"
#include "remap.h"
#include "utils.h"
#include "fmt/format.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;

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@ -16,22 +16,19 @@
------------------------------------------------------------------------- */
#include "pppm_dipole_spin.h"
#include <mpi.h>
#include <cstring>
#include <string>
#include "atom.h"
#include "comm.h"
#include "gridcomm.h"
#include "force.h"
#include "pair.h"
#include "domain.h"
#include "memory.h"
#include "error.h"
#include "update.h"
#include "utils.h"
#include "fmt/format.h"
#include "force.h"
#include "gridcomm.h"
#include "math_const.h"
#include "memory.h"
#include "pair.h"
#include "update.h"
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;

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@ -17,26 +17,24 @@
------------------------------------------------------------------------- */
#include "pppm_disp.h"
#include <mpi.h>
#include <cstring>
#include <cmath>
#include <string>
#include "math_const.h"
#include "atom.h"
#include "comm.h"
#include "gridcomm.h"
#include "neighbor.h"
#include "force.h"
#include "pair.h"
#include "bond.h"
#include "angle.h"
#include "atom.h"
#include "bond.h"
#include "comm.h"
#include "domain.h"
#include "fft3d_wrap.h"
#include "remap_wrap.h"
#include "memory.h"
#include "error.h"
#include "utils.h"
#include "fmt/format.h"
#include "fft3d_wrap.h"
#include "force.h"
#include "gridcomm.h"
#include "math_const.h"
#include "memory.h"
#include "neighbor.h"
#include "pair.h"
#include "remap_wrap.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;

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@ -12,7 +12,7 @@
------------------------------------------------------------------------- */
#include "remap_wrap.h"
#include <mpi.h>
#include "error.h"
using namespace LAMMPS_NS;

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@ -46,7 +46,6 @@
#include "text_file_reader.h"
#include "tokenizer.h"
#include <cctype>
#include <cmath>
#include <cstring>

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@ -17,15 +17,14 @@
#include "pair_eam_alloy.h"
#include <cstring>
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "memory.h"
#include "error.h"
#include "tokenizer.h"
#include "memory.h"
#include "potential_file_reader.h"
#include "tokenizer.h"
#include <cstring>
using namespace LAMMPS_NS;

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@ -17,15 +17,14 @@
#include "pair_eam_fs.h"
#include <cstring>
#include "atom.h"
#include "comm.h"
#include "force.h"
#include "memory.h"
#include "error.h"
#include "tokenizer.h"
#include "memory.h"
#include "potential_file_reader.h"
#include "tokenizer.h"
#include <cstring>
using namespace LAMMPS_NS;

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@ -17,19 +17,17 @@
#include "pair_eim.h"
#include "atom.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "memory.h"
#include "neigh_list.h"
#include "neighbor.h"
#include "tokenizer.h"
#include <cmath>
#include <cstring>
#include "atom.h"
#include "force.h"
#include "comm.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "memory.h"
#include "error.h"
#include "tokenizer.h"
#include "potential_file_reader.h"
using namespace LAMMPS_NS;

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@ -18,20 +18,17 @@
#include "pair_gw_zbl.h"
#include <cmath>
#include <cstring>
#include "atom.h"
#include "update.h"
#include "force.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
#include "tokenizer.h"
#include "potential_file_reader.h"
#include "math_const.h"
#include "memory.h"
#include "potential_file_reader.h"
#include "tokenizer.h"
#include "update.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;

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@ -26,7 +26,6 @@
#include "neigh_request.h"
#include "neighbor.h"
#include "potential_file_reader.h"
#include "text_file_reader.h"
#include "tokenizer.h"
#include <cmath>

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@ -28,7 +28,6 @@
#include "neigh_request.h"
#include "neighbor.h"
#include "potential_file_reader.h"
#include "text_file_reader.h"
#include "tokenizer.h"
#include <cmath>

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@ -18,19 +18,16 @@
#include "pair_tersoff_mod.h"
#include <cmath>
#include <cstring>
#include "atom.h"
#include "force.h"
#include "comm.h"
#include "error.h"
#include "math_const.h"
#include "math_special.h"
#include "memory.h"
#include "error.h"
#include "tokenizer.h"
#include "potential_file_reader.h"
#include "tokenizer.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;

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@ -17,17 +17,14 @@
#include "pair_tersoff_mod_c.h"
#include <cmath>
#include <cstring>
#include "atom.h"
#include "force.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
#include "tokenizer.h"
#include "memory.h"
#include "potential_file_reader.h"
#include "tokenizer.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;

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@ -18,20 +18,17 @@
#include "pair_tersoff_zbl.h"
#include <cmath>
#include <cstring>
#include "atom.h"
#include "update.h"
#include "force.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
#include "math_const.h"
#include "math_special.h"
#include "tokenizer.h"
#include "memory.h"
#include "potential_file_reader.h"
#include "tokenizer.h"
#include "update.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace MathConst;

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@ -15,38 +15,36 @@
Contributing author: Evangelos Voyiatzis (Royal DSM)
------------------------------------------------------------------------- */
#include <cmath>
#include <cstring>
#include "fix_widom.h"
#include "angle.h"
#include "atom.h"
#include "atom_vec.h"
#include "atom_vec_hybrid.h"
#include "molecule.h"
#include "update.h"
#include "modify.h"
#include "fix.h"
#include "bond.h"
#include "comm.h"
#include "compute.h"
#include "group.h"
#include "domain.h"
#include "region.h"
#include "random_park.h"
#include "force.h"
#include "pair.h"
#include "bond.h"
#include "angle.h"
#include "dihedral.h"
#include "domain.h"
#include "error.h"
#include "fix.h"
#include "force.h"
#include "group.h"
#include "improper.h"
#include "kspace.h"
#include "math_extra.h"
#include "math_const.h"
#include "math_extra.h"
#include "memory.h"
#include "error.h"
#include "thermo.h"
#include "output.h"
#include "modify.h"
#include "molecule.h"
#include "neighbor.h"
#include <iostream>
#include "pair.h"
#include "random_park.h"
#include "region.h"
#include "update.h"
#include <cmath>
#include <cstring>
using namespace std;
using namespace LAMMPS_NS;

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@ -17,18 +17,16 @@
#include "pair_dsmc.h"
#include <cmath>
#include <climits>
#include "atom.h"
#include "comm.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "memory.h"
#include "error.h"
#include "domain.h"
#include "update.h"
#include "random_mars.h"
#include "update.h"
#include <cmath>
using namespace LAMMPS_NS;

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@ -13,25 +13,24 @@
#include "fix_deposit.h"
#include <cmath>
#include <cstring>
#include "atom.h"
#include "atom_vec.h"
#include "molecule.h"
#include "force.h"
#include "update.h"
#include "modify.h"
#include "fix.h"
#include "comm.h"
#include "domain.h"
#include "lattice.h"
#include "region.h"
#include "random_park.h"
#include "math_extra.h"
#include "math_const.h"
#include "memory.h"
#include "error.h"
#include "fix.h"
#include "lattice.h"
#include "math_const.h"
#include "math_extra.h"
#include "memory.h"
#include "modify.h"
#include "molecule.h"
#include "random_park.h"
#include "region.h"
#include "update.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace FixConst;

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@ -16,13 +16,14 @@
------------------------------------------------------------------------- */
#include "fix_oneway.h"
#include <cstring>
#include "atom.h"
#include "domain.h"
#include "error.h"
#include "force.h"
#include "region.h"
#include <cstring>
using namespace LAMMPS_NS;
using namespace FixConst;

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@ -19,25 +19,21 @@
------------------------------------------------------------------------- */
#include "fix_orient_bcc.h"
#include <cmath>
#include <cstring>
#include "atom.h"
#include "update.h"
#include "respa.h"
#include "neighbor.h"
#include "citeme.h"
#include "comm.h"
#include "error.h"
#include "math_const.h"
#include "memory.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "comm.h"
#include "force.h"
#include "math_const.h"
#include "citeme.h"
#include "memory.h"
#include "error.h"
#include "neighbor.h"
#include "respa.h"
#include "update.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace FixConst;

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@ -18,13 +18,13 @@
#include "fix_viscosity.h"
#include <cmath>
#include <cstring>
#include "atom.h"
#include "domain.h"
#include "modify.h"
#include "error.h"
#include "force.h"
#include "modify.h"
#include <cmath>
#include <cstring>
using namespace LAMMPS_NS;
using namespace FixConst;

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@ -11,24 +11,15 @@
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#include <cstring>
#include <cstdlib>
#include "mliap_data.h"
#include "mliap_model_linear.h"
#include "mliap_model_quadratic.h"
#include "mliap_descriptor_snap.h"
#include "compute_mliap.h"
#include "atom.h"
#include "update.h"
#include "modify.h"
#include "neighbor.h"
#include "neigh_list.h"
#include "neigh_request.h"
#include "force.h"
#include "pair.h"
#include "comm.h"
#include "memory.h"
#include "error.h"
#include "mliap_descriptor.h"
#include "mliap_model.h"
#include "neigh_list.h"
#include <cstring>
using namespace LAMMPS_NS;

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@ -12,14 +12,9 @@
------------------------------------------------------------------------- */
#include "mliap_descriptor.h"
#include "atom.h"
#include "memory.h"
#include "error.h"
using namespace LAMMPS_NS;
#define MAXLINE 1024
#define MAXWORD 3
/* ---------------------------------------------------------------------- */

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@ -20,7 +20,6 @@
#include <cstring>
#include <utility>
#include <vector>
using namespace LAMMPS_NS;