[lammps] branch master updated (eb5d230 -> 261b490)
Anton Gladky
gladk at moszumanska.debian.org
Wed Apr 16 18:04:47 UTC 2014
This is an automated email from the git hooks/post-receive script.
gladk pushed a change to branch master
in repository lammps.
from eb5d230 Update changelog.
adds f2930e3 Imported Upstream version 0~20140415.git42bb280
new 0f0d35a Merge tag 'upstream/0_20140415.git42bb280'
new b05b302 Remove patch, applied by upstream.
new 12f95b6 Fix autotest.
new cca8000 Replace deprecated MPI-flag in debian/rules.
new 261b490 Update changelog.
The 5 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
debian/changelog | 9 +
debian/patches/fix_FTBFS_timer.patch | 22 -
debian/patches/series | 1 -
debian/rules | 2 +-
debian/tests/crack | 4 +-
doc/Eqs/pair_tersoff_zbl.jpg | Bin 65850 -> 392677 bytes
doc/Eqs/pair_tersoff_zbl.tex | 2 +-
doc/Manual.html | 6 +-
doc/Manual.txt | 7 +-
doc/Section_accelerate.html | 7 +-
doc/Section_accelerate.txt | 7 +-
doc/Section_commands.html | 18 +-
doc/Section_commands.txt | 3 +
doc/Section_howto.html | 22 +-
doc/Section_howto.txt | 22 +-
doc/Section_intro.html | 2 +
doc/Section_intro.txt | 2 +
doc/Section_packages.html | 190 +-
doc/Section_packages.txt | 190 +-
doc/delete_atoms.html | 4 +-
doc/delete_atoms.txt | 4 +-
doc/dump_molfile.html | 11 +-
doc/dump_molfile.txt | 11 +-
doc/fix_bond_break.html | 56 +-
doc/fix_bond_break.txt | 56 +-
doc/fix_bond_create.html | 26 +-
doc/fix_bond_create.txt | 26 +-
doc/fix_bond_swap.html | 25 +-
doc/fix_bond_swap.txt | 18 +-
doc/fix_oneway.html | 69 +
doc/fix_oneway.txt | 60 +
doc/fix_property_atom.html | 14 +-
doc/fix_property_atom.txt | 14 +-
doc/fix_qmmm.html | 71 +
doc/fix_qmmm.txt | 66 +
doc/fix_recenter.html | 21 +-
doc/fix_recenter.txt | 21 +-
doc/fix_rigid.html | 8 +-
doc/fix_rigid.txt | 6 +-
doc/fix_temp_csvr.html | 153 +
doc/fix_temp_csvr.txt | 143 +
doc/fix_wall_reflect.html | 2 +-
doc/fix_wall_reflect.txt | 2 +-
doc/if.html | 26 +-
doc/if.txt | 23 +-
doc/jump.html | 32 +-
doc/jump.txt | 29 +-
doc/kspace_modify.html | 51 +-
doc/kspace_modify.txt | 50 +-
doc/kspace_style.html | 34 +-
doc/kspace_style.txt | 34 +-
doc/lattice.html | 6 +-
doc/lattice.txt | 6 +-
doc/pair_dpd.html | 17 +
doc/pair_dpd.txt | 14 +
doc/pair_tersoff_zbl.html | 19 +-
doc/pair_tersoff_zbl.txt | 17 +-
doc/pair_zbl.html | 25 +-
doc/pair_zbl.txt | 25 +-
doc/prd.html | 73 +-
doc/prd.txt | 71 +-
doc/read_data.html | 28 +-
doc/read_data.txt | 28 +-
doc/read_restart.html | 5 +
doc/read_restart.txt | 5 +
doc/thermo_style.html | 4 +-
doc/thermo_style.txt | 4 +-
doc/units.html | 14 +-
doc/units.txt | 14 +-
doc/variable.html | 21 +-
doc/variable.txt | 21 +-
examples/KAPPA/in.heatflux | 2 +-
examples/USER/atc/elastic/in.bar1d_flux | 2 +-
examples/USER/atc/elastic/in.bar1d_ghost_flux | 2 +-
examples/USER/atc/elastic/in.bar1d_thermo_elastic | 2 +-
examples/USER/atc/elastic/in.cnt_electrostatic | 107 -
examples/USER/atc/elastic/in.cnt_electrostatic2 | 118 -
examples/USER/atc/elastic/in.cnt_fixed_charge | 145 -
examples/USER/atc/elastic/in.electrostatic_bending | 186 -
.../USER/atc/elastic/in.electrostatic_bending_dos | 164 -
examples/USER/awpmd/H/in.h_atom | 2 +-
examples/USER/awpmd/H/in.h_molecule | 2 +-
examples/USER/cg-cmm/README | 40 +-
examples/USER/cg-cmm/peg-verlet/data.pegc12e8.gz | Bin 696097 -> 1018275 bytes
examples/USER/cg-cmm/peg-verlet/in.pegc12e8 | 8 +-
examples/USER/cg-cmm/peg-verlet/in.pegc12e8-angle | 12 +-
examples/USER/cg-cmm/peg-verlet/log.pegc12e8 | 123 +-
examples/USER/cg-cmm/peg-verlet/log.pegc12e8-angle | 135 +-
examples/USER/cg-cmm/peg-verlet/parm.pegc12e8 | 42 -
.../USER/cg-cmm/peg-verlet/parm.pegc12e8-angle | 42 -
examples/USER/cg-cmm/peg-verlet/pegc12e8.psf.gz | Bin 209419 -> 0 bytes
examples/USER/cg-cmm/sds-monolayer/data.sds.gz | Bin 0 -> 2265938 bytes
examples/USER/cg-cmm/sds-monolayer/in.sds-hybrid | 50 +
examples/USER/cg-cmm/sds-monolayer/in.sds-regular | 43 +
examples/USER/cg-cmm/sds-monolayer/log.sds-hybrid | 127 +
examples/USER/cg-cmm/sds-monolayer/log.sds-regular | 116 +
examples/USER/colvars/in.peptide-spring | 44 +
examples/USER/colvars/in.peptide-spring2 | 39 +
examples/USER/colvars/log.peptide-colvars | 547 +
examples/USER/colvars/log.peptide-colvars2 | 225 +
examples/USER/colvars/log.peptide-spring | 150 +
examples/USER/colvars/log.peptide-spring2 | 145 +
examples/USER/colvars/peptide.colvars | 2 +-
examples/USER/eff/ECP/Si2H6/in.Si2H6 | 2 +-
examples/USER/eff/ECP/Si2H6/in.Si2H6.ang | 2 +-
examples/USER/eff/ECP/SiH4/in.SiH4 | 2 +-
examples/USER/eff/ECP/SiH4/in.SiH4.ang | 2 +-
examples/USER/eff/H/in.h_atom.spe.ang | 2 +-
examples/USER/eff/H/in.h_atom.spe.bohr | 2 +-
examples/USER/eff/H2/in.h2 | 2 +-
examples/USER/eff/H_plasma/in.h2bulk.nve.ang | 2 +-
examples/USER/eff/Li-solid/in.Li.ang | 2 +-
examples/USER/eff/Li-solid/in.Li.bohr | 2 +-
examples/USER/eff/fixed-core/C2H6/in.C2H6fc.ang | 2 +-
examples/USER/eff/fixed-core/C2H6/in.C2H6fc.bohr | 2 +-
examples/USER/eff/fixed-core/CH4/in.CH4fc.ang | 2 +-
examples/USER/eff/fixed-core/CH4/in.CH4fc.bohr | 2 +-
examples/USER/eff/fixed-core/CH4/in.CH4fc.spe.ang | 2 +-
examples/USER/eff/fixed-core/CH4/in.CH4fc.spe.bohr | 2 +-
examples/USER/misc/basal/in.basal | 4 +-
examples/comb/in.comb.Cu2O.elastic | 8 +-
examples/comb/in.comb.Si.elastic | 8 +-
examples/prd/in.prd | 2 +-
examples/tad/in.tad | 2 +-
lib/README | 2 +
lib/atc/ATC_Coupling.cpp | 55 -
lib/atc/ATC_Coupling.h | 2 +-
lib/atc/ATC_TypeDefs.h | 3 +-
lib/atc/FE_Element.cpp | 20 -
lib/atc/FE_Mesh.cpp | 7 -
lib/atc/PoissonSolver.cpp | 3 -
lib/gpu/Nvidia.makefile | 22 +-
lib/gpu/Opencl.makefile | 18 +-
lib/gpu/lal_atom.cpp | 34 +-
lib/gpu/lal_atom.h | 78 +-
lib/gpu/lal_base_dpd.cpp | 307 +
lib/gpu/lal_base_dpd.h | 203 +
lib/gpu/lal_device.cpp | 59 +-
lib/gpu/lal_device.h | 2 +-
lib/gpu/lal_dpd.cpp | 170 +
lib/gpu/lal_dpd.cu | 396 +
lib/gpu/lal_dpd.h | 86 +
lib/gpu/lal_dpd_ext.cpp | 133 +
lib/qmmm/Makefile.gfortran | 67 +
lib/qmmm/Makefile.lammps.empty | 5 +
lib/qmmm/README | 175 +
lib/qmmm/example1/mm-master/data.water | 236 +
lib/qmmm/example1/mm-master/water.in | 28 +
lib/qmmm/example1/mm-slave/data.single_water | 46 +
lib/qmmm/example1/mm-slave/water_single.in | 20 +
lib/qmmm/example1/qm-pw/pseudo/H.pbe-van_ak.UPF | 1088 +
lib/qmmm/example1/qm-pw/pseudo/O.pbe-van_bm.UPF | 3655 +++
lib/qmmm/example1/qm-pw/water.in | 38 +
lib/qmmm/example1/qmmm.inp | 24 +
lib/qmmm/libqmmm.c | 346 +
lib/qmmm/libqmmm.h | 75 +
lib/qmmm/pwqmmm.c | 365 +
src/ASPHERE/fix_nve_asphere_noforce.cpp | 1 -
src/ASPHERE/fix_nve_line.cpp | 6 +-
src/ASPHERE/fix_nve_tri.cpp | 4 +-
src/ASPHERE/pair_line_lj.cpp | 3 +-
src/ASPHERE/pair_resquared.cpp | 4 +-
src/BODY/body_nparticle.cpp | 2 +-
src/BODY/compute_body_local.cpp | 1 -
src/COLLOID/fix_wall_colloid.h | 2 +-
src/DIPOLE/pair_lj_cut_dipole_long.cpp | 1 -
src/FLD/pair_lubricate.cpp | 16 -
src/FLD/pair_lubricateU.cpp | 136 +-
src/FLD/pair_lubricateU_poly.cpp | 61 +-
src/FLD/pair_lubricate_poly.cpp | 16 -
src/GPU/Install.sh | 4 +
src/GPU/fix_gpu.cpp | 10 +-
src/GPU/pair_beck_gpu.h | 1 -
src/GPU/pair_born_coul_long_gpu.h | 1 -
src/GPU/pair_born_coul_wolf_gpu.h | 1 -
src/GPU/pair_born_gpu.h | 1 -
src/GPU/pair_buck_coul_cut_gpu.h | 1 -
src/GPU/pair_buck_coul_long_gpu.h | 1 -
src/GPU/pair_buck_gpu.h | 1 -
src/GPU/pair_colloid_gpu.h | 1 -
src/GPU/pair_coul_dsf_gpu.cpp | 5 +-
src/GPU/pair_coul_dsf_gpu.h | 1 -
src/GPU/pair_coul_long_gpu.cpp | 11 +-
src/GPU/pair_coul_long_gpu.h | 1 -
src/GPU/pair_dpd_gpu.cpp | 409 +
src/GPU/{pair_lj_cut_gpu.h => pair_dpd_gpu.h} | 15 +-
src/GPU/pair_dpd_tstat_gpu.cpp | 417 +
.../{pair_lj_cut_gpu.h => pair_dpd_tstat_gpu.h} | 15 +-
src/GPU/pair_eam_alloy_gpu.cpp | 2 +-
src/GPU/pair_eam_fs_gpu.cpp | 2 +-
src/GPU/pair_eam_gpu.cpp | 3 +-
src/GPU/pair_eam_gpu.h | 1 -
src/GPU/pair_gauss_gpu.cpp | 3 +-
src/GPU/pair_gauss_gpu.h | 1 -
src/GPU/pair_gayberne_gpu.h | 1 -
src/GPU/pair_lj96_cut_gpu.h | 1 -
src/GPU/pair_lj_charmm_coul_long_gpu.h | 1 -
src/GPU/pair_lj_class2_coul_long_gpu.h | 1 -
src/GPU/pair_lj_class2_gpu.h | 1 -
src/GPU/pair_lj_cut_coul_cut_gpu.h | 1 -
src/GPU/pair_lj_cut_coul_debye_gpu.h | 1 -
src/GPU/pair_lj_cut_coul_dsf_gpu.h | 1 -
src/GPU/pair_lj_cut_coul_long_gpu.h | 1 -
src/GPU/pair_lj_cut_coul_msm_gpu.cpp | 3 +
src/GPU/pair_lj_cut_coul_msm_gpu.h | 5 +-
src/GPU/pair_lj_cut_dipole_cut_gpu.h | 1 -
src/GPU/pair_lj_cut_gpu.h | 1 -
src/GPU/pair_lj_expand_gpu.h | 1 -
src/GPU/pair_lj_gromacs_gpu.h | 1 -
src/GPU/pair_lj_sdk_coul_long_gpu.h | 1 -
src/GPU/pair_lj_sdk_gpu.cpp | 2 +-
src/GPU/pair_lj_sdk_gpu.h | 1 -
src/GPU/pair_lj_sf_dipole_sf_gpu.h | 1 -
src/GPU/pair_mie_cut_gpu.h | 1 -
src/GPU/pair_morse_gpu.h | 1 -
src/GPU/pair_resquared_gpu.h | 1 -
src/GPU/pair_soft_gpu.h | 1 -
src/GPU/pair_sw_gpu.h | 1 -
src/GPU/pair_table_gpu.h | 1 -
src/GPU/pair_yukawa_colloid_gpu.cpp | 3 +-
src/GPU/pair_yukawa_colloid_gpu.h | 1 -
src/GPU/pair_yukawa_gpu.h | 1 -
src/GPU/pppm_gpu.cpp | 6 +
src/GRANULAR/fix_pour.cpp | 5 +-
src/GRANULAR/fix_pour.h | 2 +-
src/GRANULAR/pair_gran_hertz_history.cpp | 3 +-
src/KIM/pair_kim.cpp | 2 +-
src/KSPACE/commgrid.cpp | 4 -
src/KSPACE/ewald.cpp | 46 +-
src/KSPACE/ewald.h | 2 +-
src/KSPACE/ewald_disp.cpp | 11 +-
src/KSPACE/fft3d.cpp | 12 +-
src/KSPACE/fft3d.h | 2 +-
src/KSPACE/fft3d_wrap.cpp | 4 +-
src/KSPACE/fft3d_wrap.h | 2 +-
src/KSPACE/msm.cpp | 96 +-
src/KSPACE/msm.h | 6 +-
src/KSPACE/msm_cg.cpp | 19 +-
src/KSPACE/msm_cg.h | 4 +
src/KSPACE/pair_born_coul_msm.cpp | 84 +-
src/KSPACE/pair_born_coul_msm.h | 9 +-
src/KSPACE/pair_buck_coul_msm.cpp | 84 +-
src/KSPACE/pair_buck_coul_msm.h | 10 +-
src/KSPACE/pair_coul_msm.cpp | 22 +-
src/KSPACE/pair_coul_msm.h | 4 +
src/KSPACE/pair_lj_charmm_coul_msm.cpp | 88 +-
src/KSPACE/pair_lj_charmm_coul_msm.h | 14 +-
src/KSPACE/pair_lj_cut_coul_msm.cpp | 88 +-
src/KSPACE/pair_lj_cut_coul_msm.h | 13 +-
src/KSPACE/pair_tip4p_long.cpp | 10 +-
src/KSPACE/pppm.cpp | 69 +-
src/KSPACE/pppm.h | 1 -
src/KSPACE/pppm_cg.cpp | 29 +-
src/KSPACE/pppm_disp.cpp | 229 +-
src/KSPACE/pppm_disp.h | 1 -
src/KSPACE/pppm_disp_tip4p.cpp | 1 -
src/KSPACE/pppm_stagger.cpp | 27 +-
src/KSPACE/pppm_stagger.h | 3 +-
src/KSPACE/pppm_tip4p.cpp | 5 +-
src/KSPACE/remap.cpp | 373 +-
src/KSPACE/remap.h | 8 +-
src/KSPACE/remap_wrap.cpp | 5 +-
src/KSPACE/remap_wrap.h | 2 +-
src/MANYBODY/fix_qeq_comb.cpp | 9 -
src/MANYBODY/pair_adp.cpp | 8 +-
src/MANYBODY/pair_airebo.cpp | 3 +-
src/MANYBODY/pair_bop.cpp | 257 +-
src/MANYBODY/pair_comb.cpp | 14 +-
src/MANYBODY/pair_comb3.cpp | 57 +-
src/MANYBODY/pair_eam.cpp | 8 +-
src/MANYBODY/pair_eam_alloy.cpp | 5 +-
src/MANYBODY/pair_eam_fs.cpp | 5 +-
src/MANYBODY/pair_eim.cpp | 2 +-
src/MANYBODY/pair_lcbop.cpp | 2 +-
src/MANYBODY/pair_nb3b_harmonic.cpp | 2 +-
src/MANYBODY/pair_sw.cpp | 8 +-
src/MANYBODY/pair_tersoff.cpp | 8 +-
src/MANYBODY/pair_tersoff_mod.cpp | 8 +-
src/MANYBODY/pair_tersoff_zbl.cpp | 8 +-
src/MC/fix_bond_break.cpp | 547 +-
src/MC/fix_bond_break.h | 31 +-
src/MC/fix_bond_create.cpp | 31 +-
src/MC/fix_bond_swap.cpp | 43 +-
src/MC/fix_bond_swap.h | 2 +-
src/MEAM/pair_meam.cpp | 12 +-
src/MISC/compute_ti.cpp | 19 +-
src/MISC/fix_deposit.cpp | 37 +-
src/MISC/fix_deposit.h | 6 +-
src/MISC/fix_gld.cpp | 23 +-
src/MISC/fix_oneway.cpp | 109 +
src/{fix_recenter.h => MISC/fix_oneway.h} | 41 +-
src/MOLECULE/angle_table.cpp | 4 +-
src/MOLECULE/bond_fene.cpp | 2 +-
src/MOLECULE/bond_fene_expand.cpp | 2 +-
src/MOLECULE/bond_quartic.cpp | 2 +-
src/MOLECULE/bond_table.cpp | 2 +-
src/MPIIO/dump_atom_mpiio.cpp | 26 +-
src/MPIIO/dump_custom_mpiio.cpp | 24 +-
src/MPIIO/dump_xyz_mpiio.cpp | 20 +-
src/Make.py | 2 +-
src/Makefile | 18 +-
src/PERI/fix_peri_neigh.cpp | 3 +-
src/PERI/pair_peri_eps.cpp | 13 +-
src/PERI/pair_peri_eps.h | 1 +
src/PERI/pair_peri_lps.cpp | 6 +-
src/PERI/pair_peri_lps.h | 1 +
src/PERI/pair_peri_ves.cpp | 15 +-
src/PERI/pair_peri_ves.h | 4 +-
src/POEMS/fix_poems.cpp | 2 +-
src/Purge.list | 3 +
src/REPLICA/fix_event.cpp | 107 +-
src/REPLICA/fix_event.h | 21 +-
src/REPLICA/fix_event_prd.cpp | 4 +-
src/REPLICA/fix_event_prd.h | 2 +-
src/REPLICA/neb.cpp | 10 +-
src/REPLICA/prd.cpp | 143 +-
src/REPLICA/prd.h | 10 +-
src/REPLICA/tad.cpp | 21 +-
src/RIGID/fix_rigid_small.cpp | 39 +-
src/SRD/fix_srd.cpp | 14 +-
src/USER-CG-CMM/angle_sdk.cpp | 2 +-
src/USER-CG-CMM/pair_lj_sdk_coul_msm.cpp | 3 +
src/USER-CG-CMM/pair_lj_sdk_coul_msm.h | 9 +
src/USER-CUDA/Install.sh | 6 +-
src/USER-CUDA/cuda.cpp | 17 +-
src/USER-CUDA/fft3d_cuda.cpp | 8 +-
src/USER-CUDA/fix_addforce_cuda.cpp | 7 +-
src/USER-CUDA/fix_aveforce_cuda.cpp | 7 +-
src/USER-CUDA/fix_gravity_cuda.cpp | 23 +-
src/USER-CUDA/fix_nh_cuda.cpp | 74 +-
src/USER-CUDA/fix_set_force_cuda.cpp | 7 +-
src/USER-CUDA/fix_shake_cuda.cpp | 14 +-
src/USER-CUDA/fix_temp_berendsen_cuda.cpp | 6 +-
src/USER-CUDA/fix_temp_rescale_cuda.cpp | 10 +-
src/USER-CUDA/fix_temp_rescale_limit_cuda.cpp | 12 +-
src/USER-CUDA/pair_lj_sdk_coul_long_cuda.h | 5 +-
src/USER-CUDA/pair_lj_sdk_cuda.h | 5 +-
src/USER-CUDA/pppm_cuda.cpp | 38 +-
src/USER-CUDA/pppm_cuda.h | 1 -
src/{KSPACE => USER-CUDA}/pppm_old.cpp | 47 +-
src/{KSPACE => USER-CUDA}/pppm_old.h | 1 -
src/USER-CUDA/verlet_cuda.cpp | 9 +-
src/USER-EFF/compute_temp_eff.h | 1 -
src/USER-EFF/fix_langevin_eff.cpp | 10 -
src/USER-EFF/fix_nh_eff.cpp | 1 -
src/USER-EFF/fix_nvt_sllod_eff.cpp | 2 +-
src/USER-LB/fix_lb_fluid.cpp | 3 -
src/USER-LB/fix_lb_pc.cpp | 1 -
src/USER-LB/fix_lb_rigid_pc_sphere.cpp | 14 +-
src/USER-MISC/angle_dipole.cpp | 2 +-
src/USER-MISC/angle_quartic.cpp | 2 -
src/USER-MISC/dihedral_cosine_shift_exp.cpp | 6 +-
src/USER-MISC/dihedral_fourier.cpp | 9 +-
src/USER-MISC/dihedral_table.cpp | 6 +-
src/USER-MISC/improper_cossq.cpp | 2 +-
src/USER-MISC/pair_cdeam.cpp | 6 +-
src/USER-MISC/pair_edip.cpp | 2 +-
src/USER-MISC/pair_list.cpp | 2 +-
src/USER-MISC/pair_meam_spline.cpp | 2 +-
src/USER-MISC/pair_meam_sw_spline.cpp | 2 +-
src/USER-MISC/pair_tersoff_table.cpp | 19 +-
src/USER-MISC/pair_tersoff_table.h | 4 +-
src/USER-MOLFILE/molfile_interface.cpp | 41 -
src/USER-OMP/angle_charmm_omp.cpp | 1 +
src/USER-OMP/angle_class2_omp.cpp | 1 +
src/USER-OMP/angle_cosine_delta_omp.cpp | 1 +
src/USER-OMP/angle_cosine_omp.cpp | 1 +
src/USER-OMP/angle_cosine_periodic_omp.cpp | 1 +
src/USER-OMP/angle_cosine_shift_exp_omp.cpp | 1 +
src/USER-OMP/angle_cosine_squared_omp.cpp | 1 +
src/USER-OMP/angle_dipole_omp.cpp | 1 +
src/USER-OMP/angle_fourier_omp.cpp | 1 +
src/USER-OMP/angle_fourier_simple_omp.cpp | 1 +
src/USER-OMP/angle_harmonic_omp.cpp | 1 +
src/USER-OMP/angle_quartic_omp.cpp | 1 +
src/USER-OMP/angle_sdk_omp.cpp | 1 +
src/USER-OMP/angle_table_omp.cpp | 1 +
src/USER-OMP/bond_class2_omp.cpp | 1 +
src/USER-OMP/bond_fene_expand_omp.cpp | 1 +
src/USER-OMP/bond_fene_omp.cpp | 1 +
src/USER-OMP/bond_harmonic_omp.cpp | 1 +
src/USER-OMP/bond_harmonic_shift_cut_omp.cpp | 1 +
src/USER-OMP/bond_harmonic_shift_omp.cpp | 1 +
src/USER-OMP/bond_morse_omp.cpp | 1 +
src/USER-OMP/bond_nonlinear_omp.cpp | 1 +
src/USER-OMP/bond_table_omp.cpp | 1 +
src/USER-OMP/dihedral_charmm_omp.cpp | 2 +-
src/USER-OMP/dihedral_fourier_omp.cpp | 10 +-
src/USER-OMP/dihedral_table_omp.cpp | 2 +-
src/USER-OMP/fix_qeq_comb_omp.cpp | 15 +-
src/USER-OMP/fix_shear_history_omp.cpp | 49 +-
src/USER-OMP/msm_cg_omp.cpp | 19 +-
src/USER-OMP/msm_cg_omp.h | 4 +
src/USER-OMP/msm_omp.cpp | 3 +
src/USER-OMP/msm_omp.h | 8 +
src/USER-OMP/neigh_full_omp.cpp | 6 +-
src/USER-OMP/neigh_gran_omp.cpp | 8 +-
src/USER-OMP/neigh_half_bin_omp.cpp | 8 +-
src/USER-OMP/neigh_half_multi_omp.cpp | 6 +-
src/USER-OMP/neigh_respa_omp.cpp | 18 +-
src/USER-OMP/pair_adp_omp.cpp | 2 -
src/USER-OMP/pair_airebo_omp.cpp | 1 -
src/USER-OMP/pair_born_coul_msm_omp.cpp | 4 +
src/USER-OMP/pair_born_coul_msm_omp.h | 8 +
src/USER-OMP/pair_buck_coul_msm_omp.cpp | 4 +
src/USER-OMP/pair_buck_coul_msm_omp.h | 8 +
src/USER-OMP/pair_coul_msm_omp.cpp | 4 +
src/USER-OMP/pair_coul_msm_omp.h | 8 +
src/USER-OMP/pair_coul_wolf_omp.cpp | 3 +-
src/USER-OMP/pair_eam_alloy_omp.cpp | 3 +-
src/USER-OMP/pair_eam_fs_omp.cpp | 3 +-
src/USER-OMP/pair_gayberne_omp.cpp | 1 +
src/USER-OMP/pair_lj_charmm_coul_msm_omp.cpp | 4 +
src/USER-OMP/pair_lj_charmm_coul_msm_omp.h | 8 +
src/USER-OMP/pair_lj_cut_coul_msm_omp.cpp | 4 +
src/USER-OMP/pair_lj_cut_coul_msm_omp.h | 8 +
src/USER-OMP/pair_lj_cut_dipole_cut_omp.cpp | 2 +-
src/USER-OMP/pair_lj_gromacs_coul_gromacs_omp.cpp | 1 +
src/USER-OMP/pair_lj_sdk_coul_msm_omp.cpp | 4 +
src/USER-OMP/pair_lj_sdk_coul_msm_omp.h | 8 +
src/USER-OMP/pair_lj_sf_dipole_sf_omp.cpp | 2 +-
src/USER-OMP/pair_lj_sf_omp.cpp | 5 +-
src/USER-OMP/pair_meam_spline_omp.cpp | 10 +-
src/USER-OMP/pair_nb3b_harmonic_omp.cpp | 3 +-
src/USER-OMP/pair_resquared_omp.cpp | 1 +
src/USER-OMP/pair_table_omp.cpp | 2 +-
src/USER-OMP/pair_tersoff_table_omp.cpp | 88 +-
src/USER-OMP/pair_tersoff_table_omp.h | 9 +
src/USER-OMP/pair_tersoff_zbl_omp.cpp | 8 +-
src/USER-OMP/pair_tip4p_cut_omp.cpp | 5 +-
src/USER-OMP/pppm_cg_omp.h | 3 -
src/USER-OMP/pppm_disp_omp.cpp | 37 +-
src/USER-PHONON/fix_phonon.cpp | 20 +-
src/USER-QMMM/Install.sh | 64 +
src/USER-QMMM/README | 12 +
src/USER-QMMM/fix_qmmm.cpp | 758 +
src/USER-QMMM/fix_qmmm.h | 86 +
src/USER-REAXC/fix_qeq_reax.cpp | 10 +-
src/USER-REAXC/fix_reaxc_bonds.cpp | 12 +-
src/USER-REAXC/pair_reax_c.cpp | 34 +-
src/USER-REAXC/reaxc_allocate.cpp | 24 +-
src/USER-REAXC/reaxc_bond_orders.cpp | 1 -
src/USER-REAXC/reaxc_defs.h | 2 +-
src/USER-REAXC/reaxc_forces.cpp | 2 +-
src/USER-REAXC/reaxc_io_tools.cpp | 8 +-
src/USER-REAXC/reaxc_torsion_angles.cpp | 6 +-
src/USER-SPH/fix_meso_stationary.cpp | 3 -
src/VORONOI/compute_voronoi_atom.cpp | 4 +-
src/accelerator_cuda.h | 2 +
src/accelerator_kokkos.h | 24 +-
src/atom.cpp | 17 +-
src/atom.h | 11 +-
src/atom_map.cpp | 78 +-
src/atom_vec_body.cpp | 15 +-
src/atom_vec_sphere.h | 2 +-
src/balance.cpp | 86 +-
src/balance.h | 2 +
src/body.cpp | 2 +
src/change_box.cpp | 1 -
src/comm.cpp | 55 +
src/comm.h | 2 +
src/compute_angle_local.cpp | 2 -
src/compute_atom_molecule.h | 2 +-
src/compute_bond_local.cpp | 1 -
src/compute_bond_local.h | 2 +-
src/compute_cluster_atom.cpp | 3 +-
src/compute_dihedral_local.cpp | 7 +-
src/compute_group_group.cpp | 3 +-
src/compute_gyration_molecule.cpp | 2 +-
src/compute_improper_local.cpp | 2 -
src/compute_inertia_molecule.cpp | 6 +-
src/compute_pair_local.h | 2 +-
src/compute_pressure.cpp | 8 +-
src/compute_pressure.h | 5 +
src/compute_property_atom.cpp | 20 +
src/compute_property_atom.h | 2 +
src/compute_property_local.cpp | 2 -
src/compute_rdf.h | 19 +-
src/compute_reduce.cpp | 7 +-
src/compute_temp_profile.cpp | 1 -
src/delete_atoms.cpp | 6 +-
src/displace_atoms.cpp | 2 +-
src/domain.cpp | 2 +-
src/dump.cpp | 2 +-
src/dump_cfg.h | 2 +-
src/dump_image.cpp | 8 +-
src/finish.cpp | 41 +-
src/fix.cpp | 6 +-
src/fix.h | 5 +-
src/fix_ave_correlate.h | 1 -
src/fix_ave_histo.h | 2 +-
src/fix_ave_spatial.cpp | 8 +-
src/fix_ave_time.h | 2 +-
src/fix_balance.cpp | 5 +-
src/fix_box_relax.cpp | 12 +-
src/fix_indent.h | 2 +-
src/fix_move.cpp | 9 +-
src/fix_nh.cpp | 17 +-
src/fix_press_berendsen.cpp | 4 +-
src/fix_property_atom.cpp | 2 +-
src/fix_recenter.cpp | 36 +-
src/fix_recenter.h | 6 +-
src/fix_setforce.h | 4 +-
src/fix_spring.h | 1 -
src/fix_temp_csvr.cpp | 287 +
src/{MC/fix_bond_swap.h => fix_temp_csvr.h} | 74 +-
src/fix_vector.cpp | 7 +-
src/fix_vector.h | 2 +-
src/fix_wall_region.cpp | 2 +-
src/fix_wall_region.h | 1 -
src/force.cpp | 86 +
src/force.h | 5 +
src/group.cpp | 14 +-
src/image.cpp | 13 +-
src/input.cpp | 39 +-
src/irregular.cpp | 57 +-
src/irregular.h | 8 +-
src/kspace.cpp | 88 +-
src/kspace.h | 38 +-
src/lammps.cpp | 14 +-
src/lattice.cpp | 4 +-
src/lmptype.h | 2 +-
src/memory.h | 4 +-
src/min.cpp | 4 -
src/min_linesearch.cpp | 4 +-
src/modify.cpp | 10 +-
src/molecule.cpp | 15 +-
src/molecule.h | 2 +-
src/my_page.h | 2 +-
src/neigh_full.cpp | 6 +-
src/neigh_half_bin.cpp | 8 +-
src/neigh_half_multi.cpp | 6 +-
src/neigh_list.cpp | 2 +
src/neigh_list.h | 6 +-
src/neigh_request.cpp | 2 +
src/neigh_request.h | 5 +
src/neigh_respa.cpp | 18 +-
src/neigh_stencil.cpp | 5 +-
src/neighbor.cpp | 266 +-
src/neighbor.h | 15 +-
src/pair.cpp | 96 +-
src/pair.h | 8 +-
src/pair_born_coul_wolf.cpp | 3 +-
src/pair_coul_wolf.cpp | 14 +-
src/pair_gauss.cpp | 2 +-
src/pair_hybrid.cpp | 6 +-
src/pair_lj_cut.h | 2 +-
src/pair_lj_cut_coul_dsf.cpp | 2 +-
src/pair_lj_smooth_linear.cpp | 1 -
src/pair_mie_cut.cpp | 4 +-
src/pair_table.cpp | 2 +-
src/procmap.cpp | 10 +-
src/random_mars.h | 2 +-
src/read_data.cpp | 188 +-
src/read_data.h | 14 +-
src/read_restart.cpp | 10 +-
src/run.cpp | 2 +-
src/set.cpp | 3 -
src/special.h | 1 -
src/thermo.cpp | 54 +-
src/thermo.h | 5 +
src/universe.cpp | 2 +-
src/update.cpp | 19 +-
src/variable.cpp | 54 +-
src/version.h | 2 +-
src/write_data.cpp | 22 +-
src/write_restart.cpp | 2 +-
tools/moltemplate/LICENSE.TXT | 2 +-
tools/moltemplate/README.TXT | 2 +-
tools/moltemplate/common/oplsaa/AUTHOR.TXT | 3 +
tools/moltemplate/common/oplsaa/README.TXT | 82 +
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.../common/oplsaa/oplsaa_moltemplate.py | 319 +
tools/moltemplate/common/trappe1998.lt | 31 +-
.../moltemplate_files/CGLipidBr2005Orig.lt | 2 +-
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.../README_visualize.txt | 131 +
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.../images/vmd_colorscale_jet.tcl | 87 +
.../README_how_to_generate_system_lt.sh | 19 +
.../README_length_flexibility_details.txt | 57 +
.../moltemplate_files/calc_table.sh | 8 +
.../moltemplate_files/condensin.lt | 47 +
.../moltemplate_files/coords_orig.raw | 32768 +++++++++++++++++++
.../moltemplate_files/generate_system_lt.py | 301 +
.../moltemplate_files/interpolate_coords.py | 74 +
.../moltemplate_files/monomer.lt | 84 +
.../moltemplate_files/table_bonds_stage2.dat | 4011 +++
.../run.in.min | 41 +
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.../moltemplate_files/isobutane.lt | 4 +-
.../OPLSAA_force_field_examples/WARNING.TXT | 26 +
.../ethylene/README.TXT | 13 +
.../ethylene}/README_run.sh | 0
.../ethylene/README_setup.sh | 36 +
.../ethylene}/README_visualize.txt | 0
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.../ethylene/moltemplate_files/ethylene.lt | 42 +
.../oplsaa_lt_generator/AUTHOR.TXT | 3 +
.../oplsaa_lt_generator/README.TXT | 81 +
.../oplsaa_lt_generator/oplsaa.txt | 5968 ++++
.../oplsaa_lt_generator/oplsaa_moltemplate.py | 319 +
.../oplsaa_lt_generator/oplsaa_subset.txt | 3450 ++
.../ethylene/moltemplate_files/system.lt | 19 +
.../ethylene/run.in.npt | 57 +
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.../waterSPCE+Na+Cl/moltemplate_files/ions.lt | 9 +-
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.../src/docs_useful_scripts/docs_dump2data.txt | 109 +
tools/moltemplate/src/dump2data.py | 4 +-
tools/moltemplate/src/moltemplate.sh | 32 +-
tools/moltemplate/src/ttree_matrix_stack.py | 90 +-
tools/msi2lmp/README | 25 +-
tools/msi2lmp/src/ReadCarFile.c | 6 +-
tools/msi2lmp/src/WriteDataFile.c | 166 +-
tools/msi2lmp/src/msi2lmp.c | 26 +-
tools/msi2lmp/src/msi2lmp.h | 5 +-
tools/msi2lmp/test/reference/PyAC_bulk-clayff.data | 1608 +-
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create mode 100644 tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/oplsaa_lt_generator/oplsaa_subset.txt
create mode 100644 tools/moltemplate/examples/all_atom_examples/OPLSAA_force_field_examples/ethylene/moltemplate_files/system.lt
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