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Merge branch 'develop' into general-triclinic

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This commit is contained in:
Axel Kohlmeyer
2024-01-04 21:10:50 -05:00
parent e1be6c09f7 0e2a065f6b
commit c6d1cbef5a
536 changed files with 23786 additions and 19860 deletions
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2
tools/lammps-gui/CMakeLists.txt
View File

@ -1,6 +1,6 @@
cmake_minimum_required(VERSION 3.16)
project(lammps-gui VERSION 1.5.10 LANGUAGES CXX)
project(lammps-gui VERSION 1.5.11 LANGUAGES CXX)
set(CMAKE_AUTOUIC ON)
set(CMAKE_AUTOMOC ON)

24
tools/lammps-gui/help_index.table
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@ -254,6 +254,7 @@ compute_nbond_atom.html compute nbond/atom
compute_omega_chunk.html compute omega/chunk
compute_orientorder_atom.html compute orientorder/atom
compute_orientorder_atom.html compute orientorder/atom/kk
compute_pace.html compute pace
compute_pair_local.html compute pair/local
compute_pair.html compute pair
compute_pe_atom.html compute pe/atom
@ -267,13 +268,17 @@ compute_property_chunk.html compute property/chunk
compute_property_grid.html compute property/grid
compute_property_local.html compute property/local
compute_ptm_atom.html compute ptm/atom
compute_rattlers_atom.html compute rattlers/atom
compute_rdf.html compute rdf
compute_reaxff_atom.html compute reaxff/atom
compute_reaxff_atom.html compute reaxff/atom/kk
compute_reduce_chunk.html compute reduce/chunk
compute_reduce.html compute reduce
compute_reduce.html compute reduce/region
compute_rigid_local.html compute rigid/local
compute.html compute
compute_saed.html compute saed
compute_slcsa_atom.html compute slcsa/atom
compute_slice.html compute slice
compute_smd_contact_radius.html compute smd/contact/radius
compute_smd_damage.html compute smd/damage
@ -484,6 +489,7 @@ fix_drude_transform.html fix drude/transform/inverse
fix_dt_reset.html fix dt/reset
fix_dt_reset.html fix dt/reset/kk
fix_efield.html fix efield
fix_efield.html fix efield/kk
fix_efield.html fix efield/tip4p
fix_ehex.html fix ehex
fix_electrode.html fix electrode/conp
@ -565,6 +571,7 @@ fix_nh.html fix nvt/kk
fix_nh.html fix nvt/omp
fix_nh_uef.html fix npt/uef
fix_nh_uef.html fix nvt/uef
fix_nonaffine_displacement.html fix nonaffine/displacement
fix_nph_asphere.html fix nph/asphere
fix_nph_asphere.html fix nph/asphere/omp
fix_nph_body.html fix nph/body
@ -634,6 +641,7 @@ fix_polarize.html fix polarize/functional
fix_pour.html fix pour
fix_precession_spin.html fix precession/spin
fix_press_berendsen.html fix press/berendsen
fix_press_langevin.html fix press/langevin
fix_print.html fix print
fix_propel_self.html fix propel/self
fix_property_atom.html fix property/atom
@ -703,14 +711,17 @@ fix_spring_chunk.html fix spring/chunk
fix_spring_rg.html fix spring/rg
fix_spring.html fix spring
fix_spring_self.html fix spring/self
fix_spring_self.html fix spring/self/kk
fix_srd.html fix srd
fix_store_force.html fix store/force
fix_store_state.html fix store/state
fix_temp_berendsen.html fix temp/berendsen
fix_temp_berendsen.html fix temp/berendsen/kk
fix_temp_csvr.html fix temp/csld
fix_temp_csvr.html fix temp/csvr
fix_temp_rescale_eff.html fix temp/rescale/eff
fix_temp_rescale.html fix temp/rescale
fix_temp_rescale.html fix temp/rescale/kk
fix_tfmc.html fix tfmc
fix_tgnh_drude.html fix tgnpt/drude
fix_tgnh_drude.html fix tgnvt/drude
@ -980,6 +991,7 @@ pair_coul_shield.html pair_style coul/shield
pair_coul_slater.html pair_style coul/slater
pair_coul_slater.html pair_style coul/slater/cut
pair_coul_slater.html pair_style coul/slater/long
pair_coul_slater.html pair_style coul/slater/long/gpu
pair_coul_tt.html pair_style coul/tt
pair_cs.html pair_style born/coul/dsf/cs
pair_cs.html pair_style born/coul/long/cs
@ -1073,8 +1085,10 @@ pair_fep_soft.html pair_style lj/class2/coul/cut/soft
pair_fep_soft.html pair_style lj/class2/coul/long/soft
pair_fep_soft.html pair_style lj/class2/soft
pair_fep_soft.html pair_style lj/cut/coul/cut/soft
pair_fep_soft.html pair_style lj/cut/coul/cut/soft/gpu
pair_fep_soft.html pair_style lj/cut/coul/cut/soft/omp
pair_fep_soft.html pair_style lj/cut/coul/long/soft
pair_fep_soft.html pair_style lj/cut/coul/long/soft/gpu
pair_fep_soft.html pair_style lj/cut/coul/long/soft/omp
pair_fep_soft.html pair_style lj/cut/soft
pair_fep_soft.html pair_style lj/cut/soft/omp
@ -1225,7 +1239,9 @@ pair_meam_sw_spline.html pair_style meam/sw/spline
pair_mesocnt.html pair_style mesocnt
pair_mesocnt.html pair_style mesocnt/viscous
pair_mesodpd.html pair_style edpd
pair_mesodpd.html pair_style edpd/gpu
pair_mesodpd.html pair_style mdpd
pair_mesodpd.html pair_style mdpd/gpu
pair_mesodpd.html pair_style mdpd/rhosum
pair_mesodpd.html pair_style tdpd
pair_mgpt.html pair_style mgpt
@ -1245,7 +1261,8 @@ pair_morse.html pair_style morse/smooth/linear/omp
pair_multi_lucy.html pair_style multi/lucy
pair_multi_lucy_rx.html pair_style multi/lucy/rx
pair_multi_lucy_rx.html pair_style multi/lucy/rx/kk
pair_nb3b_harmonic.html pair_style nb3b/harmonic
pair_nb3b.html pair_style nb3b/harmonic
pair_nb3b.html pair_style nb3b/screened
pair_nm.html pair_style nm/cut
pair_nm.html pair_style nm/cut/coul/cut
pair_nm.html pair_style nm/cut/coul/cut/omp
@ -1303,16 +1320,20 @@ pair_smd_triangulated_surface.html pair_style smd/tri_surface
pair_smd_ulsph.html pair_style smd/ulsph
pair_smtbq.html pair_style smtbq
pair_snap.html pair_style snap
pair_snap.html pair_style snap/intel
pair_snap.html pair_style snap/kk
pair_soft.html pair_style soft
pair_soft.html pair_style soft/gpu
pair_soft.html pair_style soft/omp
pair_sph_heatconduction.html pair_style sph/heatconduction
pair_sph_heatconduction.html pair_style sph/heatconduction/gpu
pair_sph_idealgas.html pair_style sph/idealgas
pair_sph_lj.html pair_style sph/lj
pair_sph_lj.html pair_style sph/lj/gpu
pair_sph_rhosum.html pair_style sph/rhosum
pair_sph_taitwater_morris.html pair_style sph/taitwater/morris
pair_sph_taitwater.html pair_style sph/taitwater
pair_sph_taitwater.html pair_style sph/taitwater/gpu
pair_spica.html pair_style lj/spica
pair_spica.html pair_style lj/spica/coul/long
pair_spica.html pair_style lj/spica/coul/long/gpu
@ -1384,6 +1405,7 @@ pair_write.html pair_write
pair_ylz.html pair_style ylz
pair_yukawa_colloid.html pair_style yukawa/colloid
pair_yukawa_colloid.html pair_style yukawa/colloid/gpu
pair_yukawa_colloid.html pair_style yukawa/colloid/kk
pair_yukawa_colloid.html pair_style yukawa/colloid/omp
pair_yukawa.html pair_style yukawa
pair_yukawa.html pair_style yukawa/gpu

2
tools/lammps-gui/main.cpp
View File

@ -36,7 +36,7 @@ int main(int argc, char *argv[])
LammpsGui w(nullptr, infile);
w.show();
return a.exec();
return QApplication::exec();
}
// Local Variables:

2
tools/lammps-gui/preferences.cpp
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@ -177,7 +177,7 @@ void Preferences::accept()
msg.exec();
const char *path = mystrdup(QCoreApplication::applicationFilePath());
const char *arg0 = mystrdup(QCoreApplication::arguments().at(0));
execl(path, arg0, (char *)NULL);
execl(path, arg0, (char *)nullptr);
}
// reformatting settings

6
tools/lammps-gui/stdcapture.cpp
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@ -38,7 +38,7 @@
StdCapture::StdCapture() : m_oldStdOut(0), m_capturing(false)
{
// make stdout unbuffered so that we don't need to flush the stream
setvbuf(stdout, NULL, _IONBF, 0);
setvbuf(stdout, nullptr, _IONBF, 0);
m_pipe[READ] = 0;
m_pipe[WRITE] = 0;
@ -106,7 +106,7 @@ bool StdCapture::EndCapture()
std::string StdCapture::GetChunk()
{
if (!m_capturing) return std::string();
if (!m_capturing) return {};
int bytesRead = 0;
buf[0] = '\0';
@ -120,7 +120,7 @@ std::string StdCapture::GetChunk()
if (bytesRead > 0) {
buf[bytesRead] = '\0';
}
return std::string(buf);
return {buf};
}
std::string StdCapture::GetCapture()

4
tools/msi2lmp/src/SearchAndFill.c
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@ -93,7 +93,7 @@ void SearchAndFill(struct FrcFieldItem *item)
file_pos = ftell(FrcF);
if (file_pos < 0) {
fprintf(stderr, "Could not obtain file stream position: ", strerror(errno));
fprintf(stderr, "Could not obtain file stream position: %s\n", strerror(errno));
exit(2);
}
@ -116,7 +116,7 @@ void SearchAndFill(struct FrcFieldItem *item)
/* Read lines until keyword is found */
if (fseek(FrcF,file_pos,SEEK_SET) < 0) {
fprintf(stderr, "Resetting file stream failed: ", strerror(errno));
fprintf(stderr, "Resetting file stream failed: %s\n", strerror(errno));
exit(2);
}
strcpy(line,"empty");

41
tools/valgrind/MPICH.supp Normal file
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@ -0,0 +1,41 @@
{
MPICH_MPI_init1
Memcheck:Leak
match-leak-kinds: reachable
fun:malloc
obj:*
...
fun:psm3_init
...
fun:MPIDI_OFI_init_local
...
fun:PMPI_Init
fun:main
}
{
MPICH_MPI_init2
Memcheck:Leak
match-leak-kinds: reachable
fun:malloc
fun:strdup
obj:*
...
fun:fi_ini
...
fun:MPIDI_OFI_init_local
...
fun:PMPI_Init
fun:main
}
{
MPICH_MPI_init3
Memcheck:Leak
match-leak-kinds: reachable
fun:calloc
obj:*
...
fun:MPIDI_OFI_init_local
...
fun:PMPI_Init
fun:main
}

1
tools/valgrind/README
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@ -8,6 +8,7 @@ on running LAMMPS, use a command line like following:
valgrind --show-leak-kinds=all --track-origins=yes \
--suppressions=/path/to/lammps/tools/valgrind/OpenMP.supp \
--suppressions=/path/to/lammps/tools/valgrind/OpenMPI.supp \
--suppressions=/path/to/lammps/tools/valgrind/MPICH.supp \
--suppressions=/path/to/lammps/tools/valgrind/Python3.supp \
--suppressions=/path/to/lammps/tools/valgrind/GTest.supp \
--suppressions=/path/to/lammps/tools/valgrind/FlexiBLAS.supp \