forked from lijiext/lammps
Merge branch 'master' into improve-include-consistency
# Conflicts: # src/utils.cpp
This commit is contained in:
Axel Kohlmeyer
commit
a50d57bceb
|
|
@ -37,7 +37,7 @@ include(PreventInSourceBuilds)
|
|||
|
||||
if(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
|
||||
#release comes with -O3 by default
|
||||
set(CMAKE_BUILD_TYPE Release CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE)
|
||||
set(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING "Choose the type of build, options are: None Debug Release RelWithDebInfo MinSizeRel." FORCE)
|
||||
endif(NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CXX_FLAGS)
|
||||
string(TOUPPER "${CMAKE_BUILD_TYPE}" BTYPE)
|
||||
|
||||
|
|
@ -673,5 +673,10 @@ if(PKG_KOKKOS)
|
|||
message(STATUS "Kokkos Arch: ${KOKKOS_ARCH}")
|
||||
endif()
|
||||
if(PKG_KSPACE)
|
||||
message(STATUS "Using ${FFT} as FFT")
|
||||
message(STATUS "Using ${FFT} as primary FFT library")
|
||||
if(FFT_SINGLE)
|
||||
message(STATUS "Using single precision FFTs")
|
||||
else()
|
||||
message(STATUS "Using double precision FFTs")
|
||||
endif()
|
||||
endif()
|
||||
|
|
|
|||
|
|
@ -1,5 +1,5 @@
|
|||
if(PKG_KSPACE)
|
||||
option(FFT_SINGLE "Use single precision FFT instead of double" OFF)
|
||||
option(FFT_SINGLE "Use single precision FFTs instead of double precision FFTs" OFF)
|
||||
set(FFTW "FFTW3")
|
||||
if(FFT_SINGLE)
|
||||
set(FFTW "FFTW3F")
|
||||
|
|
@ -7,26 +7,30 @@ if(PKG_KSPACE)
|
|||
endif()
|
||||
find_package(${FFTW} QUIET)
|
||||
if(${FFTW}_FOUND)
|
||||
set(FFT "${FFTW}" CACHE STRING "FFT library for KSPACE package")
|
||||
set(FFT "FFTW3" CACHE STRING "FFT library for KSPACE package")
|
||||
else()
|
||||
set(FFT "KISS" CACHE STRING "FFT library for KSPACE package")
|
||||
endif()
|
||||
set(FFT_VALUES KISS ${FFTW} MKL)
|
||||
set(FFT_VALUES KISS FFTW3 MKL)
|
||||
set_property(CACHE FFT PROPERTY STRINGS ${FFT_VALUES})
|
||||
validate_option(FFT FFT_VALUES)
|
||||
string(TOUPPER ${FFT} FFT)
|
||||
if(NOT FFT STREQUAL "KISS")
|
||||
find_package(${FFT} REQUIRED)
|
||||
if(NOT FFT STREQUAL "FFTW3F")
|
||||
add_definitions(-DFFT_FFTW)
|
||||
else()
|
||||
add_definitions(-DFFT_${FFT})
|
||||
endif()
|
||||
include_directories(${${FFT}_INCLUDE_DIRS})
|
||||
list(APPEND LAMMPS_LINK_LIBS ${${FFT}_LIBRARIES})
|
||||
|
||||
if(FFT STREQUAL "FFTW3")
|
||||
find_package(${FFTW} REQUIRED)
|
||||
add_definitions(-DFFT_FFTW3)
|
||||
include_directories(${${FFTW}_INCLUDE_DIRS})
|
||||
list(APPEND LAMMPS_LINK_LIBS ${${FFTW}_LIBRARIES})
|
||||
elseif(FFT STREQUAL "MKL")
|
||||
find_package(MKL REQUIRED)
|
||||
add_definitions(-DFFT_MKL)
|
||||
include_directories(${MKL_INCLUDE_DIRS})
|
||||
list(APPEND LAMMPS_LINK_LIBS ${MKL_LIBRARIES})
|
||||
else()
|
||||
# last option is KISSFFT
|
||||
add_definitions(-DFFT_KISS)
|
||||
endif()
|
||||
|
||||
set(FFT_PACK "array" CACHE STRING "Optimization for FFT")
|
||||
set(FFT_PACK_VALUES array pointer memcpy)
|
||||
set_property(CACHE FFT_PACK PROPERTY STRINGS ${FFT_PACK_VALUES})
|
||||
|
|
|
|||
|
|
@ -5890,6 +5890,11 @@ The element names in the ADP file do not match those requested. :dd
|
|||
|
||||
The element names in the EAM file do not match those requested. :dd
|
||||
|
||||
{Incorrect format of ... section in data file} :dt
|
||||
|
||||
Number or type of values per line in the given section of the data file
|
||||
is not consistent with the requirements for this section. :dd
|
||||
|
||||
{Incorrect format in COMB potential file} :dt
|
||||
|
||||
Incorrect number of words per line in the potential file. :dd
|
||||
|
|
|
|||
|
|
@ -171,42 +171,40 @@ The individual style names on the "Commands
|
|||
compute"_Commands_compute.html doc page are followed by one or more of
|
||||
(g,i,k,o,t) to indicate which accelerated styles exist.
|
||||
|
||||
"ackland/atom"_compute_ackland_atom.html -
|
||||
"ackland/atom"_compute_ackland_atom.html - determines the local lattice structure based on the Ackland formulation
|
||||
"adf"_compute_adf.html - angular distribution function of triples of atoms
|
||||
"aggregate/atom"_compute_cluster_atom.html - aggregate ID for each atom
|
||||
"angle"_compute_angle.html -
|
||||
"angle/local"_compute_angle_local.html -
|
||||
"angle/local"_compute_bond_local.html - theta and energy of each angle
|
||||
"angle"_compute_angle.html - energy of each angle sub-style
|
||||
"angle/local"_compute_angle_local.html - theta and energy of each angle
|
||||
"angmom/chunk"_compute_angmom_chunk.html - angular momentum for each chunk
|
||||
"basal/atom"_compute_basal_atom.html -
|
||||
"basal/atom"_compute_basal_atom.html - calculates the hexagonal close-packed “c” lattice vector of each atom
|
||||
"body/local"_compute_body_local.html - attributes of body sub-particles
|
||||
"bond"_compute_bond.html - values computed by a bond style
|
||||
"bond"_compute_bond.html - energy of each bond sub-style
|
||||
"bond/local"_compute_bond_local.html - distance and energy of each bond
|
||||
"centro/atom"_compute_centro_atom.html - centro-symmetry parameter for each atom
|
||||
"chunk/atom"_compute_chunk_atom.html - assign chunk IDs to each atom
|
||||
"chunk/spread/atom"_compute_chunk_spread_atom.html - spreads chunk values to each atom in chunk
|
||||
"cluster/atom"_compute_cluster_atom.html - cluster ID for each atom
|
||||
"cna/atom"_compute_cna_atom.html - common neighbor analysis (CNA) for each atom
|
||||
"cnp/atom"_compute_cnp_atom.html -
|
||||
"cnp/atom"_compute_cnp_atom.html - common neighborhood parameter (CNP) for each atom
|
||||
"com"_compute_com.html - center-of-mass of group of atoms
|
||||
"com/chunk"_compute_com_chunk.html - center-of-mass for each chunk
|
||||
"contact/atom"_compute_contact_atom.html - contact count for each spherical particle
|
||||
"coord/atom"_compute_coord_atom.html - coordination number for each atom
|
||||
"damage/atom"_compute_damage_atom.html - Peridynamic damage for each atom
|
||||
"dihedral"_compute_dihedral.html -
|
||||
"dihedral"_compute_dihedral.html - energy of each dihedral sub-style
|
||||
"dihedral/local"_compute_dihedral_local.html - angle of each dihedral
|
||||
"dilatation/atom"_compute_dilatation_atom.html - Peridynamic dilatation for each atom
|
||||
"dipole/chunk"_compute_dipole_chunk.html -
|
||||
"dipole/chunk"_compute_dipole_chunk.html - dipole vector and total dipole for each chunk
|
||||
"displace/atom"_compute_displace_atom.html - displacement of each atom
|
||||
"dpd"_compute_dpd.html -
|
||||
"dpd/atom"_compute_dpd_atom.html -
|
||||
"edpd/temp/atom"_compute_edpd_temp_atom.html -
|
||||
"entropy/atom"_compute_entropy_atom.html -
|
||||
"edpd/temp/atom"_compute_edpd_temp_atom.html - per-atom temperature for each eDPD particle in a group
|
||||
"entropy/atom"_compute_entropy_atom.html - pair entropy fingerprint of each atom
|
||||
"erotate/asphere"_compute_erotate_asphere.html - rotational energy of aspherical particles
|
||||
"erotate/rigid"_compute_erotate_rigid.html - rotational energy of rigid bodies
|
||||
"erotate/sphere"_compute_erotate_sphere.html - rotational energy of spherical particles
|
||||
"erotate/sphere/atom"_compute_erotate_sphere.html - rotational energy for each spherical particle
|
||||
"erotate/sphere/atom"_compute_erotate_sphere_atom.html -
|
||||
"erotate/sphere/atom"_compute_erotate_sphere_atom.html - rotational energy for each spherical particle
|
||||
"event/displace"_compute_event_displace.html - detect event on atom displacement
|
||||
"fep"_compute_fep.html -
|
||||
"force/tally"_compute_tally.html -
|
||||
|
|
@ -218,17 +216,17 @@ compute"_Commands_compute.html doc page are followed by one or more of
|
|||
"heat/flux"_compute_heat_flux.html - heat flux through a group of atoms
|
||||
"heat/flux/tally"_compute_tally.html -
|
||||
"hexorder/atom"_compute_hexorder_atom.html - bond orientational order parameter q6
|
||||
"improper"_compute_improper.html -
|
||||
"improper"_compute_improper.html - energy of each improper sub-style
|
||||
"improper/local"_compute_improper_local.html - angle of each improper
|
||||
"inertia/chunk"_compute_inertia_chunk.html - inertia tensor for each chunk
|
||||
"ke"_compute_ke.html - translational kinetic energy
|
||||
"ke/atom"_compute_ke_atom.html - kinetic energy for each atom
|
||||
"ke/atom/eff"_compute_ke_atom_eff.html -
|
||||
"ke/eff"_compute_ke_eff.html -
|
||||
"ke/atom/eff"_compute_ke_atom_eff.html - per-atom translational and radial kinetic energy in the electron force field model
|
||||
"ke/eff"_compute_ke_eff.html - kinetic energy of a group of nuclei and electrons in the electron force field model
|
||||
"ke/rigid"_compute_ke_rigid.html - translational kinetic energy of rigid bodies
|
||||
"meso/e/atom"_compute_meso_e_atom.html -
|
||||
"meso/rho/atom"_compute_meso_rho_atom.html -
|
||||
"meso/t/atom"_compute_meso_t_atom.html -
|
||||
"meso/e/atom"_compute_meso_e_atom.html - per-atom internal energy of Smooth-Particle Hydrodynamics atoms
|
||||
"meso/rho/atom"_compute_meso_rho_atom.html - per-atom mesoscopic density of Smooth-Particle Hydrodynamics atoms
|
||||
"meso/t/atom"_compute_meso_t_atom.html - per-atom internal temperature of Smooth-Particle Hydrodynamics atoms
|
||||
"msd"_compute_msd.html - mean-squared displacement of group of atoms
|
||||
"msd/chunk"_compute_msd_chunk.html - mean-squared displacement for each chunk
|
||||
"msd/nongauss"_compute_msd_nongauss.html - MSD and non-Gaussian parameter of group of atoms
|
||||
|
|
@ -242,73 +240,72 @@ compute"_Commands_compute.html doc page are followed by one or more of
|
|||
"pe/tally"_compute_tally.html -
|
||||
"plasticity/atom"_compute_plasticity_atom.html - Peridynamic plasticity for each atom
|
||||
"pressure"_compute_pressure.html - total pressure and pressure tensor
|
||||
"pressure/cylinder"_compute_pressure_cylinder.html -
|
||||
"pressure/uef"_compute_pressure_uef.html -
|
||||
"pressure/cylinder"_compute_pressure_cylinder.html - pressure tensor in cylindrical coordinates
|
||||
"pressure/uef"_compute_pressure_uef.html - pressure tensor in the reference frame of an applied flow field
|
||||
"property/atom"_compute_property_atom.html - convert atom attributes to per-atom vectors/arrays
|
||||
"property/chunk"_compute_property_chunk.html - extract various per-chunk attributes
|
||||
"property/local"_compute_property_local.html - convert local attributes to localvectors/arrays
|
||||
"ptm/atom"_compute_ptm_atom.html -
|
||||
"ptm/atom"_compute_ptm_atom.html - determines the local lattice structure based on the Polyhedral Template Matching method
|
||||
"rdf"_compute_rdf.html - radial distribution function g(r) histogram of group of atoms
|
||||
"reduce"_compute_reduce.html - combine per-atom quantities into a single global value
|
||||
"reduce/chunk"_compute_reduce_chunk.html - reduce per-atom quantities within each chunk
|
||||
"reduce/region"_compute_reduce.html - same as compute reduce, within a region
|
||||
"rigid/local"_compute_rigid_local.html - extract rigid body attributes
|
||||
"saed"_compute_saed.html -
|
||||
"saed"_compute_saed.html - electron diffraction intensity on a mesh of reciprocal lattice nodes
|
||||
"slice"_compute_slice.html - extract values from global vector or array
|
||||
"smd/contact/radius"_compute_smd_contact_radius.html -
|
||||
"smd/damage"_compute_smd_damage.html -
|
||||
"smd/damage"_compute_smd_damage.html - damage status of SPH particles in Smooth Mach Dynamics
|
||||
"smd/hourglass/error"_compute_smd_hourglass_error.html -
|
||||
"smd/internal/energy"_compute_smd_internal_energy.html -
|
||||
"smd/plastic/strain"_compute_smd_plastic_strain.html -
|
||||
"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html -
|
||||
"smd/rho"_compute_smd_rho.html -
|
||||
"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html -
|
||||
"smd/tlsph/dt"_compute_smd_tlsph_dt.html -
|
||||
"smd/internal/energy"_compute_smd_internal_energy.html - per-particle enthalpy in Smooth Mach Dynamics
|
||||
"smd/plastic/strain"_compute_smd_plastic_strain.html - equivalent plastic strain per particle in Smooth Mach Dynamics
|
||||
"smd/plastic/strain/rate"_compute_smd_plastic_strain_rate.html - time rate of the equivalent plastic strain in Smooth Mach Dynamics
|
||||
"smd/rho"_compute_smd_rho.html - per-particle mass density in Smooth Mach Dynamics
|
||||
"smd/tlsph/defgrad"_compute_smd_tlsph_defgrad.html - deformation gradient in Smooth Mach Dynamics
|
||||
"smd/tlsph/dt"_compute_smd_tlsph_dt.html - CFL-stable time increment per particle in Smooth Mach Dynamics
|
||||
"smd/tlsph/num/neighs"_compute_smd_tlsph_num_neighs.html -
|
||||
"smd/tlsph/shape"_compute_smd_tlsph_shape.html -
|
||||
"smd/tlsph/strain"_compute_smd_tlsph_strain.html -
|
||||
"smd/tlsph/strain/rate"_compute_smd_tlsph_strain_rate.html -
|
||||
"smd/tlsph/stress"_compute_smd_tlsph_stress.html -
|
||||
"smd/triangle/vertices"_compute_smd_triangle_vertices.html -
|
||||
"smd/tlsph/stress"_compute_smd_tlsph_stress.html - per-particle Cauchy stress tensor for SPH particles
|
||||
"smd/triangle/vertices"_compute_smd_triangle_vertices.html -
|
||||
"smd/ulsph/num/neighs"_compute_smd_ulsph_num_neighs.html -
|
||||
"smd/ulsph/strain"_compute_smd_ulsph_strain.html -
|
||||
"smd/ulsph/strain/rate"_compute_smd_ulsph_strain_rate.html -
|
||||
"smd/ulsph/stress"_compute_smd_ulsph_stress.html -
|
||||
"smd/vol"_compute_smd_vol.html -
|
||||
"smd/ulsph/stress"_compute_smd_ulsph_stress.html - per-particle Cauchy stress tensor and von Mises equivalent stress in Smooth Mach Dynamics
|
||||
"smd/vol"_compute_smd_vol.html - per-particle volumes and their sum in Smooth Mach Dynamics
|
||||
"sna/atom"_compute_sna_atom.html - calculate bispectrum coefficients for each atom
|
||||
"snad/atom"_compute_sna_atom.html - derivative of bispectrum coefficients for each atom
|
||||
"snav/atom"_compute_sna_atom.html - virial contribution from bispectrum coefficients for each atom
|
||||
"spin"_compute_spin.html -
|
||||
"spin"_compute_spin.html - magnetic quantities for a system of atoms having spins
|
||||
"stress/atom"_compute_stress_atom.html - stress tensor for each atom
|
||||
"stress/mop"_compute_stress_mop.html -
|
||||
"stress/mop/profile"_compute_stress_mop.html -
|
||||
"stress/mop"_compute_stress_mop.html - normal components of the local stress tensor using the method of planes
|
||||
"stress/mop/profile"_compute_stress_mop.html - profile of the normal components of the local stress tensor using the method of planes
|
||||
"stress/tally"_compute_tally.html -
|
||||
"tdpd/cc/atom"_compute_tdpd_cc_atom.html -
|
||||
"tdpd/cc/atom"_compute_tdpd_cc_atom.html - per-atom chemical concentration of a specified species for each tDPD particle
|
||||
"temp"_compute_temp.html - temperature of group of atoms
|
||||
"temp/asphere"_compute_temp_asphere.html - temperature of aspherical particles
|
||||
"temp/body"_compute_temp_body.html - temperature of body particles
|
||||
"temp/chunk"_compute_temp_chunk.html - temperature of each chunk
|
||||
"temp/com"_compute_temp_com.html - temperature after subtracting center-of-mass velocity
|
||||
"temp/cs"_compute_temp_cs.html -
|
||||
"temp/cs"_compute_temp_cs.html - temperature based on the center-of-mass velocity of atom pairs that are bonded to each other
|
||||
"temp/deform"_compute_temp_deform.html - temperature excluding box deformation velocity
|
||||
"temp/deform/eff"_compute_temp_deform_eff.html -
|
||||
"temp/drude"_compute_temp_drude.html -
|
||||
"temp/eff"_compute_temp_eff.html -
|
||||
"temp/deform/eff"_compute_temp_deform_eff.html - temperature excluding box deformation velocity in the electron force field model
|
||||
"temp/drude"_compute_temp_drude.html - temperature of Core-Drude pairs
|
||||
"temp/eff"_compute_temp_eff.html - temperature of a group of nuclei and electrons in the electron force field model
|
||||
"temp/partial"_compute_temp_partial.html - temperature excluding one or more dimensions of velocity
|
||||
"temp/profile"_compute_temp_profile.html - temperature excluding a binned velocity profile
|
||||
"temp/ramp"_compute_temp_ramp.html - temperature excluding ramped velocity component
|
||||
"temp/region"_compute_temp_region.html - temperature of a region of atoms
|
||||
"temp/region/eff"_compute_temp_region_eff.html -
|
||||
"temp/rotate"_compute_temp_rotate.html -
|
||||
"temp/region/eff"_compute_temp_region_eff.html - temperature of a region of nuclei and electrons in the electron force field model
|
||||
"temp/rotate"_compute_temp_rotate.html - temperature of a group of atoms after subtracting out their center-of-mass and angular velocities
|
||||
"temp/sphere"_compute_temp_sphere.html - temperature of spherical particles
|
||||
"temp/uef"_compute_temp_uef.html -
|
||||
"temp/uef"_compute_temp_uef.html - kinetic energy tensor in the reference frame of an applied flow field
|
||||
"ti"_compute_ti.html - thermodynamic integration free energy values
|
||||
"torque/chunk"_compute_torque_chunk.html - torque applied on each chunk
|
||||
"vacf"_compute_vacf.html - velocity auto-correlation function of group of atoms
|
||||
"vcm/chunk"_compute_vcm_chunk.html - velocity of center-of-mass for each chunk
|
||||
"voronoi/atom"_compute_voronoi_atom.html - Voronoi volume and neighbors for each atom
|
||||
"xrd"_compute_xrd.html - :ul
|
||||
"xrd"_compute_xrd.html - x-ray diffraction intensity on a mesh of reciprocal lattice nodes :ul
|
||||
|
||||
[Restrictions:] none
|
||||
|
||||
|
|
|
|||
|
|
@ -301,12 +301,6 @@ void PPPMKokkos<DeviceType>::init()
|
|||
|
||||
if (me == 0) {
|
||||
|
||||
#ifdef FFT_SINGLE
|
||||
const char fft_prec[] = "single";
|
||||
#else
|
||||
const char fft_prec[] = "double";
|
||||
#endif
|
||||
|
||||
if (screen) {
|
||||
fprintf(screen," G vector (1/distance) = %g\n",g_ewald);
|
||||
fprintf(screen," grid = %d %d %d\n",nx_pppm,ny_pppm,nz_pppm);
|
||||
|
|
@ -315,7 +309,7 @@ void PPPMKokkos<DeviceType>::init()
|
|||
estimated_accuracy);
|
||||
fprintf(screen," estimated relative force accuracy = %g\n",
|
||||
estimated_accuracy/two_charge_force);
|
||||
fprintf(screen," using %s precision FFTs\n",fft_prec);
|
||||
fprintf(screen," using " LMP_FFT_PREC " precision " LMP_FFT_LIB "\n");
|
||||
fprintf(screen," 3d grid and FFT values/proc = %d %d\n",
|
||||
ngrid_max,nfft_both_max);
|
||||
}
|
||||
|
|
@ -327,7 +321,7 @@ void PPPMKokkos<DeviceType>::init()
|
|||
estimated_accuracy);
|
||||
fprintf(logfile," estimated relative force accuracy = %g\n",
|
||||
estimated_accuracy/two_charge_force);
|
||||
fprintf(logfile," using %s precision FFTs\n",fft_prec);
|
||||
fprintf(logfile," using " LMP_FFT_PREC " precision " LMP_FFT_LIB "\n");
|
||||
fprintf(logfile," 3d grid and FFT values/proc = %d %d\n",
|
||||
ngrid_max,nfft_both_max);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -348,12 +348,6 @@ void PPPM::init()
|
|||
|
||||
if (me == 0) {
|
||||
|
||||
#ifdef FFT_SINGLE
|
||||
const char fft_prec[] = "single";
|
||||
#else
|
||||
const char fft_prec[] = "double";
|
||||
#endif
|
||||
|
||||
if (screen) {
|
||||
fprintf(screen," G vector (1/distance) = %g\n",g_ewald);
|
||||
fprintf(screen," grid = %d %d %d\n",nx_pppm,ny_pppm,nz_pppm);
|
||||
|
|
@ -362,7 +356,7 @@ void PPPM::init()
|
|||
estimated_accuracy);
|
||||
fprintf(screen," estimated relative force accuracy = %g\n",
|
||||
estimated_accuracy/two_charge_force);
|
||||
fprintf(screen," using %s precision FFTs\n",fft_prec);
|
||||
fprintf(screen," using " LMP_FFT_PREC " precision " LMP_FFT_LIB "\n");
|
||||
fprintf(screen," 3d grid and FFT values/proc = %d %d\n",
|
||||
ngrid_max,nfft_both_max);
|
||||
}
|
||||
|
|
@ -374,7 +368,7 @@ void PPPM::init()
|
|||
estimated_accuracy);
|
||||
fprintf(logfile," estimated relative force accuracy = %g\n",
|
||||
estimated_accuracy/two_charge_force);
|
||||
fprintf(logfile," using %s precision FFTs\n",fft_prec);
|
||||
fprintf(logfile," using " LMP_FFT_PREC " precision " LMP_FFT_LIB "\n");
|
||||
fprintf(logfile," 3d grid and FFT values/proc = %d %d\n",
|
||||
ngrid_max,nfft_both_max);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -22,11 +22,22 @@ KSpaceStyle(pppm,PPPM)
|
|||
|
||||
#include "kspace.h"
|
||||
|
||||
#if defined(FFT_FFTW3)
|
||||
#define LMP_FFT_LIB "FFTW3"
|
||||
#elif defined(FFT_MKL)
|
||||
#define LMP_FFT_LIB "MKL FFT"
|
||||
#else
|
||||
#define LMP_FFT_LIB "KISS FFT"
|
||||
#endif
|
||||
|
||||
#ifdef FFT_SINGLE
|
||||
typedef float FFT_SCALAR;
|
||||
#define LMP_FFT_PREC "single"
|
||||
#define MPI_FFT_SCALAR MPI_FLOAT
|
||||
#else
|
||||
|
||||
typedef double FFT_SCALAR;
|
||||
#define LMP_FFT_PREC "double"
|
||||
#define MPI_FFT_SCALAR MPI_DOUBLE
|
||||
#endif
|
||||
|
||||
|
|
|
|||
|
|
@ -472,12 +472,6 @@ void PPPMDisp::init()
|
|||
MPI_Allreduce(&nfft_both,&nfft_both_max,1,MPI_INT,MPI_MAX,world);
|
||||
|
||||
if (me == 0) {
|
||||
#ifdef FFT_SINGLE
|
||||
const char fft_prec[] = "single";
|
||||
#else
|
||||
const char fft_prec[] = "double";
|
||||
#endif
|
||||
|
||||
if (screen) {
|
||||
fprintf(screen," Coulomb G vector (1/distance)= %g\n",g_ewald);
|
||||
fprintf(screen," Coulomb grid = %d %d %d\n",nx_pppm,ny_pppm,nz_pppm);
|
||||
|
|
@ -486,7 +480,7 @@ void PPPMDisp::init()
|
|||
acc);
|
||||
fprintf(screen," Coulomb estimated relative force accuracy = %g\n",
|
||||
acc/two_charge_force);
|
||||
fprintf(screen," using %s precision FFTs\n",fft_prec);
|
||||
fprintf(screen," using " LMP_FFT_PREC " precision " LMP_FFT_LIB "\n");
|
||||
fprintf(screen," 3d grid and FFT values/proc = %d %d\n",
|
||||
ngrid_max, nfft_both_max);
|
||||
}
|
||||
|
|
@ -499,7 +493,7 @@ void PPPMDisp::init()
|
|||
acc);
|
||||
fprintf(logfile," Coulomb estimated relative force accuracy = %g\n",
|
||||
acc/two_charge_force);
|
||||
fprintf(logfile," using %s precision FFTs\n",fft_prec);
|
||||
fprintf(logfile," using " LMP_FFT_PREC " precision " LMP_FFT_LIB "\n");
|
||||
fprintf(logfile," 3d grid and FFT values/proc = %d %d\n",
|
||||
ngrid_max, nfft_both_max);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -22,11 +22,21 @@ KSpaceStyle(pppm/disp,PPPMDisp)
|
|||
|
||||
#include "kspace.h"
|
||||
|
||||
#if defined(FFT_FFTW3)
|
||||
#define LMP_FFT_LIB "FFTW3"
|
||||
#elif defined(FFT_MKL)
|
||||
#define LMP_FFT_LIB "MKL FFT"
|
||||
#else
|
||||
#define LMP_FFT_LIB "KISS FFT"
|
||||
#endif
|
||||
|
||||
#ifdef FFT_SINGLE
|
||||
typedef float FFT_SCALAR;
|
||||
#define LMP_FFT_PREC "single"
|
||||
#define MPI_FFT_SCALAR MPI_FLOAT
|
||||
#else
|
||||
typedef double FFT_SCALAR;
|
||||
#define LMP_FFT_PREC "double"
|
||||
#define MPI_FFT_SCALAR MPI_DOUBLE
|
||||
#endif
|
||||
|
||||
|
|
|
|||
|
|
@ -53,7 +53,7 @@ AtomVecPeri::AtomVecPeri(LAMMPS *lmp) : AtomVec(lmp)
|
|||
comm_f_only = 1;
|
||||
size_forward = 4;
|
||||
size_reverse = 3;
|
||||
size_border = 11;
|
||||
size_border = 12;
|
||||
size_velocity = 3;
|
||||
size_data_atom = 7;
|
||||
size_data_vel = 4;
|
||||
|
|
@ -355,6 +355,7 @@ int AtomVecPeri::pack_border(int n, int *list, double *buf,
|
|||
buf[m++] = ubuf(type[j]).d;
|
||||
buf[m++] = ubuf(mask[j]).d;
|
||||
buf[m++] = vfrac[j];
|
||||
buf[m++] = rmass[j];
|
||||
buf[m++] = s0[j];
|
||||
buf[m++] = x0[j][0];
|
||||
buf[m++] = x0[j][1];
|
||||
|
|
@ -379,6 +380,7 @@ int AtomVecPeri::pack_border(int n, int *list, double *buf,
|
|||
buf[m++] = ubuf(type[j]).d;
|
||||
buf[m++] = ubuf(mask[j]).d;
|
||||
buf[m++] = vfrac[j];
|
||||
buf[m++] = rmass[j];
|
||||
buf[m++] = s0[j];
|
||||
buf[m++] = x0[j][0];
|
||||
buf[m++] = x0[j][1];
|
||||
|
|
@ -412,6 +414,7 @@ int AtomVecPeri::pack_border_vel(int n, int *list, double *buf,
|
|||
buf[m++] = ubuf(type[j]).d;
|
||||
buf[m++] = ubuf(mask[j]).d;
|
||||
buf[m++] = vfrac[j];
|
||||
buf[m++] = rmass[j];
|
||||
buf[m++] = s0[j];
|
||||
buf[m++] = x0[j][0];
|
||||
buf[m++] = x0[j][1];
|
||||
|
|
@ -440,6 +443,7 @@ int AtomVecPeri::pack_border_vel(int n, int *list, double *buf,
|
|||
buf[m++] = ubuf(type[j]).d;
|
||||
buf[m++] = ubuf(mask[j]).d;
|
||||
buf[m++] = vfrac[j];
|
||||
buf[m++] = rmass[j];
|
||||
buf[m++] = s0[j];
|
||||
buf[m++] = x0[j][0];
|
||||
buf[m++] = x0[j][1];
|
||||
|
|
@ -461,6 +465,7 @@ int AtomVecPeri::pack_border_vel(int n, int *list, double *buf,
|
|||
buf[m++] = ubuf(type[j]).d;
|
||||
buf[m++] = ubuf(mask[j]).d;
|
||||
buf[m++] = vfrac[j];
|
||||
buf[m++] = rmass[j];
|
||||
buf[m++] = s0[j];
|
||||
buf[m++] = x0[j][0];
|
||||
buf[m++] = x0[j][1];
|
||||
|
|
@ -495,6 +500,7 @@ int AtomVecPeri::pack_border_hybrid(int n, int *list, double *buf)
|
|||
for (i = 0; i < n; i++) {
|
||||
j = list[i];
|
||||
buf[m++] = vfrac[j];
|
||||
buf[m++] = rmass[j];
|
||||
buf[m++] = s0[j];
|
||||
buf[m++] = x0[j][0];
|
||||
buf[m++] = x0[j][1];
|
||||
|
|
@ -520,6 +526,7 @@ void AtomVecPeri::unpack_border(int n, int first, double *buf)
|
|||
type[i] = (int) ubuf(buf[m++]).i;
|
||||
mask[i] = (int) ubuf(buf[m++]).i;
|
||||
vfrac[i] = buf[m++];
|
||||
rmass[i] = buf[m++];
|
||||
s0[i] = buf[m++];
|
||||
x0[i][0] = buf[m++];
|
||||
x0[i][1] = buf[m++];
|
||||
|
|
@ -549,6 +556,7 @@ void AtomVecPeri::unpack_border_vel(int n, int first, double *buf)
|
|||
type[i] = (int) ubuf(buf[m++]).i;
|
||||
mask[i] = (int) ubuf(buf[m++]).i;
|
||||
vfrac[i] = buf[m++];
|
||||
rmass[i] = buf[m++];
|
||||
s0[i] = buf[m++];
|
||||
x0[i][0] = buf[m++];
|
||||
x0[i][1] = buf[m++];
|
||||
|
|
@ -574,6 +582,7 @@ int AtomVecPeri::unpack_border_hybrid(int n, int first, double *buf)
|
|||
last = first + n;
|
||||
for (i = first; i < last; i++) {
|
||||
vfrac[i] = buf[m++];
|
||||
rmass[i] = buf[m++];
|
||||
s0[i] = buf[m++];
|
||||
x0[i][0] = buf[m++];
|
||||
x0[i][1] = buf[m++];
|
||||
|
|
|
|||
|
|
@ -392,28 +392,33 @@ void NEB::readfile(char *file, int flag)
|
|||
open(file);
|
||||
while (1) {
|
||||
eof = fgets(line,MAXLINE,fp);
|
||||
if (eof == NULL) error->one(FLERR,"Unexpected end of neb file");
|
||||
if (eof == NULL) error->one(FLERR,"Unexpected end of NEB file");
|
||||
start = &line[strspn(line," \t\n\v\f\r")];
|
||||
if (*start != '\0' && *start != '#') break;
|
||||
}
|
||||
sscanf(line,"%d",&nlines);
|
||||
int rv = sscanf(line,"%d",&nlines);
|
||||
if (rv != 1) nlines = -1;
|
||||
}
|
||||
MPI_Bcast(&nlines,1,MPI_INT,0,uworld);
|
||||
|
||||
if (nlines < 0)
|
||||
error->universe_all(FLERR,"Incorrectly formatted NEB file");
|
||||
} else {
|
||||
if (me == 0) {
|
||||
if (ireplica) {
|
||||
open(file);
|
||||
while (1) {
|
||||
eof = fgets(line,MAXLINE,fp);
|
||||
if (eof == NULL) error->one(FLERR,"Unexpected end of neb file");
|
||||
if (eof == NULL) error->one(FLERR,"Unexpected end of NEB file");
|
||||
start = &line[strspn(line," \t\n\v\f\r")];
|
||||
if (*start != '\0' && *start != '#') break;
|
||||
}
|
||||
sscanf(line,"%d",&nlines);
|
||||
int rv = sscanf(line,"%d",&nlines);
|
||||
if (rv != 1) nlines = -1;
|
||||
} else nlines = 0;
|
||||
}
|
||||
MPI_Bcast(&nlines,1,MPI_INT,0,world);
|
||||
if (nlines < 0)
|
||||
error->all(FLERR,"Incorrectly formatted NEB file");
|
||||
}
|
||||
|
||||
char *buffer = new char[CHUNK*MAXLINE];
|
||||
|
|
@ -437,7 +442,7 @@ void NEB::readfile(char *file, int flag)
|
|||
eofflag = comm->read_lines_from_file_universe(fp,nchunk,MAXLINE,buffer);
|
||||
else
|
||||
eofflag = comm->read_lines_from_file(fp,nchunk,MAXLINE,buffer);
|
||||
if (eofflag) error->all(FLERR,"Unexpected end of neb file");
|
||||
if (eofflag) error->all(FLERR,"Unexpected end of NEB file");
|
||||
|
||||
buf = buffer;
|
||||
next = strchr(buf,'\n');
|
||||
|
|
@ -446,7 +451,7 @@ void NEB::readfile(char *file, int flag)
|
|||
*next = '\n';
|
||||
|
||||
if (nwords != ATTRIBUTE_PERLINE)
|
||||
error->all(FLERR,"Incorrect atom format in neb file");
|
||||
error->all(FLERR,"Incorrect atom format in NEB file");
|
||||
|
||||
// loop over lines of atom coords
|
||||
// tokenize the line into values
|
||||
|
|
@ -504,12 +509,12 @@ void NEB::readfile(char *file, int flag)
|
|||
int ntotal;
|
||||
MPI_Allreduce(&ncount,&ntotal,1,MPI_INT,MPI_SUM,uworld);
|
||||
if (ntotal != nreplica*nlines)
|
||||
error->universe_all(FLERR,"Invalid atom IDs in neb file");
|
||||
error->universe_all(FLERR,"Invalid atom IDs in NEB file");
|
||||
} else {
|
||||
int ntotal;
|
||||
MPI_Allreduce(&ncount,&ntotal,1,MPI_INT,MPI_SUM,world);
|
||||
if (ntotal != nlines)
|
||||
error->all(FLERR,"Invalid atom IDs in neb file");
|
||||
error->all(FLERR,"Invalid atom IDs in NEB file");
|
||||
}
|
||||
|
||||
// clean up
|
||||
|
|
|
|||
|
|
@ -199,7 +199,7 @@ void FixQEqReax::pertype_parameters(char *arg)
|
|||
return;
|
||||
}
|
||||
|
||||
int i,itype,ntypes;
|
||||
int i,itype,ntypes,rv;
|
||||
double v1,v2,v3;
|
||||
FILE *pf;
|
||||
|
||||
|
|
@ -215,9 +215,11 @@ void FixQEqReax::pertype_parameters(char *arg)
|
|||
error->one(FLERR,"Fix qeq/reax parameter file could not be found");
|
||||
|
||||
for (i = 1; i <= ntypes && !feof(pf); i++) {
|
||||
fscanf(pf,"%d %lg %lg %lg",&itype,&v1,&v2,&v3);
|
||||
rv = fscanf(pf,"%d %lg %lg %lg",&itype,&v1,&v2,&v3);
|
||||
if (rv != 4)
|
||||
error->one(FLERR,"Fix qeq/reax: Incorrect format of param file");
|
||||
if (itype < 1 || itype > ntypes)
|
||||
error->one(FLERR,"Fix qeq/reax invalid atom type in param file");
|
||||
error->one(FLERR,"Fix qeq/reax: invalid atom type in param file");
|
||||
chi[itype] = v1;
|
||||
eta[itype] = v2;
|
||||
gamma[itype] = v3;
|
||||
|
|
|
|||
36
src/atom.cpp
36
src/atom.cpp
|
|
@ -1066,7 +1066,7 @@ void Atom::data_vels(int n, char *buf, tagint id_offset)
|
|||
void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset,
|
||||
int type_offset)
|
||||
{
|
||||
int m,tmp,itype;
|
||||
int m,tmp,itype,rv;
|
||||
tagint atom1,atom2;
|
||||
char *next;
|
||||
int newton_bond = force->newton_bond;
|
||||
|
|
@ -1074,8 +1074,10 @@ void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset,
|
|||
for (int i = 0; i < n; i++) {
|
||||
next = strchr(buf,'\n');
|
||||
*next = '\0';
|
||||
sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT,
|
||||
&tmp,&itype,&atom1,&atom2);
|
||||
rv = sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT,
|
||||
&tmp,&itype,&atom1,&atom2);
|
||||
if (rv != 4)
|
||||
error->one(FLERR,"Incorrect format of Bonds section in data file");
|
||||
if (id_offset) {
|
||||
atom1 += id_offset;
|
||||
atom2 += id_offset;
|
||||
|
|
@ -1119,7 +1121,7 @@ void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset,
|
|||
void Atom::data_angles(int n, char *buf, int *count, tagint id_offset,
|
||||
int type_offset)
|
||||
{
|
||||
int m,tmp,itype;
|
||||
int m,tmp,itype,rv;
|
||||
tagint atom1,atom2,atom3;
|
||||
char *next;
|
||||
int newton_bond = force->newton_bond;
|
||||
|
|
@ -1127,8 +1129,10 @@ void Atom::data_angles(int n, char *buf, int *count, tagint id_offset,
|
|||
for (int i = 0; i < n; i++) {
|
||||
next = strchr(buf,'\n');
|
||||
*next = '\0';
|
||||
sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
|
||||
&tmp,&itype,&atom1,&atom2,&atom3);
|
||||
rv = sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
|
||||
&tmp,&itype,&atom1,&atom2,&atom3);
|
||||
if (rv != 5)
|
||||
error->one(FLERR,"Incorrect format of Angles section in data file");
|
||||
if (id_offset) {
|
||||
atom1 += id_offset;
|
||||
atom2 += id_offset;
|
||||
|
|
@ -1189,7 +1193,7 @@ void Atom::data_angles(int n, char *buf, int *count, tagint id_offset,
|
|||
void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset,
|
||||
int type_offset)
|
||||
{
|
||||
int m,tmp,itype;
|
||||
int m,tmp,itype,rv;
|
||||
tagint atom1,atom2,atom3,atom4;
|
||||
char *next;
|
||||
int newton_bond = force->newton_bond;
|
||||
|
|
@ -1197,9 +1201,11 @@ void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset,
|
|||
for (int i = 0; i < n; i++) {
|
||||
next = strchr(buf,'\n');
|
||||
*next = '\0';
|
||||
sscanf(buf,"%d %d "
|
||||
TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
|
||||
&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
|
||||
rv = sscanf(buf,"%d %d " TAGINT_FORMAT " " TAGINT_FORMAT
|
||||
" " TAGINT_FORMAT " " TAGINT_FORMAT,
|
||||
&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
|
||||
if (rv != 6)
|
||||
error->one(FLERR,"Incorrect format of Dihedrals section in data file");
|
||||
if (id_offset) {
|
||||
atom1 += id_offset;
|
||||
atom2 += id_offset;
|
||||
|
|
@ -1278,7 +1284,7 @@ void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset,
|
|||
void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset,
|
||||
int type_offset)
|
||||
{
|
||||
int m,tmp,itype;
|
||||
int m,tmp,itype,rv;
|
||||
tagint atom1,atom2,atom3,atom4;
|
||||
char *next;
|
||||
int newton_bond = force->newton_bond;
|
||||
|
|
@ -1286,9 +1292,11 @@ void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset,
|
|||
for (int i = 0; i < n; i++) {
|
||||
next = strchr(buf,'\n');
|
||||
*next = '\0';
|
||||
sscanf(buf,"%d %d "
|
||||
TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
|
||||
&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
|
||||
rv = sscanf(buf,"%d %d "
|
||||
TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT " " TAGINT_FORMAT,
|
||||
&tmp,&itype,&atom1,&atom2,&atom3,&atom4);
|
||||
if (rv != 6)
|
||||
error->one(FLERR,"Incorrect format of Impropers section in data file");
|
||||
if (id_offset) {
|
||||
atom1 += id_offset;
|
||||
atom2 += id_offset;
|
||||
|
|
|
|||
|
|
@ -426,6 +426,11 @@ E: Incorrect atom format in data file
|
|||
Number of values per atom line in the data file is not consistent with
|
||||
the atom style.
|
||||
|
||||
E: Incorrect format of ... section in data file
|
||||
|
||||
Number or type of values per line in the given section of the data file
|
||||
is not consistent with the requirements for this section.
|
||||
|
||||
E: Invalid atom type in Atoms section of data file
|
||||
|
||||
Atom types must range from 1 to specified # of types.
|
||||
|
|
|
|||
|
|
@ -40,7 +40,7 @@ AtomVecEllipsoid::AtomVecEllipsoid(LAMMPS *lmp) : AtomVec(lmp)
|
|||
comm_x_only = comm_f_only = 0;
|
||||
size_forward = 7;
|
||||
size_reverse = 6;
|
||||
size_border = 14;
|
||||
size_border = 15;
|
||||
size_velocity = 6;
|
||||
size_data_atom = 7;
|
||||
size_data_vel = 7;
|
||||
|
|
@ -543,6 +543,7 @@ int AtomVecEllipsoid::pack_border(int n, int *list, double *buf,
|
|||
buf[m++] = ubuf(tag[j]).d;
|
||||
buf[m++] = ubuf(type[j]).d;
|
||||
buf[m++] = ubuf(mask[j]).d;
|
||||
buf[m++] = rmass[j];
|
||||
if (ellipsoid[j] < 0) buf[m++] = ubuf(0).d;
|
||||
else {
|
||||
buf[m++] = ubuf(1).d;
|
||||
|
|
@ -575,6 +576,7 @@ int AtomVecEllipsoid::pack_border(int n, int *list, double *buf,
|
|||
buf[m++] = ubuf(tag[j]).d;
|
||||
buf[m++] = ubuf(type[j]).d;
|
||||
buf[m++] = ubuf(mask[j]).d;
|
||||
buf[m++] = rmass[j];
|
||||
if (ellipsoid[j] < 0) buf[m++] = ubuf(0).d;
|
||||
else {
|
||||
buf[m++] = ubuf(1).d;
|
||||
|
|
@ -617,6 +619,7 @@ int AtomVecEllipsoid::pack_border_vel(int n, int *list, double *buf,
|
|||
buf[m++] = ubuf(tag[j]).d;
|
||||
buf[m++] = ubuf(type[j]).d;
|
||||
buf[m++] = ubuf(mask[j]).d;
|
||||
buf[m++] = rmass[j];
|
||||
if (ellipsoid[j] < 0) buf[m++] = ubuf(0).d;
|
||||
else {
|
||||
buf[m++] = ubuf(1).d;
|
||||
|
|
@ -656,6 +659,7 @@ int AtomVecEllipsoid::pack_border_vel(int n, int *list, double *buf,
|
|||
buf[m++] = ubuf(tag[j]).d;
|
||||
buf[m++] = ubuf(type[j]).d;
|
||||
buf[m++] = ubuf(mask[j]).d;
|
||||
buf[m++] = rmass[j];
|
||||
if (ellipsoid[j] < 0) buf[m++] = ubuf(0).d;
|
||||
else {
|
||||
buf[m++] = ubuf(1).d;
|
||||
|
|
@ -688,6 +692,7 @@ int AtomVecEllipsoid::pack_border_vel(int n, int *list, double *buf,
|
|||
buf[m++] = ubuf(tag[j]).d;
|
||||
buf[m++] = ubuf(type[j]).d;
|
||||
buf[m++] = ubuf(mask[j]).d;
|
||||
buf[m++] = rmass[j];
|
||||
if (ellipsoid[j] < 0) buf[m++] = ubuf(0).d;
|
||||
else {
|
||||
buf[m++] = ubuf(1).d;
|
||||
|
|
@ -734,6 +739,7 @@ int AtomVecEllipsoid::pack_border_hybrid(int n, int *list, double *buf)
|
|||
m = 0;
|
||||
for (i = 0; i < n; i++) {
|
||||
j = list[i];
|
||||
buf[m++] = rmass[j];
|
||||
if (ellipsoid[j] < 0) buf[m++] = ubuf(0).d;
|
||||
else {
|
||||
buf[m++] = ubuf(1).d;
|
||||
|
|
@ -768,6 +774,7 @@ void AtomVecEllipsoid::unpack_border(int n, int first, double *buf)
|
|||
tag[i] = (tagint) ubuf(buf[m++]).i;
|
||||
type[i] = (int) ubuf(buf[m++]).i;
|
||||
mask[i] = (int) ubuf(buf[m++]).i;
|
||||
rmass[i] = buf[m++];
|
||||
ellipsoid[i] = (int) ubuf(buf[m++]).i;
|
||||
if (ellipsoid[i] == 0) ellipsoid[i] = -1;
|
||||
else {
|
||||
|
|
@ -811,6 +818,7 @@ void AtomVecEllipsoid::unpack_border_vel(int n, int first, double *buf)
|
|||
tag[i] = (tagint) ubuf(buf[m++]).i;
|
||||
type[i] = (int) ubuf(buf[m++]).i;
|
||||
mask[i] = (int) ubuf(buf[m++]).i;
|
||||
rmass[i] = buf[m++];
|
||||
ellipsoid[i] = (int) ubuf(buf[m++]).i;
|
||||
if (ellipsoid[i] == 0) ellipsoid[i] = -1;
|
||||
else {
|
||||
|
|
@ -853,6 +861,7 @@ int AtomVecEllipsoid::unpack_border_hybrid(int n, int first, double *buf)
|
|||
m = 0;
|
||||
last = first + n;
|
||||
for (i = first; i < last; i++) {
|
||||
rmass[i] = buf[m++];
|
||||
ellipsoid[i] = (int) ubuf(buf[m++]).i;
|
||||
if (ellipsoid[i] == 0) ellipsoid[i] = -1;
|
||||
else {
|
||||
|
|
|
|||
|
|
@ -29,6 +29,7 @@
|
|||
#include "force.h"
|
||||
#include "memory.h"
|
||||
#include "error.h"
|
||||
#include "utils.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
using namespace FixConst;
|
||||
|
|
@ -163,7 +164,7 @@ void FixTMD::init()
|
|||
|
||||
dtv = update->dt;
|
||||
dtf = update->dt * force->ftm2v;
|
||||
if (strstr(update->integrate_style,"respa"))
|
||||
if (utils::strmatch(update->integrate_style,"^respa"))
|
||||
step_respa = ((Respa *) update->integrate)->step;
|
||||
}
|
||||
|
||||
|
|
@ -422,21 +423,27 @@ void FixTMD::readfile(char *file)
|
|||
*next = '\0';
|
||||
|
||||
if (firstline) {
|
||||
if (strstr(bufptr,"xlo xhi")) {
|
||||
if (utils::strmatch(bufptr,"^\\s*\\f+\\s+\\f+\\s+xlo\\s+xhi")) {
|
||||
double lo,hi;
|
||||
sscanf(bufptr,"%lg %lg",&lo,&hi);
|
||||
n = sscanf(bufptr,"%lg %lg",&lo,&hi);
|
||||
if (n != 2)
|
||||
error->all(FLERR,"Incorrect format in TMD target file");
|
||||
xprd = hi - lo;
|
||||
bufptr = next + 1;
|
||||
continue;
|
||||
} else if (strstr(bufptr,"ylo yhi")) {
|
||||
} else if (utils::strmatch(bufptr,"^\\s*\\f+\\s+\\f+\\s+ylo\\s+yhi")) {
|
||||
double lo,hi;
|
||||
sscanf(bufptr,"%lg %lg",&lo,&hi);
|
||||
n = sscanf(bufptr,"%lg %lg",&lo,&hi);
|
||||
if (n != 2)
|
||||
error->all(FLERR,"Incorrect format in TMD target file");
|
||||
yprd = hi - lo;
|
||||
bufptr = next + 1;
|
||||
continue;
|
||||
} else if (strstr(bufptr,"zlo zhi")) {
|
||||
} else if (utils::strmatch(bufptr,"^\\s*\\f+\\s+\\f+\\s+zlo\\s+zhi")) {
|
||||
double lo,hi;
|
||||
sscanf(bufptr,"%lg %lg",&lo,&hi);
|
||||
n = sscanf(bufptr,"%lg %lg",&lo,&hi);
|
||||
if (n != 2)
|
||||
error->all(FLERR,"Incorrect format in TMD target file");
|
||||
zprd = hi - lo;
|
||||
bufptr = next + 1;
|
||||
continue;
|
||||
|
|
@ -454,14 +461,13 @@ void FixTMD::readfile(char *file)
|
|||
}
|
||||
|
||||
if (imageflag)
|
||||
n = sscanf(bufptr,TAGINT_FORMAT " %lg %lg %lg %d %d %d",
|
||||
&itag,&x,&y,&z,&ix,&iy,&iz);
|
||||
n = 7 - sscanf(bufptr,TAGINT_FORMAT " %lg %lg %lg %d %d %d",
|
||||
&itag,&x,&y,&z,&ix,&iy,&iz);
|
||||
else
|
||||
n = sscanf(bufptr,TAGINT_FORMAT " %lg %lg %lg",&itag,&x,&y,&z);
|
||||
n = 4 - sscanf(bufptr,TAGINT_FORMAT " %lg %lg %lg",&itag,&x,&y,&z);
|
||||
|
||||
if (n < 0) {
|
||||
if (me == 0) error->warning(FLERR,"Ignoring empty or incorrectly"
|
||||
" formatted line in target file");
|
||||
if (n != 0) {
|
||||
error->all(FLERR,"Incorrectly formatted line in TMD target file");
|
||||
bufptr = next + 1;
|
||||
continue;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -304,7 +304,8 @@ void ProcMap::custom_grid(char *cfile, int nprocs,
|
|||
MPI_Bcast(&n,1,MPI_INT,0,world);
|
||||
MPI_Bcast(line,n,MPI_CHAR,0,world);
|
||||
|
||||
sscanf(line,"%d %d %d",&procgrid[0],&procgrid[1],&procgrid[2]);
|
||||
int rv = sscanf(line,"%d %d %d",&procgrid[0],&procgrid[1],&procgrid[2]);
|
||||
if (rv != 3) error->all(FLERR,"Processors custom grid file is inconsistent");
|
||||
|
||||
int flag = 0;
|
||||
if (procgrid[0]*procgrid[1]*procgrid[2] != nprocs) flag = 1;
|
||||
|
|
@ -323,8 +324,10 @@ void ProcMap::custom_grid(char *cfile, int nprocs,
|
|||
for (int i = 0; i < nprocs; i++) {
|
||||
if (!fgets(line,MAXLINE,fp))
|
||||
error->one(FLERR,"Unexpected end of custom file");
|
||||
sscanf(line,"%d %d %d %d",
|
||||
&cmap[i][0],&cmap[i][1],&cmap[i][2],&cmap[i][3]);
|
||||
rv = sscanf(line,"%d %d %d %d",
|
||||
&cmap[i][0],&cmap[i][1],&cmap[i][2],&cmap[i][3]);
|
||||
if (rv != 4)
|
||||
error->one(FLERR,"Processors custom grid file is inconsistent");
|
||||
}
|
||||
fclose(fp);
|
||||
}
|
||||
|
|
|
|||
|
|
@ -41,6 +41,7 @@
|
|||
#include "irregular.h"
|
||||
#include "error.h"
|
||||
#include "memory.h"
|
||||
#include "utils.h"
|
||||
|
||||
using namespace LAMMPS_NS;
|
||||
|
||||
|
|
@ -995,74 +996,115 @@ void ReadData::header(int firstpass)
|
|||
// customize for new header lines
|
||||
// check for triangles before angles so "triangles" not matched as "angles"
|
||||
int extra_flag_value = 0;
|
||||
int rv;
|
||||
|
||||
if (strstr(line,"atoms")) {
|
||||
sscanf(line,BIGINT_FORMAT,&natoms);
|
||||
if (utils::strmatch(line,"^\\s*\\d+\\s+atoms\\s")) {
|
||||
rv = sscanf(line,BIGINT_FORMAT,&natoms);
|
||||
if (rv != 1)
|
||||
error->all(FLERR,"Could not parse 'atoms' line in data file header");
|
||||
if (addflag == NONE) atom->natoms = natoms;
|
||||
else if (firstpass) atom->natoms += natoms;
|
||||
|
||||
} else if (strstr(line,"ellipsoids")) {
|
||||
} else if (utils::strmatch(line,"^\\s*\\d+\\s+ellipsoids\\s")) {
|
||||
if (!avec_ellipsoid)
|
||||
error->all(FLERR,"No ellipsoids allowed with this atom style");
|
||||
sscanf(line,BIGINT_FORMAT,&nellipsoids);
|
||||
rv = sscanf(line,BIGINT_FORMAT,&nellipsoids);
|
||||
if (rv != 1)
|
||||
error->all(FLERR,"Could not parse 'ellipsoids' line in data file header");
|
||||
if (addflag == NONE) atom->nellipsoids = nellipsoids;
|
||||
else if (firstpass) atom->nellipsoids += nellipsoids;
|
||||
|
||||
} else if (strstr(line,"lines")) {
|
||||
} else if (utils::strmatch(line,"^\\s*\\d+\\s+lines\\s")) {
|
||||
if (!avec_line)
|
||||
error->all(FLERR,"No lines allowed with this atom style");
|
||||
sscanf(line,BIGINT_FORMAT,&nlines);
|
||||
rv = sscanf(line,BIGINT_FORMAT,&nlines);
|
||||
if (rv != 1)
|
||||
error->all(FLERR,"Could not parse 'lines' line in data file header");
|
||||
if (addflag == NONE) atom->nlines = nlines;
|
||||
else if (firstpass) atom->nlines += nlines;
|
||||
|
||||
} else if (strstr(line,"triangles")) {
|
||||
} else if (utils::strmatch(line,"^\\s*\\d+\\s+triangles\\s")) {
|
||||
if (!avec_tri)
|
||||
error->all(FLERR,"No triangles allowed with this atom style");
|
||||
sscanf(line,BIGINT_FORMAT,&ntris);
|
||||
rv = sscanf(line,BIGINT_FORMAT,&ntris);
|
||||
if (rv != 1)
|
||||
error->all(FLERR,"Could not parse 'triangles' line in data file header");
|
||||
if (addflag == NONE) atom->ntris = ntris;
|
||||
else if (firstpass) atom->ntris += ntris;
|
||||
|
||||
} else if (strstr(line,"bodies")) {
|
||||
} else if (utils::strmatch(line,"^\\s*\\d+\\s+bodies\\s")) {
|
||||
if (!avec_body)
|
||||
error->all(FLERR,"No bodies allowed with this atom style");
|
||||
sscanf(line,BIGINT_FORMAT,&nbodies);
|
||||
rv = sscanf(line,BIGINT_FORMAT,&nbodies);
|
||||
if (rv != 1)
|
||||
error->all(FLERR,"Could not parse 'bodies' line in data file header");
|
||||
if (addflag == NONE) atom->nbodies = nbodies;
|
||||
else if (firstpass) atom->nbodies += nbodies;
|
||||
|
||||
} else if (strstr(line,"bonds")) {
|
||||
sscanf(line,BIGINT_FORMAT,&nbonds);
|
||||
} else if (utils::strmatch(line,"^\\s*\\d+\\s+bonds\\s")) {
|
||||
rv = sscanf(line,BIGINT_FORMAT,&nbonds);
|
||||
if (rv != 1)
|
||||
error->all(FLERR,"Could not parse 'bonds' line in data file header");
|
||||
if (addflag == NONE) atom->nbonds = nbonds;
|
||||
else if (firstpass) atom->nbonds += nbonds;
|
||||
} else if (strstr(line,"angles")) {
|
||||
sscanf(line,BIGINT_FORMAT,&nangles);
|
||||
|
||||
} else if (utils::strmatch(line,"^\\s*\\d+\\s+angles\\s")) {
|
||||
rv = sscanf(line,BIGINT_FORMAT,&nangles);
|
||||
if (rv != 1)
|
||||
error->all(FLERR,"Could not parse 'angles' line in data file header");
|
||||
if (addflag == NONE) atom->nangles = nangles;
|
||||
else if (firstpass) atom->nangles += nangles;
|
||||
} else if (strstr(line,"dihedrals")) {
|
||||
sscanf(line,BIGINT_FORMAT,&ndihedrals);
|
||||
|
||||
} else if (utils::strmatch(line,"^\\s*\\d+\\s+dihedrals\\s")) {
|
||||
rv = sscanf(line,BIGINT_FORMAT,&ndihedrals);
|
||||
if (rv != 1)
|
||||
error->all(FLERR,"Could not parse 'dihedrals' line in data file header");
|
||||
if (addflag == NONE) atom->ndihedrals = ndihedrals;
|
||||
else if (firstpass) atom->ndihedrals += ndihedrals;
|
||||
} else if (strstr(line,"impropers")) {
|
||||
sscanf(line,BIGINT_FORMAT,&nimpropers);
|
||||
|
||||
} else if (utils::strmatch(line,"^\\s*\\d+\\s+impropers\\s")) {
|
||||
rv = sscanf(line,BIGINT_FORMAT,&nimpropers);
|
||||
if (rv != 1)
|
||||
error->all(FLERR,"Could not parse 'impropers' line in data file header");
|
||||
if (addflag == NONE) atom->nimpropers = nimpropers;
|
||||
else if (firstpass) atom->nimpropers += nimpropers;
|
||||
|
||||
// Atom class type settings are only set by first data file
|
||||
|
||||
} else if (strstr(line,"atom types")) {
|
||||
sscanf(line,"%d",&ntypes);
|
||||
} else if (utils::strmatch(line,"^\\s*\\d+\\s+atom\\s+types\\s")) {
|
||||
rv = sscanf(line,"%d",&ntypes);
|
||||
if (rv != 1)
|
||||
error->all(FLERR,"Could not parse 'atom types' line "
|
||||
"in data file header");
|
||||
if (addflag == NONE) atom->ntypes = ntypes + extra_atom_types;
|
||||
} else if (strstr(line,"bond types")) {
|
||||
sscanf(line,"%d",&nbondtypes);
|
||||
|
||||
} else if (utils::strmatch(line,"\\s*\\d+\\s+bond\\s+types\\s")) {
|
||||
rv = sscanf(line,"%d",&nbondtypes);
|
||||
if (rv != 1)
|
||||
error->all(FLERR,"Could not parse 'bond types' line "
|
||||
"in data file header");
|
||||
if (addflag == NONE) atom->nbondtypes = nbondtypes + extra_bond_types;
|
||||
} else if (strstr(line,"angle types")) {
|
||||
sscanf(line,"%d",&nangletypes);
|
||||
|
||||
} else if (utils::strmatch(line,"^\\s*\\d+\\s+angle\\s+types\\s")) {
|
||||
rv = sscanf(line,"%d",&nangletypes);
|
||||
if (rv != 1)
|
||||
error->all(FLERR,"Could not parse 'angle types' line "
|
||||
"in data file header");
|
||||
if (addflag == NONE) atom->nangletypes = nangletypes + extra_angle_types;
|
||||
} else if (strstr(line,"dihedral types")) {
|
||||
sscanf(line,"%d",&ndihedraltypes);
|
||||
|
||||
} else if (utils::strmatch(line,"^\\s*\\d+\\s+dihedral\\s+types\\s")) {
|
||||
rv = sscanf(line,"%d",&ndihedraltypes);
|
||||
if (rv != 1)
|
||||
error->all(FLERR,"Could not parse 'dihedral types' line "
|
||||
"in data file header");
|
||||
if (addflag == NONE)
|
||||
atom->ndihedraltypes = ndihedraltypes + extra_dihedral_types;
|
||||
} else if (strstr(line,"improper types")) {
|
||||
sscanf(line,"%d",&nimpropertypes);
|
||||
|
||||
} else if (utils::strmatch(line,"^\\s*\\d+\\s+improper\\s+types\\s")) {
|
||||
rv = sscanf(line,"%d",&nimpropertypes);
|
||||
if (rv != 1)
|
||||
error->all(FLERR,"Could not parse 'improper types' line "
|
||||
"in data file header");
|
||||
if (addflag == NONE)
|
||||
atom->nimpropertypes = nimpropertypes + extra_improper_types;
|
||||
|
||||
|
|
@ -1091,15 +1133,27 @@ void ReadData::header(int firstpass)
|
|||
// local copy of box info
|
||||
// so can treat differently for first vs subsequent data files
|
||||
|
||||
} else if (strstr(line,"xlo xhi")) {
|
||||
sscanf(line,"%lg %lg",&boxlo[0],&boxhi[0]);
|
||||
} else if (strstr(line,"ylo yhi")) {
|
||||
sscanf(line,"%lg %lg",&boxlo[1],&boxhi[1]);
|
||||
} else if (strstr(line,"zlo zhi")) {
|
||||
sscanf(line,"%lg %lg",&boxlo[2],&boxhi[2]);
|
||||
} else if (strstr(line,"xy xz yz")) {
|
||||
} else if (utils::strmatch(line,"^\\s*\\f+\\s+\\f+\\s+xlo\\s+xhi\\s")) {
|
||||
rv = sscanf(line,"%lg %lg",&boxlo[0],&boxhi[0]);
|
||||
if (rv != 2)
|
||||
error->all(FLERR,"Could not parse 'xlo xhi' line in data file header");
|
||||
|
||||
} else if (utils::strmatch(line,"^\\s*\\f+\\s+\\f+\\s+ylo\\s+yhi\\s")) {
|
||||
rv = sscanf(line,"%lg %lg",&boxlo[1],&boxhi[1]);
|
||||
if (rv != 2)
|
||||
error->all(FLERR,"Could not parse 'ylo yhi' line in data file header");
|
||||
|
||||
} else if (utils::strmatch(line,"^\\s*\\f+\\s+\\f+\\s+zlo\\s+zhi\\s")) {
|
||||
rv = sscanf(line,"%lg %lg",&boxlo[2],&boxhi[2]);
|
||||
if (rv != 2)
|
||||
error->all(FLERR,"Could not parse 'zlo zhi' line in data file header");
|
||||
|
||||
} else if (utils::strmatch(line,"^\\s*\\f+\\s+\\f+\\s+\\f+"
|
||||
"\\s+xy\\s+xz\\s+yz\\s")) {
|
||||
triclinic = 1;
|
||||
sscanf(line,"%lg %lg %lg",&xy,&xz,&yz);
|
||||
rv = sscanf(line,"%lg %lg %lg",&xy,&xz,&yz);
|
||||
if (rv != 3)
|
||||
error->all(FLERR,"Could not parse 'xy xz yz' line in data file header");
|
||||
|
||||
} else break;
|
||||
}
|
||||
|
|
@ -1634,7 +1688,7 @@ void ReadData::bonus(bigint nbonus, AtomVec *ptr, const char *type)
|
|||
|
||||
void ReadData::bodies(int firstpass)
|
||||
{
|
||||
int m,nchunk,nline,nmax,ninteger,ndouble,nword,ncount,onebody,tmp;
|
||||
int m,nchunk,nline,nmax,ninteger,ndouble,nword,ncount,onebody,tmp,rv;
|
||||
char *eof;
|
||||
|
||||
int mapflag = 0;
|
||||
|
|
@ -1662,7 +1716,9 @@ void ReadData::bodies(int firstpass)
|
|||
while (nchunk < nmax && nline <= CHUNK-MAXBODY) {
|
||||
eof = fgets(&buffer[m],MAXLINE,fp);
|
||||
if (eof == NULL) error->one(FLERR,"Unexpected end of data file");
|
||||
sscanf(&buffer[m],"%d %d %d",&tmp,&ninteger,&ndouble);
|
||||
rv = sscanf(&buffer[m],"%d %d %d",&tmp,&ninteger,&ndouble);
|
||||
if (rv != 3)
|
||||
error->one(FLERR,"Incorrect format in Bodies section of data file");
|
||||
m += strlen(&buffer[m]);
|
||||
|
||||
// read lines one at a time into buffer and count words
|
||||
|
|
|
|||
|
|
@ -59,8 +59,9 @@ int ReaderNative::read_time(bigint &ntimestep)
|
|||
if (strstr(line,"ITEM: TIMESTEP") != line)
|
||||
error->one(FLERR,"Dump file is incorrectly formatted");
|
||||
read_lines(1);
|
||||
sscanf(line,BIGINT_FORMAT,&ntimestep);
|
||||
|
||||
int rv = sscanf(line,BIGINT_FORMAT,&ntimestep);
|
||||
if (rv != 1)
|
||||
error->one(FLERR,"Dump file is incorrectly formatted");
|
||||
return 0;
|
||||
}
|
||||
|
||||
|
|
@ -73,7 +74,9 @@ void ReaderNative::skip()
|
|||
{
|
||||
read_lines(2);
|
||||
bigint natoms;
|
||||
sscanf(line,BIGINT_FORMAT,&natoms);
|
||||
int rv = sscanf(line,BIGINT_FORMAT,&natoms);
|
||||
if (rv != 1)
|
||||
error->one(FLERR,"Dump file is incorrectly formatted");
|
||||
|
||||
read_lines(5);
|
||||
|
||||
|
|
@ -110,8 +113,12 @@ bigint ReaderNative::read_header(double box[3][3], int &boxinfo, int &triclinic,
|
|||
int &xflag, int &yflag, int &zflag)
|
||||
{
|
||||
bigint natoms;
|
||||
int rv;
|
||||
|
||||
read_lines(2);
|
||||
sscanf(line,BIGINT_FORMAT,&natoms);
|
||||
rv = sscanf(line,BIGINT_FORMAT,&natoms);
|
||||
if (rv != 1)
|
||||
error->one(FLERR,"Dump file is incorrectly formatted");
|
||||
|
||||
boxinfo = 1;
|
||||
triclinic = 0;
|
||||
|
|
@ -120,14 +127,19 @@ bigint ReaderNative::read_header(double box[3][3], int &boxinfo, int &triclinic,
|
|||
if (line[strlen("ITEM: BOX BOUNDS ")] == 'x') triclinic = 1;
|
||||
|
||||
read_lines(1);
|
||||
if (!triclinic) sscanf(line,"%lg %lg",&box[0][0],&box[0][1]);
|
||||
else sscanf(line,"%lg %lg %lg",&box[0][0],&box[0][1],&box[0][2]);
|
||||
if (!triclinic) rv = 2 - sscanf(line,"%lg %lg",&box[0][0],&box[0][1]);
|
||||
else rv = 3 - sscanf(line,"%lg %lg %lg",&box[0][0],&box[0][1],&box[0][2]);
|
||||
if (rv != 0) error->one(FLERR,"Dump file is incorrectly formatted");
|
||||
|
||||
read_lines(1);
|
||||
if (!triclinic) sscanf(line,"%lg %lg",&box[1][0],&box[1][1]);
|
||||
else sscanf(line,"%lg %lg %lg",&box[1][0],&box[1][1],&box[1][2]);
|
||||
if (!triclinic) rv = 2 - sscanf(line,"%lg %lg",&box[1][0],&box[1][1]);
|
||||
else rv = 3 - sscanf(line,"%lg %lg %lg",&box[1][0],&box[1][1],&box[1][2]);
|
||||
if (rv != 0) error->one(FLERR,"Dump file is incorrectly formatted");
|
||||
|
||||
read_lines(1);
|
||||
if (!triclinic) sscanf(line,"%lg %lg",&box[2][0],&box[2][1]);
|
||||
else sscanf(line,"%lg %lg %lg",&box[2][0],&box[2][1],&box[2][2]);
|
||||
if (!triclinic) rv = 2 - sscanf(line,"%lg %lg",&box[2][0],&box[2][1]);
|
||||
else rv = 3 - sscanf(line,"%lg %lg %lg",&box[2][0],&box[2][1],&box[2][2]);
|
||||
if (rv != 0) error->one(FLERR,"Dump file is incorrectly formatted");
|
||||
|
||||
read_lines(1);
|
||||
|
||||
|
|
|
|||
|
|
@ -168,7 +168,7 @@ bigint ReaderXYZ::read_header(double /*box*/[3][3], int &boxinfo, int &/*triclin
|
|||
|
||||
void ReaderXYZ::read_atoms(int n, int nfield, double **fields)
|
||||
{
|
||||
int i,m;
|
||||
int i,m,rv;
|
||||
char *eof;
|
||||
int mytype;
|
||||
double myx, myy, myz;
|
||||
|
|
@ -178,7 +178,9 @@ void ReaderXYZ::read_atoms(int n, int nfield, double **fields)
|
|||
if (eof == NULL) error->one(FLERR,"Unexpected end of dump file");
|
||||
|
||||
++nid;
|
||||
sscanf(line,"%*s%lg%lg%lg", &myx, &myy, &myz);
|
||||
rv = sscanf(line,"%*s%lg%lg%lg", &myx, &myy, &myz);
|
||||
if (rv != 3)
|
||||
error->one(FLERR,"Dump file is incorrectly formatted");
|
||||
|
||||
// XXX: we could insert an element2type translation here
|
||||
// XXX: for now we flag unrecognized types as type 0,
|
||||
|
|
|
|||
|
|
@ -113,19 +113,19 @@ void Universe::reorder(char *style, char *arg)
|
|||
// read nprocs lines
|
||||
// uni2orig = inverse mapping
|
||||
|
||||
int me_orig,me_new;
|
||||
sscanf(line,"%d %d",&me_orig,&me_new);
|
||||
int me_orig,me_new,rv;
|
||||
rv = sscanf(line,"%d %d",&me_orig,&me_new);
|
||||
if (me_orig < 0 || me_orig >= nprocs ||
|
||||
me_new < 0 || me_new >= nprocs)
|
||||
me_new < 0 || me_new >= nprocs || rv != 2)
|
||||
error->one(FLERR,"Invalid entry in -reorder file");
|
||||
uni2orig[me_new] = me_orig;
|
||||
|
||||
for (int i = 1; i < nprocs; i++) {
|
||||
if (!fgets(line,MAXLINE,fp))
|
||||
error->one(FLERR,"Unexpected end of -reorder file");
|
||||
sscanf(line,"%d %d",&me_orig,&me_new);
|
||||
rv = sscanf(line,"%d %d",&me_orig,&me_new);
|
||||
if (me_orig < 0 || me_orig >= nprocs ||
|
||||
me_new < 0 || me_new >= nprocs)
|
||||
me_new < 0 || me_new >= nprocs || rv != 2)
|
||||
error->one(FLERR,"Invalid entry in -reorder file");
|
||||
uni2orig[me_new] = me_orig;
|
||||
}
|
||||
|
|
|
|||
|
|
@ -13,6 +13,7 @@
|
|||
|
||||
#include "utils.h"
|
||||
#include <cstring>
|
||||
#include <cstdlib>
|
||||
#include "lammps.h"
|
||||
#include "error.h"
|
||||
|
||||
|
|
@ -38,6 +39,10 @@
|
|||
* '\W' Non-alphanumeric
|
||||
* '\d' Digits, [0-9]
|
||||
* '\D' Non-digits
|
||||
* '\i' Integer chars, [0-9], '+' and '-'
|
||||
* '\I' Non-integers
|
||||
* '\f' Floating point number chars, [0-9], '.', 'e', 'E', '+' and '-'
|
||||
* '\F' Non-floats
|
||||
*
|
||||
* *NOT* supported:
|
||||
* '[^abc]' Inverted class
|
||||
|
|
@ -306,6 +311,7 @@ extern "C" {
|
|||
|
||||
enum { UNUSED, DOT, BEGIN, END, QUESTIONMARK, STAR, PLUS,
|
||||
CHAR, CHAR_CLASS, INV_CHAR_CLASS, DIGIT, NOT_DIGIT,
|
||||
INTEGER, NOT_INTEGER, FLOAT, NOT_FLOAT,
|
||||
ALPHA, NOT_ALPHA, WHITESPACE, NOT_WHITESPACE /*, BRANCH */ };
|
||||
|
||||
typedef struct regex_t {
|
||||
|
|
@ -323,6 +329,8 @@ extern "C" {
|
|||
static int matchplus(regex_t p, regex_t *pattern, const char *text);
|
||||
static int matchone(regex_t p, char c);
|
||||
static int matchdigit(char c);
|
||||
static int matchint(char c);
|
||||
static int matchfloat(char c);
|
||||
static int matchalpha(char c);
|
||||
static int matchwhitespace(char c);
|
||||
static int matchmetachar(char c, const char *str);
|
||||
|
|
@ -394,6 +402,10 @@ extern "C" {
|
|||
/* Meta-character: */
|
||||
case 'd': { re_compiled[j].type = DIGIT; } break;
|
||||
case 'D': { re_compiled[j].type = NOT_DIGIT; } break;
|
||||
case 'i': { re_compiled[j].type = INTEGER; } break;
|
||||
case 'I': { re_compiled[j].type = NOT_INTEGER; } break;
|
||||
case 'f': { re_compiled[j].type = FLOAT; } break;
|
||||
case 'F': { re_compiled[j].type = NOT_FLOAT; } break;
|
||||
case 'w': { re_compiled[j].type = ALPHA; } break;
|
||||
case 'W': { re_compiled[j].type = NOT_ALPHA; } break;
|
||||
case 's': { re_compiled[j].type = WHITESPACE; } break;
|
||||
|
|
@ -466,6 +478,16 @@ extern "C" {
|
|||
return ((c >= '0') && (c <= '9'));
|
||||
}
|
||||
|
||||
static int matchint(char c)
|
||||
{
|
||||
return (matchdigit(c) || (c == '-') || (c == '+'));
|
||||
}
|
||||
|
||||
static int matchfloat(char c)
|
||||
{
|
||||
return (matchint(c) || (c == '.') || (c == 'e') || (c == 'E'));
|
||||
}
|
||||
|
||||
static int matchalpha(char c)
|
||||
{
|
||||
return ((c >= 'a') && (c <= 'z')) || ((c >= 'A') && (c <= 'Z'));
|
||||
|
|
@ -501,6 +523,10 @@ extern "C" {
|
|||
switch (str[0]) {
|
||||
case 'd': return matchdigit(c);
|
||||
case 'D': return !matchdigit(c);
|
||||
case 'i': return matchint(c);
|
||||
case 'I': return !matchint(c);
|
||||
case 'f': return matchfloat(c);
|
||||
case 'F': return !matchfloat(c);
|
||||
case 'w': return matchalphanum(c);
|
||||
case 'W': return !matchalphanum(c);
|
||||
case 's': return matchwhitespace(c);
|
||||
|
|
@ -543,6 +569,10 @@ extern "C" {
|
|||
case INV_CHAR_CLASS: return !matchcharclass(c, (const char *)p.ccl);
|
||||
case DIGIT: return matchdigit(c);
|
||||
case NOT_DIGIT: return !matchdigit(c);
|
||||
case INTEGER: return matchint(c);
|
||||
case NOT_INTEGER: return !matchint(c);
|
||||
case FLOAT: return matchfloat(c);
|
||||
case NOT_FLOAT: return !matchfloat(c);
|
||||
case ALPHA: return matchalphanum(c);
|
||||
case NOT_ALPHA: return !matchalphanum(c);
|
||||
case WHITESPACE: return matchwhitespace(c);
|
||||
|
|
|
|||
|
|
@ -5163,8 +5163,8 @@ int VarReader::read_peratom()
|
|||
for (i = 0; i < nchunk; i++) {
|
||||
next = strchr(buf,'\n');
|
||||
*next = '\0';
|
||||
sscanf(buf,TAGINT_FORMAT " %lg",&tag,&value);
|
||||
if (tag <= 0 || tag > map_tag_max)
|
||||
int rv = sscanf(buf,TAGINT_FORMAT " %lg",&tag,&value);
|
||||
if (tag <= 0 || tag > map_tag_max || rv != 2)
|
||||
error->one(FLERR,"Invalid atom ID in variable file");
|
||||
if ((m = atom->map(tag)) >= 0) vstore[m] = value;
|
||||
buf = next + 1;
|
||||
|
|
|
|||
Loading…
Reference in New Issue