update example for dynamically loading LAMMPS with current library API
This commit is contained in:
Axel Kohlmeyer
@ -13,7 +13,7 @@ like below.
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mpicc -c -O -Wall -g -I$HOME/lammps/src liblammpsplugin.c
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mpicc -c -O -Wall -g simple.c
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mpicc simple.o liblammsplugin.o -ldl -o simpleC
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mpicc simple.o liblammpsplugin.o -ldl -o simpleC
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You also need to build LAMMPS as a shared library
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(see examples/COUPLE/README), e.g.
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@ -31,51 +31,105 @@ liblammpsplugin_t *liblammpsplugin_load(const char *lib)
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if (lib == NULL) return NULL;
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handle = dlopen(lib,RTLD_NOW|RTLD_GLOBAL);
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if (handle == NULL) return NULL;
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lmp = (liblammpsplugin_t *) malloc(sizeof(liblammpsplugin_t));
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lmp->handle = handle;
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#define ADDSYM(symbol) lmp->symbol = dlsym(handle,"lammps_" #symbol)
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ADDSYM(open);
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ADDSYM(open_no_mpi);
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ADDSYM(open_fortran);
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ADDSYM(close);
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ADDSYM(version);
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ADDSYM(mpi_init);
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ADDSYM(mpi_finalize);
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ADDSYM(kokkos_finalize);
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ADDSYM(python_finalize);
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ADDSYM(file);
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ADDSYM(command);
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ADDSYM(commands_list);
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ADDSYM(commands_string);
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ADDSYM(free);
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ADDSYM(extract_setting);
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ADDSYM(extract_global);
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ADDSYM(get_natoms);
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ADDSYM(get_thermo);
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ADDSYM(extract_box);
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ADDSYM(reset_box);
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ADDSYM(memory_usage);
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ADDSYM(get_mpi_comm);
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ADDSYM(extract_setting);
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ADDSYM(extract_global_datatype);
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ADDSYM(extract_global);
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ADDSYM(extract_atom_datatype);
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ADDSYM(extract_atom);
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ADDSYM(extract_compute);
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ADDSYM(extract_fix);
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ADDSYM(extract_variable);
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ADDSYM(get_thermo);
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ADDSYM(get_natoms);
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ADDSYM(set_variable);
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ADDSYM(reset_box);
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ADDSYM(gather_atoms);
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ADDSYM(gather_atoms_concat);
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ADDSYM(gather_atoms_subset);
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ADDSYM(scatter_atoms);
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ADDSYM(scatter_atoms_subset);
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ADDSYM(gather_bonds);
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ADDSYM(set_fix_external_callback);
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ADDSYM(create_atoms);
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ADDSYM(config_has_package);
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ADDSYM(config_package_count);
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ADDSYM(config_package_name);
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ADDSYM(find_pair_neighlist);
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ADDSYM(find_fix_neighlist);
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ADDSYM(find_compute_neighlist);
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ADDSYM(neighlist_num_elements);
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ADDSYM(neighlist_element_neighbors);
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ADDSYM(version);
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ADDSYM(get_os_info);
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ADDSYM(config_has_mpi_support);
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ADDSYM(config_has_gzip_support);
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ADDSYM(config_has_png_support);
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ADDSYM(config_has_jpeg_support);
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ADDSYM(config_has_ffmpeg_support);
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ADDSYM(config_has_exceptions);
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ADDSYM(create_atoms);
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ADDSYM(config_has_package);
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ADDSYM(config_package_count);
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ADDSYM(config_package_name);
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ADDSYM(config_accelerator);
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ADDSYM(has_gpu_device);
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ADDSYM(get_gpu_device_info);
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ADDSYM(has_style);
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ADDSYM(style_count);
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ADDSYM(style_name);
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ADDSYM(has_id);
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ADDSYM(id_count);
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ADDSYM(id_name);
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ADDSYM(plugin_count);
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ADDSYM(plugin_name);
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ADDSYM(set_fix_external_callback);
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ADDSYM(fix_external_get_force);
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ADDSYM(fix_external_set_energy_global);
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ADDSYM(fix_external_set_energy_peratom);
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ADDSYM(fix_external_set_virial_global);
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ADDSYM(fix_external_set_virial_peratom);
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ADDSYM(fix_external_set_vector_length);
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ADDSYM(fix_external_set_vector);
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ADDSYM(free);
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ADDSYM(is_running);
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ADDSYM(force_timeout);
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#ifdef LAMMPS_EXCEPTIONS
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lmp->has_exceptions = 1;
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ADDSYM(has_error);
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@ -39,75 +39,121 @@ extern "C" {
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#if defined(LAMMPS_BIGBIG)
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typedef void (*FixExternalFnPtr)(void *, int64_t, int, int64_t *, double **, double **);
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#elif defined(LAMMPS_SMALLBIG)
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typedef void (*FixExternalFnPtr)(void *, int64_t, int, int *, double **, double **);
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#else
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#elif defined(LAMMPS_SMALLSMALL)
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typedef void (*FixExternalFnPtr)(void *, int, int, int *, double **, double **);
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#else
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typedef void (*FixExternalFnPtr)(void *, int64_t, int, int *, double **, double **);
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#endif
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struct _liblammpsplugin {
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int abiversion;
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int has_exceptions;
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void *handle;
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void (*open)(int, char **, MPI_Comm, void **);
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void (*open_no_mpi)(int, char **, void **);
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void *(*open)(int, char **, MPI_Comm, void **);
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void *(*open_no_mpi)(int, char **, void **);
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void *(*open_fortran)(int, char **, void **, int);
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void (*close)(void *);
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int (*version)(void *);
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void (*mpi_init)();
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void (*mpi_finalize)();
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void (*kokkos_finalize)();
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void (*python_finalize)();
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void (*file)(void *, char *);
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char *(*command)(void *, char *);
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void (*commands_list)(void *, int, char **);
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void (*commands_string)(void *, char *);
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void (*free)(void *);
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int (*extract_setting)(void *, char *);
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void *(*extract_global)(void *, char *);
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void (*extract_box)(void *, double *, double *,
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double *, double *, double *, int *, int *);
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void *(*extract_atom)(void *, char *);
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void *(*extract_compute)(void *, char *, int, int);
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void *(*extract_fix)(void *, char *, int, int, int, int);
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void *(*extract_variable)(void *, char *, char *);
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char *(*command)(void *, const char *);
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void (*commands_list)(void *, int, const char **);
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void (*commands_string)(void *, const char *);
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double (*get_natoms)(void *);
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double (*get_thermo)(void *, char *);
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int (*get_natoms)(void *);
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int (*set_variable)(void *, char *, char *);
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void (*extract_box)(void *, double *, double *,
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double *, double *, double *, int *, int *);
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void (*reset_box)(void *, double *, double *, double, double, double);
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void (*memory_usage)(void *, double *);
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int (*get_mpi_comm)(void *);
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int (*extract_setting)(void *, const char *);
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int *(*extract_global_datatype)(void *, const char *);
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void *(*extract_global)(void *, const char *);
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void *(*extract_atom_datatype)(void *, const char *);
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void *(*extract_atom)(void *, const char *);
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void *(*extract_compute)(void *, const char *, int, int);
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void *(*extract_fix)(void *, const char *, int, int, int, int);
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void *(*extract_variable)(void *, const char *, char *);
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int (*set_variable)(void *, char *, char *);
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void (*gather_atoms)(void *, char *, int, int, void *);
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void (*gather_atoms_concat)(void *, char *, int, int, void *);
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void (*gather_atoms_subset)(void *, char *, int, int, int, int *, void *);
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void (*scatter_atoms)(void *, char *, int, int, void *);
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void (*scatter_atoms_subset)(void *, char *, int, int, int, int *, void *);
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void (*set_fix_external_callback)(void *, char *, FixExternalFnPtr, void*);
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void (*gather_bonds)(void *, void *);
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// lammps_create_atoms() takes tagint and imageint as args
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// ifdef insures they are compatible with rest of LAMMPS
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// caller must match to how LAMMPS library is built
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int (*config_has_package)(char * package_name);
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int (*config_package_count)();
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int (*config_package_name)(int index, char * buffer, int max_size);
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#ifndef LAMMPS_BIGBIG
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void (*create_atoms)(void *, int, int *, int *, double *,
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double *, int *, int);
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#else
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void (*create_atoms)(void *, int, int64_t *, int *, double *,
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double *, int64_t *, int);
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#endif
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int (*find_pair_neighlist)(void *, const char *, int, int, int);
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int (*find_fix_neighlist)(void *, const char *, int);
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int (*find_compute_neighlist)(void *, char *, int);
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int (*neighlist_num_elements)(void *, int);
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void (*neighlist_element_neighbors)(void *, int, int, int *, int *, int **);
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int (*version)(void *);
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void (*get_os_info)(char *, int);
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int (*config_has_mpi_support)();
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int (*config_has_gzip_support)();
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int (*config_has_png_support)();
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int (*config_has_jpeg_support)();
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int (*config_has_ffmpeg_support)();
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int (*config_has_exceptions)();
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int (*find_pair_neighlist)(void* ptr, char * style, int exact, int nsub, int request);
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int (*find_fix_neighlist)(void* ptr, char * id, int request);
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int (*find_compute_neighlist)(void* ptr, char * id, int request);
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int (*neighlist_num_elements)(void* ptr, int idx);
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void (*neighlist_element_neighbors)(void * ptr, int idx, int element, int * iatom, int * numneigh, int ** neighbors);
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int (*config_has_package)(const char *);
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int (*config_package_count)();
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int (*config_package_name)(int, char *, int);
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// lammps_create_atoms() takes tagint and imageint as args
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// ifdef insures they are compatible with rest of LAMMPS
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// caller must match to how LAMMPS library is built
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int (*config_accelerator)(const char *, const char *, const char *);
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int (*has_gpu_device)();
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void (*get_gpu_device_info)(char *, int);
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#ifdef LAMMPS_BIGBIG
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void (*create_atoms)(void *, int, int64_t *, int *,
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double *, double *, int64_t *, int);
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#else
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void (*create_atoms)(void *, int, int *, int *,
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double *, double *, int *, int);
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#endif
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int (*has_style)(void *, const char *, const char *);
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int (*style_count)(void *, const char *);
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int (*style_name)(void *, const char *, int, char *, int);
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int (*has_id)(void *, const char *, const char *);
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int (*id_count)(void *, const char *);
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int (*id_name)(void *, const char *, int, char *, int);
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int (*plugin_count)();
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int (*plugin_name)(int, char *, char *, int);
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void (*set_fix_external_callback)(void *, const char *, FixExternalFnPtr, void*);
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void (*fix_external_get_force)(void *, const char *);
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void (*fix_external_set_energy_global)(void *, const char *, double);
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void (*fix_external_set_energy_peratom)(void *, const char *, double *);
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void (*fix_external_set_virial_global)(void *, const char *, double *);
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void (*fix_external_set_virial_peratom)(void *, const char *, double **);
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void (*fix_external_set_vector_length)(void *, const char *, int);
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void (*fix_external_set_vector)(void *, const char *, int, double);
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void (*free)(void *);
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void (*is_running)(void *);
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void (*force_timeout)(void *);
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int (*has_error)(void *);
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int (*get_last_error_message)(void *, char *, int);
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@ -117,7 +163,7 @@ typedef struct _liblammpsplugin liblammpsplugin_t;
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liblammpsplugin_t *liblammpsplugin_load(const char *);
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int liblammpsplugin_release(liblammpsplugin_t *);
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#undef LAMMPS
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#ifdef __cplusplus
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}
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@ -1,9 +1,12 @@
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LAMMPS (18 Feb 2020)
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Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
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Created orthogonal box = (0 0 0) to (6.71838 6.71838 6.71838)
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LAMMPS (31 Aug 2021)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
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Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (6.7183848 6.7183848 6.7183848)
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1 by 1 by 1 MPI processor grid
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Created 256 atoms
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create_atoms CPU = 0.000297844 secs
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using lattice units in orthogonal box = (0.0000000 0.0000000 0.0000000) to (6.7183848 6.7183848 6.7183848)
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create_atoms CPU = 0.001 seconds
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Neighbor list info ...
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update every 20 steps, delay 0 steps, check no
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max neighbors/atom: 2000, page size: 100000
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@ -14,108 +17,108 @@ Neighbor list info ...
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d/newton
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stencil: half/bin/3d
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bin: standard
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Setting up Verlet run ...
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Unit style : lj
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Current step : 0
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Time step : 0.005
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Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
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Per MPI rank memory allocation (min/avg/max) = 2.630 | 2.630 | 2.630 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1.44 -6.7733681 0 -4.6218056 -5.0244179
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10 1.1298532 -6.3095502 0 -4.6213906 -2.6058175
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Loop time of 0.00164276 on 1 procs for 10 steps with 256 atoms
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Loop time of 0.00239712 on 1 procs for 10 steps with 256 atoms
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Performance: 2629719.113 tau/day, 6087.313 timesteps/s
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93.7% CPU use with 1 MPI tasks x no OpenMP threads
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Performance: 1802163.347 tau/day, 4171.674 timesteps/s
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97.2% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.0014956 | 0.0014956 | 0.0014956 | 0.0 | 91.04
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Pair | 0.0020572 | 0.0020572 | 0.0020572 | 0.0 | 85.82
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 8.045e-05 | 8.045e-05 | 8.045e-05 | 0.0 | 4.90
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Output | 1.1399e-05 | 1.1399e-05 | 1.1399e-05 | 0.0 | 0.69
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Modify | 3.7431e-05 | 3.7431e-05 | 3.7431e-05 | 0.0 | 2.28
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Other | | 1.789e-05 | | | 1.09
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Comm | 0.00018731 | 0.00018731 | 0.00018731 | 0.0 | 7.81
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Output | 4.478e-05 | 4.478e-05 | 4.478e-05 | 0.0 | 1.87
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Modify | 6.3637e-05 | 6.3637e-05 | 6.3637e-05 | 0.0 | 2.65
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Other | | 4.419e-05 | | | 1.84
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Nlocal: 256 ave 256 max 256 min
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Nlocal: 256.000 ave 256 max 256 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 1431 ave 1431 max 1431 min
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Nghost: 1431.00 ave 1431 max 1431 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 9984 ave 9984 max 9984 min
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Neighs: 9984.00 ave 9984 max 9984 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 9984
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Ave neighs/atom = 39
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Ave neighs/atom = 39.000000
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Neighbor list builds = 0
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Dangerous builds not checked
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Setting up Verlet run ...
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Unit style : lj
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Current step : 10
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Time step : 0.005
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Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
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Per MPI rank memory allocation (min/avg/max) = 2.630 | 2.630 | 2.630 Mbytes
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Step Temp E_pair E_mol TotEng Press
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10 1.1298532 -6.3095502 0 -4.6213906 -2.6058175
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20 0.6239063 -5.557644 0 -4.6254403 0.97451173
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Loop time of 0.00199768 on 1 procs for 10 steps with 256 atoms
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Loop time of 0.00329271 on 1 procs for 10 steps with 256 atoms
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Performance: 2162504.180 tau/day, 5005.797 timesteps/s
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99.8% CPU use with 1 MPI tasks x no OpenMP threads
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Performance: 1311987.619 tau/day, 3037.008 timesteps/s
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96.4% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.0018518 | 0.0018518 | 0.0018518 | 0.0 | 92.70
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Pair | 0.0029015 | 0.0029015 | 0.0029015 | 0.0 | 88.12
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 7.9768e-05 | 7.9768e-05 | 7.9768e-05 | 0.0 | 3.99
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Output | 1.1433e-05 | 1.1433e-05 | 1.1433e-05 | 0.0 | 0.57
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Modify | 3.6904e-05 | 3.6904e-05 | 3.6904e-05 | 0.0 | 1.85
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Other | | 1.773e-05 | | | 0.89
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Comm | 0.00021807 | 0.00021807 | 0.00021807 | 0.0 | 6.62
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Output | 4.9163e-05 | 4.9163e-05 | 4.9163e-05 | 0.0 | 1.49
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Modify | 7.0573e-05 | 7.0573e-05 | 7.0573e-05 | 0.0 | 2.14
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Other | | 5.339e-05 | | | 1.62
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Nlocal: 256 ave 256 max 256 min
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Nlocal: 256.000 ave 256 max 256 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1431 ave 1431 max 1431 min
|
||||
Nghost: 1431.00 ave 1431 max 1431 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 9952 ave 9952 max 9952 min
|
||||
Neighs: 9952.00 ave 9952 max 9952 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 9952
|
||||
Ave neighs/atom = 38.875
|
||||
Ave neighs/atom = 38.875000
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Setting up Verlet run ...
|
||||
Unit style : lj
|
||||
Current step : 20
|
||||
Time step : 0.005
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.630 | 2.630 | 2.630 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
20 0.6239063 -5.5404291 0 -4.6082254 1.0394285
|
||||
21 0.63845863 -5.5628733 0 -4.6089263 0.99398278
|
||||
Loop time of 0.000304321 on 1 procs for 1 steps with 256 atoms
|
||||
Loop time of 0.000638039 on 1 procs for 1 steps with 256 atoms
|
||||
|
||||
Performance: 1419553.695 tau/day, 3286.004 timesteps/s
|
||||
98.9% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 677074.599 tau/day, 1567.302 timesteps/s
|
||||
98.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00027815 | 0.00027815 | 0.00027815 | 0.0 | 91.40
|
||||
Pair | 0.00042876 | 0.00042876 | 0.00042876 | 0.0 | 67.20
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 8.321e-06 | 8.321e-06 | 8.321e-06 | 0.0 | 2.73
|
||||
Output | 1.0513e-05 | 1.0513e-05 | 1.0513e-05 | 0.0 | 3.45
|
||||
Modify | 3.968e-06 | 3.968e-06 | 3.968e-06 | 0.0 | 1.30
|
||||
Other | | 3.365e-06 | | | 1.11
|
||||
Comm | 5.2872e-05 | 5.2872e-05 | 5.2872e-05 | 0.0 | 8.29
|
||||
Output | 0.00012218 | 0.00012218 | 0.00012218 | 0.0 | 19.15
|
||||
Modify | 1.3762e-05 | 1.3762e-05 | 1.3762e-05 | 0.0 | 2.16
|
||||
Other | | 2.047e-05 | | | 3.21
|
||||
|
||||
Nlocal: 256 ave 256 max 256 min
|
||||
Nlocal: 256.000 ave 256 max 256 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1431 ave 1431 max 1431 min
|
||||
Nghost: 1431.00 ave 1431 max 1431 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 9705 ave 9705 max 9705 min
|
||||
Neighs: 9705.00 ave 9705 max 9705 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 9705
|
||||
Ave neighs/atom = 37.9102
|
||||
Ave neighs/atom = 37.910156
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Force on 1 atom via extract_atom: 26.9581
|
||||
@ -124,136 +127,136 @@ Setting up Verlet run ...
|
||||
Unit style : lj
|
||||
Current step : 21
|
||||
Time step : 0.005
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.630 | 2.630 | 2.630 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
21 0.63845863 -5.5628733 0 -4.6089263 0.99398278
|
||||
31 0.7494946 -5.7306417 0 -4.6107913 0.41043597
|
||||
Loop time of 0.00196027 on 1 procs for 10 steps with 256 atoms
|
||||
Loop time of 0.00281277 on 1 procs for 10 steps with 256 atoms
|
||||
|
||||
Performance: 2203779.175 tau/day, 5101.341 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 1535852.558 tau/day, 3555.214 timesteps/s
|
||||
92.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0018146 | 0.0018146 | 0.0018146 | 0.0 | 92.57
|
||||
Pair | 0.0024599 | 0.0024599 | 0.0024599 | 0.0 | 87.45
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 8.0268e-05 | 8.0268e-05 | 8.0268e-05 | 0.0 | 4.09
|
||||
Output | 1.0973e-05 | 1.0973e-05 | 1.0973e-05 | 0.0 | 0.56
|
||||
Modify | 3.6913e-05 | 3.6913e-05 | 3.6913e-05 | 0.0 | 1.88
|
||||
Other | | 1.756e-05 | | | 0.90
|
||||
Comm | 0.00020234 | 0.00020234 | 0.00020234 | 0.0 | 7.19
|
||||
Output | 3.6436e-05 | 3.6436e-05 | 3.6436e-05 | 0.0 | 1.30
|
||||
Modify | 6.7542e-05 | 6.7542e-05 | 6.7542e-05 | 0.0 | 2.40
|
||||
Other | | 4.655e-05 | | | 1.65
|
||||
|
||||
Nlocal: 256 ave 256 max 256 min
|
||||
Nlocal: 256.000 ave 256 max 256 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1431 ave 1431 max 1431 min
|
||||
Nghost: 1431.00 ave 1431 max 1431 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 9688 ave 9688 max 9688 min
|
||||
Neighs: 9688.00 ave 9688 max 9688 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 9688
|
||||
Ave neighs/atom = 37.8438
|
||||
Ave neighs/atom = 37.843750
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Setting up Verlet run ...
|
||||
Unit style : lj
|
||||
Current step : 31
|
||||
Time step : 0.005
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.630 | 2.630 | 2.630 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
31 0.7494946 -5.7306417 0 -4.6107913 0.41043597
|
||||
51 0.71349216 -5.6772387 0 -4.6111811 0.52117681
|
||||
Loop time of 0.00433063 on 1 procs for 20 steps with 256 atoms
|
||||
Loop time of 0.00560916 on 1 procs for 20 steps with 256 atoms
|
||||
|
||||
Performance: 1995088.941 tau/day, 4618.261 timesteps/s
|
||||
99.3% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 1540338.414 tau/day, 3565.598 timesteps/s
|
||||
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0035121 | 0.0035121 | 0.0035121 | 0.0 | 81.10
|
||||
Neigh | 0.00050258 | 0.00050258 | 0.00050258 | 0.0 | 11.61
|
||||
Comm | 0.00019444 | 0.00019444 | 0.00019444 | 0.0 | 4.49
|
||||
Output | 1.2092e-05 | 1.2092e-05 | 1.2092e-05 | 0.0 | 0.28
|
||||
Modify | 7.2917e-05 | 7.2917e-05 | 7.2917e-05 | 0.0 | 1.68
|
||||
Other | | 3.647e-05 | | | 0.84
|
||||
Pair | 0.0044403 | 0.0044403 | 0.0044403 | 0.0 | 79.16
|
||||
Neigh | 0.00056186 | 0.00056186 | 0.00056186 | 0.0 | 10.02
|
||||
Comm | 0.00036797 | 0.00036797 | 0.00036797 | 0.0 | 6.56
|
||||
Output | 3.676e-05 | 3.676e-05 | 3.676e-05 | 0.0 | 0.66
|
||||
Modify | 0.00011282 | 0.00011282 | 0.00011282 | 0.0 | 2.01
|
||||
Other | | 8.943e-05 | | | 1.59
|
||||
|
||||
Nlocal: 256 ave 256 max 256 min
|
||||
Nlocal: 256.000 ave 256 max 256 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1421 ave 1421 max 1421 min
|
||||
Nghost: 1421.00 ave 1421 max 1421 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 9700 ave 9700 max 9700 min
|
||||
Neighs: 9700.00 ave 9700 max 9700 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 9700
|
||||
Ave neighs/atom = 37.8906
|
||||
Ave neighs/atom = 37.890625
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds not checked
|
||||
Setting up Verlet run ...
|
||||
Unit style : lj
|
||||
Current step : 51
|
||||
Time step : 0.005
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.630 | 2.630 | 2.630 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
51 0.71349216 -5.6772387 0 -4.6111811 0.52117681
|
||||
61 0.78045421 -5.7781094 0 -4.6120011 0.093808941
|
||||
Loop time of 0.00196567 on 1 procs for 10 steps with 256 atoms
|
||||
Loop time of 0.00373815 on 1 procs for 10 steps with 256 atoms
|
||||
|
||||
Performance: 2197727.285 tau/day, 5087.332 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 1155650.623 tau/day, 2675.117 timesteps/s
|
||||
98.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0018222 | 0.0018222 | 0.0018222 | 0.0 | 92.70
|
||||
Pair | 0.0030908 | 0.0030908 | 0.0030908 | 0.0 | 82.68
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 7.8285e-05 | 7.8285e-05 | 7.8285e-05 | 0.0 | 3.98
|
||||
Output | 1.0862e-05 | 1.0862e-05 | 1.0862e-05 | 0.0 | 0.55
|
||||
Modify | 3.6719e-05 | 3.6719e-05 | 3.6719e-05 | 0.0 | 1.87
|
||||
Other | | 1.764e-05 | | | 0.90
|
||||
Comm | 0.00038189 | 0.00038189 | 0.00038189 | 0.0 | 10.22
|
||||
Output | 4.1615e-05 | 4.1615e-05 | 4.1615e-05 | 0.0 | 1.11
|
||||
Modify | 0.00013851 | 0.00013851 | 0.00013851 | 0.0 | 3.71
|
||||
Other | | 8.533e-05 | | | 2.28
|
||||
|
||||
Nlocal: 256 ave 256 max 256 min
|
||||
Nlocal: 256.000 ave 256 max 256 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1421 ave 1421 max 1421 min
|
||||
Nghost: 1421.00 ave 1421 max 1421 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 9700 ave 9700 max 9700 min
|
||||
Neighs: 9700.00 ave 9700 max 9700 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 9700
|
||||
Ave neighs/atom = 37.8906
|
||||
Ave neighs/atom = 37.890625
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Setting up Verlet run ...
|
||||
Unit style : lj
|
||||
Current step : 61
|
||||
Time step : 0.005
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.630 | 2.630 | 2.630 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
61 0.78045421 -5.7781094 0 -4.6120011 0.093808941
|
||||
81 0.77743907 -5.7735004 0 -4.6118971 0.090822641
|
||||
Loop time of 0.00430528 on 1 procs for 20 steps with 256 atoms
|
||||
Loop time of 0.00612177 on 1 procs for 20 steps with 256 atoms
|
||||
|
||||
Performance: 2006838.581 tau/day, 4645.460 timesteps/s
|
||||
99.8% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 1411356.519 tau/day, 3267.029 timesteps/s
|
||||
98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0034931 | 0.0034931 | 0.0034931 | 0.0 | 81.13
|
||||
Neigh | 0.00050437 | 0.00050437 | 0.00050437 | 0.0 | 11.72
|
||||
Comm | 0.0001868 | 0.0001868 | 0.0001868 | 0.0 | 4.34
|
||||
Output | 1.1699e-05 | 1.1699e-05 | 1.1699e-05 | 0.0 | 0.27
|
||||
Modify | 7.3308e-05 | 7.3308e-05 | 7.3308e-05 | 0.0 | 1.70
|
||||
Other | | 3.604e-05 | | | 0.84
|
||||
Pair | 0.0047211 | 0.0047211 | 0.0047211 | 0.0 | 77.12
|
||||
Neigh | 0.00083088 | 0.00083088 | 0.00083088 | 0.0 | 13.57
|
||||
Comm | 0.00032716 | 0.00032716 | 0.00032716 | 0.0 | 5.34
|
||||
Output | 3.9891e-05 | 3.9891e-05 | 3.9891e-05 | 0.0 | 0.65
|
||||
Modify | 0.00010926 | 0.00010926 | 0.00010926 | 0.0 | 1.78
|
||||
Other | | 9.346e-05 | | | 1.53
|
||||
|
||||
Nlocal: 256 ave 256 max 256 min
|
||||
Nlocal: 256.000 ave 256 max 256 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1405 ave 1405 max 1405 min
|
||||
Nghost: 1405.00 ave 1405 max 1405 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 9701 ave 9701 max 9701 min
|
||||
Neighs: 9701.00 ave 9701 max 9701 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 9701
|
||||
Ave neighs/atom = 37.8945
|
||||
Ave neighs/atom = 37.894531
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds not checked
|
||||
Deleted 256 atoms, new total = 0
|
||||
@ -261,34 +264,34 @@ Setting up Verlet run ...
|
||||
Unit style : lj
|
||||
Current step : 81
|
||||
Time step : 0.005
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.63 | 2.63 | 2.63 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 2.630 | 2.630 | 2.630 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
81 0.6239063 -5.5404291 0 -4.6082254 1.0394285
|
||||
91 0.75393007 -5.7375259 0 -4.6110484 0.39357367
|
||||
Loop time of 0.00195843 on 1 procs for 10 steps with 256 atoms
|
||||
Loop time of 0.00319065 on 1 procs for 10 steps with 256 atoms
|
||||
|
||||
Performance: 2205851.941 tau/day, 5106.139 timesteps/s
|
||||
99.7% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
Performance: 1353954.393 tau/day, 3134.154 timesteps/s
|
||||
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0018143 | 0.0018143 | 0.0018143 | 0.0 | 92.64
|
||||
Pair | 0.0027828 | 0.0027828 | 0.0027828 | 0.0 | 87.22
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 7.8608e-05 | 7.8608e-05 | 7.8608e-05 | 0.0 | 4.01
|
||||
Output | 1.0786e-05 | 1.0786e-05 | 1.0786e-05 | 0.0 | 0.55
|
||||
Modify | 3.7106e-05 | 3.7106e-05 | 3.7106e-05 | 0.0 | 1.89
|
||||
Other | | 1.762e-05 | | | 0.90
|
||||
Comm | 0.00023286 | 0.00023286 | 0.00023286 | 0.0 | 7.30
|
||||
Output | 4.0459e-05 | 4.0459e-05 | 4.0459e-05 | 0.0 | 1.27
|
||||
Modify | 7.3576e-05 | 7.3576e-05 | 7.3576e-05 | 0.0 | 2.31
|
||||
Other | | 6.094e-05 | | | 1.91
|
||||
|
||||
Nlocal: 256 ave 256 max 256 min
|
||||
Nlocal: 256.000 ave 256 max 256 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1431 ave 1431 max 1431 min
|
||||
Nghost: 1431.00 ave 1431 max 1431 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 9705 ave 9705 max 9705 min
|
||||
Neighs: 9705.00 ave 9705 max 9705 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 9705
|
||||
Ave neighs/atom = 37.9102
|
||||
Ave neighs/atom = 37.910156
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:00
|
||||
|
||||
@ -1,9 +1,12 @@
|
||||
LAMMPS (18 Feb 2020)
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
Created orthogonal box = (0 0 0) to (6.71838 6.71838 6.71838)
|
||||
LAMMPS (31 Aug 2021)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
Lattice spacing in x,y,z = 1.6795962 1.6795962 1.6795962
|
||||
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (6.7183848 6.7183848 6.7183848)
|
||||
1 by 1 by 2 MPI processor grid
|
||||
Created 256 atoms
|
||||
create_atoms CPU = 0.000265157 secs
|
||||
using lattice units in orthogonal box = (0.0000000 0.0000000 0.0000000) to (6.7183848 6.7183848 6.7183848)
|
||||
create_atoms CPU = 0.003 seconds
|
||||
Neighbor list info ...
|
||||
update every 20 steps, delay 0 steps, check no
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
@ -14,7 +17,7 @@ Neighbor list info ...
|
||||
(1) pair lj/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : lj
|
||||
@ -24,30 +27,30 @@ Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7733681 0 -4.6218056 -5.0244179
|
||||
10 1.1298532 -6.3095502 0 -4.6213906 -2.6058175
|
||||
Loop time of 0.00115264 on 2 procs for 10 steps with 256 atoms
|
||||
Loop time of 0.00330899 on 2 procs for 10 steps with 256 atoms
|
||||
|
||||
Performance: 3747912.946 tau/day, 8675.724 timesteps/s
|
||||
94.5% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
Performance: 1305535.501 tau/day, 3022.073 timesteps/s
|
||||
75.7% CPU use with 2 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00074885 | 0.00075021 | 0.00075156 | 0.0 | 65.09
|
||||
Pair | 0.0013522 | 0.0013813 | 0.0014104 | 0.1 | 41.74
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00031829 | 0.00031943 | 0.00032056 | 0.0 | 27.71
|
||||
Output | 9.306e-06 | 2.6673e-05 | 4.4041e-05 | 0.0 | 2.31
|
||||
Modify | 2.0684e-05 | 2.0891e-05 | 2.1098e-05 | 0.0 | 1.81
|
||||
Other | | 3.544e-05 | | | 3.07
|
||||
Comm | 0.00049139 | 0.00054241 | 0.00059342 | 0.0 | 16.39
|
||||
Output | 3.6986e-05 | 0.00056588 | 0.0010948 | 0.0 | 17.10
|
||||
Modify | 4.3909e-05 | 4.3924e-05 | 4.3939e-05 | 0.0 | 1.33
|
||||
Other | | 0.0007755 | | | 23.44
|
||||
|
||||
Nlocal: 128 ave 128 max 128 min
|
||||
Nlocal: 128.000 ave 128 max 128 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1109 ave 1109 max 1109 min
|
||||
Nghost: 1109.00 ave 1109 max 1109 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 4992 ave 4992 max 4992 min
|
||||
Neighs: 4992.00 ave 4992 max 4992 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 9984
|
||||
Ave neighs/atom = 39
|
||||
Ave neighs/atom = 39.000000
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Setting up Verlet run ...
|
||||
@ -58,30 +61,30 @@ Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
10 1.1298532 -6.3095502 0 -4.6213906 -2.6058175
|
||||
20 0.6239063 -5.557644 0 -4.6254403 0.97451173
|
||||
Loop time of 0.00120443 on 2 procs for 10 steps with 256 atoms
|
||||
Loop time of 0.00648485 on 2 procs for 10 steps with 256 atoms
|
||||
|
||||
Performance: 3586761.860 tau/day, 8302.689 timesteps/s
|
||||
95.5% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
Performance: 666168.017 tau/day, 1542.056 timesteps/s
|
||||
44.3% CPU use with 2 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00087798 | 0.00091359 | 0.0009492 | 0.0 | 75.85
|
||||
Pair | 0.0022373 | 0.0024405 | 0.0026437 | 0.4 | 37.63
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00016739 | 0.00020368 | 0.00023997 | 0.0 | 16.91
|
||||
Output | 1.0124e-05 | 3.0513e-05 | 5.0901e-05 | 0.0 | 2.53
|
||||
Modify | 1.89e-05 | 1.9812e-05 | 2.0725e-05 | 0.0 | 1.64
|
||||
Other | | 3.683e-05 | | | 3.06
|
||||
Comm | 0.0024446 | 0.0026464 | 0.0028481 | 0.4 | 40.81
|
||||
Output | 3.9069e-05 | 0.00059734 | 0.0011556 | 0.0 | 9.21
|
||||
Modify | 4.869e-05 | 4.912e-05 | 4.9551e-05 | 0.0 | 0.76
|
||||
Other | | 0.0007515 | | | 11.59
|
||||
|
||||
Nlocal: 128 ave 134 max 122 min
|
||||
Nlocal: 128.000 ave 134 max 122 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 1109 ave 1115 max 1103 min
|
||||
Nghost: 1109.00 ave 1115 max 1103 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 4976 ave 5205 max 4747 min
|
||||
Neighs: 4976.00 ave 5205 max 4747 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 9952
|
||||
Ave neighs/atom = 38.875
|
||||
Ave neighs/atom = 38.875000
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Setting up Verlet run ...
|
||||
@ -92,34 +95,34 @@ Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
20 0.6239063 -5.5404291 0 -4.6082254 1.0394285
|
||||
21 0.63845863 -5.5628733 0 -4.6089263 0.99398278
|
||||
Loop time of 0.000206062 on 2 procs for 1 steps with 256 atoms
|
||||
Loop time of 0.00128072 on 2 procs for 1 steps with 256 atoms
|
||||
|
||||
Performance: 2096456.406 tau/day, 4852.908 timesteps/s
|
||||
94.1% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
Performance: 337310.921 tau/day, 780.812 timesteps/s
|
||||
60.2% CPU use with 2 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00012947 | 0.00013524 | 0.00014101 | 0.0 | 65.63
|
||||
Pair | 0.00047351 | 0.00049064 | 0.00050777 | 0.0 | 38.31
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 1.858e-05 | 2.4113e-05 | 2.9647e-05 | 0.0 | 11.70
|
||||
Output | 8.699e-06 | 2.4204e-05 | 3.9708e-05 | 0.0 | 11.75
|
||||
Modify | 2.34e-06 | 2.3705e-06 | 2.401e-06 | 0.0 | 1.15
|
||||
Other | | 2.013e-05 | | | 9.77
|
||||
Comm | 7.6767e-05 | 9.3655e-05 | 0.00011054 | 0.0 | 7.31
|
||||
Output | 5.4217e-05 | 0.00026297 | 0.00047172 | 0.0 | 20.53
|
||||
Modify | 1.1554e-05 | 1.2026e-05 | 1.2498e-05 | 0.0 | 0.94
|
||||
Other | | 0.0004214 | | | 32.91
|
||||
|
||||
Nlocal: 128 ave 135 max 121 min
|
||||
Nlocal: 128.000 ave 135 max 121 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 1109 ave 1116 max 1102 min
|
||||
Nghost: 1109.00 ave 1116 max 1102 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 4852.5 ave 5106 max 4599 min
|
||||
Neighs: 4852.50 ave 5106 max 4599 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 9705
|
||||
Ave neighs/atom = 37.9102
|
||||
Force on 1 atom via extract_atom: -18.109
|
||||
Force on 1 atom via extract_variable: -18.109
|
||||
Ave neighs/atom = 37.910156
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Force on 1 atom via extract_atom: -18.109
|
||||
Force on 1 atom via extract_variable: -18.109
|
||||
Force on 1 atom via extract_atom: 26.9581
|
||||
Force on 1 atom via extract_variable: 26.9581
|
||||
Setting up Verlet run ...
|
||||
@ -130,30 +133,30 @@ Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
21 0.63845863 -5.5628733 0 -4.6089263 0.99398278
|
||||
31 0.7494946 -5.7306417 0 -4.6107913 0.41043597
|
||||
Loop time of 0.00119048 on 2 procs for 10 steps with 256 atoms
|
||||
Loop time of 0.00784933 on 2 procs for 10 steps with 256 atoms
|
||||
|
||||
Performance: 3628802.105 tau/day, 8400.005 timesteps/s
|
||||
98.0% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
Performance: 550365.761 tau/day, 1273.995 timesteps/s
|
||||
59.6% CPU use with 2 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00085276 | 0.00089699 | 0.00094123 | 0.0 | 75.35
|
||||
Pair | 0.0019235 | 0.0033403 | 0.0047572 | 2.5 | 42.56
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00016896 | 0.00021444 | 0.00025992 | 0.0 | 18.01
|
||||
Output | 9.413e-06 | 2.5939e-05 | 4.2465e-05 | 0.0 | 2.18
|
||||
Modify | 1.8977e-05 | 2.0009e-05 | 2.1042e-05 | 0.0 | 1.68
|
||||
Other | | 3.31e-05 | | | 2.78
|
||||
Comm | 0.0016948 | 0.003118 | 0.0045411 | 2.5 | 39.72
|
||||
Output | 3.6445e-05 | 0.00064636 | 0.0012563 | 0.0 | 8.23
|
||||
Modify | 6.2842e-05 | 6.3209e-05 | 6.3577e-05 | 0.0 | 0.81
|
||||
Other | | 0.0006814 | | | 8.68
|
||||
|
||||
Nlocal: 128 ave 135 max 121 min
|
||||
Nlocal: 128.000 ave 135 max 121 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 1109 ave 1116 max 1102 min
|
||||
Nghost: 1109.00 ave 1116 max 1102 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 4844 ave 5096 max 4592 min
|
||||
Neighs: 4844.00 ave 5096 max 4592 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 9688
|
||||
Ave neighs/atom = 37.8438
|
||||
Ave neighs/atom = 37.843750
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Setting up Verlet run ...
|
||||
@ -164,30 +167,30 @@ Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
31 0.7494946 -5.7306417 0 -4.6107913 0.41043597
|
||||
51 0.71349216 -5.6772387 0 -4.6111811 0.52117681
|
||||
Loop time of 0.00252603 on 2 procs for 20 steps with 256 atoms
|
||||
Loop time of 0.00696051 on 2 procs for 20 steps with 256 atoms
|
||||
|
||||
Performance: 3420382.192 tau/day, 7917.551 timesteps/s
|
||||
99.2% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
Performance: 1241287.730 tau/day, 2873.351 timesteps/s
|
||||
79.2% CPU use with 2 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0016245 | 0.0017014 | 0.0017784 | 0.2 | 67.36
|
||||
Neigh | 0.00025359 | 0.0002563 | 0.00025901 | 0.0 | 10.15
|
||||
Comm | 0.00036863 | 0.00045124 | 0.00053385 | 0.0 | 17.86
|
||||
Output | 9.839e-06 | 2.8031e-05 | 4.6223e-05 | 0.0 | 1.11
|
||||
Modify | 3.7027e-05 | 3.9545e-05 | 4.2063e-05 | 0.0 | 1.57
|
||||
Other | | 4.948e-05 | | | 1.96
|
||||
Pair | 0.0028267 | 0.0036088 | 0.004391 | 1.3 | 51.85
|
||||
Neigh | 0.00040272 | 0.00040989 | 0.00041707 | 0.0 | 5.89
|
||||
Comm | 0.00081061 | 0.0015825 | 0.0023544 | 1.9 | 22.74
|
||||
Output | 3.6006e-05 | 0.00062106 | 0.0012061 | 0.0 | 8.92
|
||||
Modify | 6.8937e-05 | 7.1149e-05 | 7.336e-05 | 0.0 | 1.02
|
||||
Other | | 0.0006671 | | | 9.58
|
||||
|
||||
Nlocal: 128 ave 132 max 124 min
|
||||
Nlocal: 128.000 ave 132 max 124 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 1100 ave 1101 max 1099 min
|
||||
Nghost: 1100.00 ave 1101 max 1099 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 4850 ave 4953 max 4747 min
|
||||
Neighs: 4850.00 ave 4953 max 4747 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 9700
|
||||
Ave neighs/atom = 37.8906
|
||||
Ave neighs/atom = 37.890625
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds not checked
|
||||
Setting up Verlet run ...
|
||||
@ -198,30 +201,30 @@ Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
51 0.71349216 -5.6772387 0 -4.6111811 0.52117681
|
||||
61 0.78045421 -5.7781094 0 -4.6120011 0.093808941
|
||||
Loop time of 0.00115444 on 2 procs for 10 steps with 256 atoms
|
||||
Loop time of 0.00155862 on 2 procs for 10 steps with 256 atoms
|
||||
|
||||
Performance: 3742065.976 tau/day, 8662.190 timesteps/s
|
||||
96.5% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
Performance: 2771678.197 tau/day, 6415.922 timesteps/s
|
||||
95.0% CPU use with 2 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00087346 | 0.00089311 | 0.00091275 | 0.0 | 77.36
|
||||
Pair | 0.0012369 | 0.001266 | 0.001295 | 0.1 | 81.22
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00016192 | 0.0001823 | 0.00020269 | 0.0 | 15.79
|
||||
Output | 9.49e-06 | 2.6234e-05 | 4.2978e-05 | 0.0 | 2.27
|
||||
Modify | 1.9095e-05 | 1.9843e-05 | 2.0591e-05 | 0.0 | 1.72
|
||||
Other | | 3.296e-05 | | | 2.85
|
||||
Comm | 0.00019462 | 0.00022315 | 0.00025169 | 0.0 | 14.32
|
||||
Output | 2.0217e-05 | 2.1945e-05 | 2.3673e-05 | 0.0 | 1.41
|
||||
Modify | 2.562e-05 | 2.5759e-05 | 2.5898e-05 | 0.0 | 1.65
|
||||
Other | | 2.181e-05 | | | 1.40
|
||||
|
||||
Nlocal: 128 ave 132 max 124 min
|
||||
Nlocal: 128.000 ave 132 max 124 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 1100 ave 1101 max 1099 min
|
||||
Nghost: 1100.00 ave 1101 max 1099 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 4850 ave 4953 max 4747 min
|
||||
Neighs: 4850.00 ave 4953 max 4747 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 9700
|
||||
Ave neighs/atom = 37.8906
|
||||
Ave neighs/atom = 37.890625
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Setting up Verlet run ...
|
||||
@ -232,30 +235,30 @@ Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
61 0.78045421 -5.7781094 0 -4.6120011 0.093808941
|
||||
81 0.77743907 -5.7735004 0 -4.6118971 0.090822641
|
||||
Loop time of 0.00244325 on 2 procs for 20 steps with 256 atoms
|
||||
Loop time of 0.00351607 on 2 procs for 20 steps with 256 atoms
|
||||
|
||||
Performance: 3536279.919 tau/day, 8185.833 timesteps/s
|
||||
99.0% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
Performance: 2457288.612 tau/day, 5688.168 timesteps/s
|
||||
97.9% CPU use with 2 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0016916 | 0.0017038 | 0.001716 | 0.0 | 69.73
|
||||
Neigh | 0.00025229 | 0.00025512 | 0.00025795 | 0.0 | 10.44
|
||||
Comm | 0.00035772 | 0.00036918 | 0.00038064 | 0.0 | 15.11
|
||||
Output | 1.0858e-05 | 2.7875e-05 | 4.4891e-05 | 0.0 | 1.14
|
||||
Modify | 3.817e-05 | 3.9325e-05 | 4.048e-05 | 0.0 | 1.61
|
||||
Other | | 4.796e-05 | | | 1.96
|
||||
Pair | 0.0023896 | 0.0024147 | 0.0024397 | 0.1 | 68.67
|
||||
Neigh | 0.00037331 | 0.00040456 | 0.0004358 | 0.0 | 11.51
|
||||
Comm | 0.00050571 | 0.00051343 | 0.00052116 | 0.0 | 14.60
|
||||
Output | 2.6424e-05 | 5.6547e-05 | 8.667e-05 | 0.0 | 1.61
|
||||
Modify | 5.0287e-05 | 5.1071e-05 | 5.1856e-05 | 0.0 | 1.45
|
||||
Other | | 7.58e-05 | | | 2.16
|
||||
|
||||
Nlocal: 128 ave 128 max 128 min
|
||||
Nlocal: 128.000 ave 128 max 128 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1088.5 ave 1092 max 1085 min
|
||||
Nghost: 1088.50 ave 1092 max 1085 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 4850.5 ave 4851 max 4850 min
|
||||
Neighs: 4850.50 ave 4851 max 4850 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 9701
|
||||
Ave neighs/atom = 37.8945
|
||||
Ave neighs/atom = 37.894531
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds not checked
|
||||
Deleted 256 atoms, new total = 0
|
||||
@ -267,30 +270,30 @@ Per MPI rank memory allocation (min/avg/max) = 2.624 | 2.624 | 2.624 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
81 0.6239063 -5.5404291 0 -4.6082254 1.0394285
|
||||
91 0.75393007 -5.7375259 0 -4.6110484 0.39357367
|
||||
Loop time of 0.00118092 on 2 procs for 10 steps with 256 atoms
|
||||
Loop time of 0.0109747 on 2 procs for 10 steps with 256 atoms
|
||||
|
||||
Performance: 3658158.625 tau/day, 8467.960 timesteps/s
|
||||
98.6% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
Performance: 393631.731 tau/day, 911.185 timesteps/s
|
||||
53.5% CPU use with 2 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0008476 | 0.00089265 | 0.00093771 | 0.0 | 75.59
|
||||
Pair | 0.0012057 | 0.0012732 | 0.0013407 | 0.2 | 11.60
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00016335 | 0.00020946 | 0.00025557 | 0.0 | 17.74
|
||||
Output | 8.87e-06 | 2.5733e-05 | 4.2595e-05 | 0.0 | 2.18
|
||||
Modify | 1.8755e-05 | 1.9814e-05 | 2.0872e-05 | 0.0 | 1.68
|
||||
Other | | 3.326e-05 | | | 2.82
|
||||
Comm | 0.00018882 | 0.00025686 | 0.00032489 | 0.0 | 2.34
|
||||
Output | 2.1943e-05 | 0.0047067 | 0.0093915 | 6.8 | 42.89
|
||||
Modify | 2.4614e-05 | 2.5439e-05 | 2.6264e-05 | 0.0 | 0.23
|
||||
Other | | 0.004712 | | | 42.94
|
||||
|
||||
Nlocal: 128 ave 135 max 121 min
|
||||
Nlocal: 128.000 ave 135 max 121 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 1109 ave 1116 max 1102 min
|
||||
Nghost: 1109.00 ave 1116 max 1102 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 4852.5 ave 5106 max 4599 min
|
||||
Neighs: 4852.50 ave 5106 max 4599 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 9705
|
||||
Ave neighs/atom = 37.9102
|
||||
Ave neighs/atom = 37.910156
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds not checked
|
||||
Total wall time: 0:00:00
|
||||
|
||||
@ -87,7 +87,7 @@ int main(int narg, char **arg)
|
||||
MPI_Abort(MPI_COMM_WORLD,1);
|
||||
}
|
||||
}
|
||||
if (lammps == 1) plugin->open(0,NULL,comm_lammps,&lmp);
|
||||
if (lammps == 1) lmp = plugin->open(0,NULL,comm_lammps,NULL);
|
||||
|
||||
while (1) {
|
||||
if (me == 0) {
|
||||
@ -139,7 +139,7 @@ int main(int narg, char **arg)
|
||||
|
||||
cmds[0] = (char *)"run 10";
|
||||
cmds[1] = (char *)"run 20";
|
||||
if (lammps == 1) plugin->commands_list(lmp,2,cmds);
|
||||
if (lammps == 1) plugin->commands_list(lmp,2,(const char **)cmds);
|
||||
|
||||
/* delete all atoms
|
||||
create_atoms() to create new ones with old coords, vels
|
||||
@ -164,12 +164,13 @@ int main(int narg, char **arg)
|
||||
|
||||
if (lammps == 1) {
|
||||
plugin->close(lmp);
|
||||
MPI_Barrier(comm_lammps);
|
||||
MPI_Comm_free(&comm_lammps);
|
||||
liblammpsplugin_release(plugin);
|
||||
}
|
||||
|
||||
/* close down MPI */
|
||||
|
||||
if (lammps == 1) MPI_Comm_free(&comm_lammps);
|
||||
MPI_Barrier(MPI_COMM_WORLD);
|
||||
MPI_Finalize();
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user