Merge branch 'collected-small-changes' into progguide (9a36fac3) · Commits · 郑智淋 / lammps

.github/codecov.yml

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+29 −0

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		comment: false
		coverage:
		notify:
		slack:
		default:
		url: "secret:HWZbvgtc6OD7F3v3PfrK3/rzCJvScbh69Fi1CkLwuHK0+wIBIHVR+Q5i7q6F9Ln4OChbiRGtYAEUUsT8/jmBu4qDpIi8mx746codc0z/Z3aafLd24pBrCEPLvdCfIZxqPnw3TuUgGhwmMDZf0+thg8YNUr/MbOZ7Li2L6+ZbYuA="
		threshold: 10%
		only_pulls: false
		branches:
		- "master"
		flags:
		- "unit"
		paths:
		- "src"
		status:
		project:
		default:
		branches:
		- "master"
		paths:
		- "src"
		informational: true
		patch:
		default:
		branches:
		- "master"
		paths:
		- "src"
		informational: true

doc/src/Errors_warnings.rst

+18 −0

Original line number	Diff line number	Diff line
		@@ -118,6 +118,24 @@ Doc page with :doc:`ERROR messages <Errors_messages>`
		incorrect periodic images of atoms in interaction lists. To avoid, either use
		:doc:`pair style zero <pair_zero>` with a suitable cutoff or use :doc:`comm_modify cutoff <comm_modify>`.

		Communication cutoff is shorter than a bond length based estimate. This may lead to errors.

		Since LAMMPS stores topology data with individual atoms, all atoms
		comprising a bond, angle, dihedral or improper must be present on any
		sub-domain that "owns" the atom with the information, either as a
		local or a ghost atom. The communication cutoff is what determines up
		to what distance from a sub-domain boundary ghost atoms are created.
		The communication cutoff is by default the largest non-bonded cutoff
		plus the neighbor skin distance, but for short or non-bonded cutoffs
		and/or long bonds, this may not be sufficient. This warning indicates
		that there is an increased risk of a simulation stopping unexpectedly
		because of Bond/Angle/Dihedral/Improper atoms missing. It can be
		silenced by manually setting the communication cutoff via
		:doc:`comm_modify cutoff <comm_modify>`. However, since the
		heuristic used to determine the estimate is not always accurate, it
		is not changed automatically and the warning may be ignored depending
		on the specific system being simulated.

		Communication cutoff is too small for SNAP micro load balancing, increased to %lf
		Self-explanatory.

src/USER-MISC/pair_lennard_mdf.cpp

+38 −14

Original line number	Diff line number	Diff line
		@@ -32,11 +32,11 @@ using namespace LAMMPS_NS;

		/* ---------------------------------------------------------------------- */

		PairLJ_AB_MDF::PairLJ_AB_MDF(LAMMPS *lmp) : Pair(lmp) {}
		PairLennardMDF::PairLennardMDF(LAMMPS *lmp) : Pair(lmp) {}

		/* ---------------------------------------------------------------------- */

		PairLJ_AB_MDF::~PairLJ_AB_MDF()
		PairLennardMDF::~PairLennardMDF()
		{
		if (allocated) {
		memory->destroy(setflag);
		@@ -56,7 +56,7 @@ PairLJ_AB_MDF::~PairLJ_AB_MDF()

		/* ---------------------------------------------------------------------- */

		void PairLJ_AB_MDF::compute(int eflag, int vflag)
		void PairLennardMDF::compute(int eflag, int vflag)
		{
		int i,j,ii,jj,inum,jnum,itype,jtype;
		double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
		@@ -153,7 +153,7 @@ void PairLJ_AB_MDF::compute(int eflag, int vflag)
		allocate all arrays
		------------------------------------------------------------------------- */

		void PairLJ_AB_MDF::allocate()
		void PairLennardMDF::allocate()
		{
		allocated = 1;
		int n = atom->ntypes;
		@@ -180,7 +180,7 @@ void PairLJ_AB_MDF::allocate()
		global settings
		------------------------------------------------------------------------- */

		void PairLJ_AB_MDF::settings(int narg, char **arg)
		void PairLennardMDF::settings(int narg, char **arg)
		{
		if (narg != 2) error->all(FLERR,"Illegal pair_style command");

		@@ -207,7 +207,7 @@ void PairLJ_AB_MDF::settings(int narg, char **arg)
		set coeffs for one or more type pairs
		------------------------------------------------------------------------- */

		void PairLJ_AB_MDF::coeff(int narg, char **arg)
		void PairLennardMDF::coeff(int narg, char **arg)
		{
		if (narg != 4 && narg != 6)
		error->all(FLERR,"Incorrect args for pair coefficients");
		@@ -248,7 +248,7 @@ void PairLJ_AB_MDF::coeff(int narg, char **arg)
		init for one type pair i,j and corresponding j,i
		------------------------------------------------------------------------- */

		double PairLJ_AB_MDF::init_one(int i, int j)
		double PairLennardMDF::init_one(int i, int j)
		{
		if (setflag[i][j] == 0) error->all(FLERR,"All pair coeffs are not set");

		@@ -259,6 +259,7 @@ double PairLJ_AB_MDF::init_one(int i, int j)
		lj3[i][j] = aparm[i][j];
		lj4[i][j] = bparm[i][j];

		cut[j][i] = cut[i][j];
		cut_inner[j][i] = cut_inner[i][j];
		cut_inner_sq[j][i] = cut_inner_sq[i][j];
		lj1[j][i] = lj1[i][j];
		@@ -273,7 +274,7 @@ double PairLJ_AB_MDF::init_one(int i, int j)
		proc 0 writes to restart file
		------------------------------------------------------------------------- */

		void PairLJ_AB_MDF::write_restart(FILE *fp)
		void PairLennardMDF::write_restart(FILE *fp)
		{
		write_restart_settings(fp);

		@@ -294,7 +295,7 @@ void PairLJ_AB_MDF::write_restart(FILE *fp)
		proc 0 reads from restart file, bcasts
		------------------------------------------------------------------------- */

		void PairLJ_AB_MDF::read_restart(FILE *fp)
		void PairLennardMDF::read_restart(FILE *fp)
		{
		read_restart_settings(fp);
		allocate();
		@@ -324,7 +325,7 @@ void PairLJ_AB_MDF::read_restart(FILE *fp)
		proc 0 writes to restart file
		------------------------------------------------------------------------- */

		void PairLJ_AB_MDF::write_restart_settings(FILE *fp)
		void PairLennardMDF::write_restart_settings(FILE *fp)
		{
		fwrite(&mix_flag,sizeof(int),1,fp);
		}
		@@ -333,7 +334,7 @@ void PairLJ_AB_MDF::write_restart_settings(FILE *fp)
		proc 0 reads from restart file, bcasts
		------------------------------------------------------------------------- */

		void PairLJ_AB_MDF::read_restart_settings(FILE *fp)
		void PairLennardMDF::read_restart_settings(FILE *fp)
		{
		int me = comm->me;
		if (me == 0) {
		@@ -342,9 +343,32 @@ void PairLJ_AB_MDF::read_restart_settings(FILE *fp)
		MPI_Bcast(&mix_flag,1,MPI_INT,0,world);
		}

		/* ----------------------------------------------------------------------
		proc 0 writes to data file
		------------------------------------------------------------------------- */

		void PairLennardMDF::write_data(FILE *fp)
		{
		for (int i = 1; i <= atom->ntypes; i++)
		fprintf(fp,"%d %g %g\n",i,aparm[i][i],bparm[i][i]);
		}

		/* ----------------------------------------------------------------------
		proc 0 writes all pairs to data file
		------------------------------------------------------------------------- */

		void PairLennardMDF::write_data_all(FILE *fp)
		{
		for (int i = 1; i <= atom->ntypes; i++)
		for (int j = i; j <= atom->ntypes; j++)
		fprintf(fp,"%d %d %g %g %g %g\n",
		i,j,aparm[i][j],bparm[i][j],
		cut_inner[i][j],cut[i][j]);
		}

		/* ---------------------------------------------------------------------- */

		double PairLJ_AB_MDF::single(int /i/, int /j/, int itype, int jtype,
		double PairLennardMDF::single(int /i/, int /j/, int itype, int jtype,
		double rsq,
		double /factor_coul/, double factor_lj,
		double &fforce)
		@@ -368,7 +392,7 @@ double PairLJ_AB_MDF::single(int /i/, int /j/, int itype, int jtype,
		dt = 30.* dd dddd rr / dp;

		forcelj = forceljtt + philjdt;
		philj *= dt;
		philj *= tt;
		}

		fforce = factor_ljforceljr2inv;
		@@ -378,7 +402,7 @@ double PairLJ_AB_MDF::single(int /i/, int /j/, int itype, int jtype,

		/* ---------------------------------------------------------------------- */

		void PairLJ_AB_MDF::extract(const char str, int &dim)
		void PairLennardMDF::extract(const char str, int &dim)
		{
		dim = 2;
		if (strcmp(str,"a") == 0) return (void *) aparm;

src/USER-MISC/pair_lennard_mdf.h

+8 −6

Original line number	Diff line number	Diff line
		@@ -13,21 +13,21 @@

		#ifdef PAIR_CLASS

		PairStyle(lennard/mdf,PairLJ_AB_MDF)
		PairStyle(lennard/mdf,PairLennardMDF)

		#else

		#ifndef LMP_PAIR_LJ_AB_MDF_H
		#define LMP_PAIR_LJ_AB_MDF_H
		#ifndef LMP_PAIR_LENNARD_MDF_H
		#define LMP_PAIR_LENNARD_MDF_H

		#include "pair.h"

		namespace LAMMPS_NS {

		class PairLJ_AB_MDF : public Pair {
		class PairLennardMDF : public Pair {
		public:
		PairLJ_AB_MDF(class LAMMPS *);
		virtual ~PairLJ_AB_MDF();
		PairLennardMDF(class LAMMPS *);
		virtual ~PairLennardMDF();

		virtual void compute(int, int);
		void settings(int, char **);
		@@ -37,6 +37,8 @@ class PairLJ_AB_MDF : public Pair {
		void read_restart(FILE *);
		void write_restart_settings(FILE *);
		void read_restart_settings(FILE *);
		void write_data(FILE *);
		void write_data_all(FILE *);
		double single(int, int, int, int, double, double, double, double &);
		void extract(const char , int &);

src/USER-OMP/reaxc_init_md_omp.cpp

+48 −63

Original line number	Diff line number	Diff line
		@@ -36,6 +36,7 @@
		#include "reaxc_lookup.h"
		#include "reaxc_tool_box.h"
		#include "error.h"
		#include "fmt/format.h"

		// Functions defined in reaxc_init_md.cpp
		extern int Init_MPI_Datatypes(reax_system, storage, mpi_datatypes, MPI_Comm, char);
		@@ -55,6 +56,7 @@ int Init_ListsOMP(reax_system system, control_params control,
		int mincap = system->mincap;
		double safezone = system->safezone;
		double saferzone = system->saferzone;
		LAMMPS_NS::Error *error = system->error_ptr;

		bond_top = (int*) calloc(system->total_cap, sizeof(int));
		hb_top = (int*) calloc(system->local_cap, sizeof(int));
		@@ -72,7 +74,7 @@ int Init_ListsOMP(reax_system system, control_params control,

		if(!Make_List(system->Hcap, total_hbonds, TYP_HBOND,
		*lists+HBONDS)) {
		system->error_ptr->one( FLERR, "Not enough space for hbonds list. Terminating!" );
		error->one(FLERR, "Not enough space for hbonds list. Terminating!");
		}
		}

		@@ -85,7 +87,7 @@ int Init_ListsOMP(reax_system system, control_params control,

		if(!Make_List(system->total_cap, bond_cap, TYP_BOND,
		*lists+BONDS)) {
		system->error_ptr->one( FLERR, "Not enough space for bonds list. Terminating!\n" );
		error->one(FLERR, "Not enough space for bonds list. Terminating!\n");
		}

		int nthreads = control->nthreads;
		@@ -93,14 +95,14 @@ int Init_ListsOMP(reax_system system, control_params control,

		for (i = 0; i < bonds->num_intrs; ++i)
		bonds->select.bond_list[i].bo_data.CdboReduction =
		(double) smalloc(system->error_ptr, sizeof(double)nthreads, "CdboReduction");
		(double) smalloc(error, sizeof(double)nthreads, "CdboReduction");

		/* 3bodies list */
		cap_3body = (int)(MAX(num_3body*safezone, MIN_3BODIES));
		if(!Make_List(bond_cap, cap_3body, TYP_THREE_BODY,
		*lists+THREE_BODIES)){

		system->error_ptr->one( FLERR, "Problem in initializing angles list. Terminating!" );
		error->one(FLERR, "Problem in initializing angles list. Terminating!");
		}

		free(hb_top);
		@@ -118,53 +120,36 @@ void InitializeOMP( reax_system system, control_params control,
		mpi_datatypes *mpi_data, MPI_Comm comm)
		{
		char msg[MAX_STR];
		char errmsg[512];
		LAMMPS_NS::Error *error = system->error_ptr;

		if (Init_MPI_Datatypes(system,workspace,mpi_data,comm,msg) == FAILURE)
		error->one(FLERR,"init_mpi_datatypes: could not create datatypes. "
		"Mpi_data could not be initialized! Terminating.");

		if (Init_MPI_Datatypes(system, workspace, mpi_data, comm, msg) == FAILURE) {
		system->error_ptr->one( FLERR, "init_mpi_datatypes: could not create datatypes. "
		"Mpi_data couldn't be initialized! Terminating.");
		}

		if (Init_System(system, control, msg) == FAILURE) {
		snprintf( errmsg, 512, "Error on: %s. "
		"System could not be initialized! Terminating.", msg );
		system->error_ptr->one(FLERR, errmsg);
		}

		if (Init_Simulation_Data( system, control, data, msg ) == FAILURE) {
		snprintf( errmsg, 512, "Error on: %s. "
		"Sim_data couldn't be initialized! Terminating.", msg );
		system->error_ptr->one(FLERR, errmsg);
		}
		if (Init_System(system,control,msg) == FAILURE)
		error->one(FLERR,fmt::format("Error on: {}. System could not be "
		"initialized! Terminating.",msg));

		if (Init_Workspace( system, control, workspace, msg ) ==
		FAILURE) {
		system->error_ptr->one(FLERR, "init_workspace: not enough memory. "
		"Workspace couldn't be initialized! Terminating.");
		}
		if (Init_Simulation_Data(system,control,data,msg) == FAILURE)
		error->one(FLERR,fmt::format("Error on: {}. Sim_data could not be "
		"initialized! Terminating.",msg));

		if (Init_ListsOMP( system, control, data, workspace, lists, mpi_data, msg ) ==
		FAILURE) {
		snprintf( errmsg, 512, "Error on: %s. "
		"System could not be initialized! Terminating.", msg );
		system->error_ptr->one(FLERR, errmsg);
		}
		if (Init_Workspace(system,control,workspace,msg) == FAILURE)
		error->one(FLERR,"init_workspace: not enough memory. "
		"Workspace could not be initialized. Terminating.");

		if (Init_Output_Files(system,control,out_control,mpi_data,msg)== FAILURE) {
		snprintf( errmsg, 512, "Error on: %s"
		"Could not open output files! Terminating.", msg );
		system->error_ptr->one(FLERR, errmsg);
		}
		if (Init_ListsOMP(system,control,data,workspace,lists,mpi_data,msg) == FAILURE)
		error->one(FLERR,fmt::format("Error on: {}. System could not be "
		"initialized. Terminating.",msg));

		if (control->tabulate) {
		if (Init_Lookup_Tables( system, control, workspace, mpi_data, msg ) == FAILURE) {
		snprintf( errmsg, 512, "Error on: %s."
		" Couldn't create lookup table! Terminating.", msg );
		system->error_ptr->one(FLERR, errmsg);
		}
		}
		if (Init_Output_Files(system,control,out_control,mpi_data,msg)== FAILURE)
		error->one(FLERR,fmt::format("Error on: {}. Could not open output files! "
		"Terminating.",msg));

		if (control->tabulate)
		if (Init_Lookup_Tables(system,control,workspace,mpi_data,msg) == FAILURE)
		error->one(FLERR,fmt::format("Error on: {}. Could not create lookup "
		"table. Terminating.",msg));

		Init_Force_FunctionsOMP(control);
		}

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