Merge branch 'collected-small-changes' into collected-post-stable-patches (980f7e3b) · Commits · 郑智淋 / lammps

doc/src/fix_nh.txt

+3 −3

Original line number	Diff line number	Diff line
		@@ -626,10 +626,10 @@ over time or the atom count becomes very small.

		[Default:]

		The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop =
		The keyword defaults are tchain = 3, pchain = 3, mtk = yes, tloop = 1,
		ploop = 1, nreset = 0, drag = 0.0, dilate = all, couple = none,
		scaleyz = scalexz = scalexy = yes if periodic in 2nd dimension and
		not coupled to barostat, otherwise no.
		flip = yes, scaleyz = scalexz = scalexy = yes if periodic in 2nd
		dimension and not coupled to barostat, otherwise no.

		:line

doc/src/region.txt

+9 −4

Original line number	Diff line number	Diff line
		@@ -26,7 +26,7 @@ style = {delete} or {block} or {cone} or {cylinder} or {plane} or {prism} or {sp
		dim = {x} or {y} or {z} = axis of cylinder
		c1,c2 = coords of cylinder axis in other 2 dimensions (distance units)
		radius = cylinder radius (distance units)
		radius can be a variable (see below)
		c1,c2, and radius can be a variable (see below)
		lo,hi = bounds of cylinder in dim (distance units)
		{plane} args = px py pz nx ny nz
		px,py,pz = point on the plane (distance units)
		@@ -39,7 +39,7 @@ style = {delete} or {block} or {cone} or {cylinder} or {plane} or {prism} or {sp
		{sphere} args = x y z radius
		x,y,z = center of sphere (distance units)
		radius = radius of sphere (distance units)
		radius can be a variable (see below)
		x,y,z, and radius can be a variable (see below)
		{union} args = N reg-ID1 reg-ID2 ...
		N = # of regions to follow, must be 2 or greater
		reg-ID1,reg-ID2, ... = IDs of regions to join together
		@@ -179,12 +179,17 @@ The {radius} value for style {sphere} and {cylinder} can be specified
		as an equal-style "variable"_variable.html. If the value is a
		variable, it should be specified as v_name, where name is the variable
		name. In this case, the variable will be evaluated each timestep, and
		its value used to determine the radius of the region.
		its value used to determine the radius of the region. For style {sphere}
		also the x-, y-, and z- coordinate of the center of the sphere and for
		style {cylinder} the two center positions c1 and c2 for the location of
		the cylinder axes can be a variable with the same kind of effect and
		requirements than for the radius.

		Equal-style variables can specify formulas with various mathematical
		functions, and include "thermo_style"_thermo_style.html command
		keywords for the simulation box parameters and timestep and elapsed
		time. Thus it is easy to specify a time-dependent radius.
		time. Thus it is easy to specify a time-dependent radius or have
		a time dependent position of the sphere or cylinder region.

		See the "Howto tricilinc"_Howto_triclinic.html doc page for a
		geometric description of triclinic boxes, as defined by LAMMPS, and

src/info.cpp

+79 −38

Original line number	Diff line number	Diff line
		@@ -262,11 +262,20 @@ void Info::command(int narg, char **arg)
		if (flags & CONFIG) {
		fprintf(out,"\nLAMMPS version: %s / %s\n\n",
		universe->version, universe->num_ver);

		char *infobuf = get_os_info();
		fprintf(out,"OS information: %s\n\n",infobuf);
		delete[] infobuf;

		fprintf(out,"sizeof(smallint): %3d-bit\n",(int)sizeof(smallint)*8);
		fprintf(out,"sizeof(imageint): %3d-bit\n",(int)sizeof(imageint)*8);
		fprintf(out,"sizeof(tagint): %3d-bit\n",(int)sizeof(tagint)*8);
		fprintf(out,"sizeof(bigint): %3d-bit\n",(int)sizeof(bigint)*8);

		infobuf = get_compiler_info();
		fprintf(out,"\nCompiler: %s\n",infobuf);
		delete[] infobuf;

		fputs("\nActive compile time flags:\n\n",out);
		if (has_gzip_support()) fputs("-DLAMMPS_GZIP\n",out);
		if (has_png_support()) fputs("-DLAMMPS_PNG\n",out);
		@@ -274,6 +283,14 @@ void Info::command(int narg, char **arg)
		if (has_ffmpeg_support()) fputs("-DLAMMPS_FFMPEG\n",out);
		if (has_exceptions()) fputs("-DLAMMPS_EXCEPTIONS\n",out);

		#if defined(LAMMPS_BIGBIG)
		fputs("-DLAMMPS_BIGBIG\n",out);
		#elif defined(LAMMPS_SMALLBIG)
		fputs("-DLAMMPS_SMALLBIG\n",out);
		#else // defined(LAMMPS_SMALLSMALL)
		fputs("-DLAMMPS_SMALLSMALL\n",out);
		#endif

		const char *pkg;
		int ncword, ncline = 0;

		@@ -288,44 +305,6 @@ void Info::command(int narg, char **arg)
		ncline += ncword + 1;
		}
		fputs("\n",out);

		#if defined(_WIN32)
		DWORD fullversion,majorv,minorv,buildv=0;

		fullversion = GetVersion();
		majorv = (DWORD) (LOBYTE(LOWORD(fullversion)));
		minorv = (DWORD) (HIBYTE(LOWORD(fullversion)));
		if (fullversion < 0x80000000)
		buildv = (DWORD) (HIWORD(fullversion));

		SYSTEM_INFO si;
		GetSystemInfo(&si);

		const char *machine;
		switch (si.wProcessorArchitecture) {
		case PROCESSOR_ARCHITECTURE_AMD64:
		machine = (const char *) "x86_64";
		break;
		case PROCESSOR_ARCHITECTURE_ARM:
		machine = (const char *) "arm";
		break;
		case PROCESSOR_ARCHITECTURE_IA64:
		machine = (const char *) "ia64";
		break;
		case PROCESSOR_ARCHITECTURE_INTEL:
		machine = (const char *) "i386";
		break;
		default:
		machine = (const char *) "(unknown)";
		}
		fprintf(out,"\nOS information: Windows %d.%d (%d) on %s\n",
		majorv,minorv,buildv,machine);
		#else
		struct utsname ut;
		uname(&ut);
		fprintf(out,"\nOS information: %s %s on %s\n",
		ut.sysname, ut.release, ut.machine);
		#endif
		}

		if (flags & MEMORY) {
		@@ -1103,6 +1082,68 @@ bool Info::has_package(const char * package_name) {
		return false;
		}

		/* ---------------------------------------------------------------------- */
		#define _INFOBUF_SIZE 256

		char *Info::get_os_info()
		{
		char *buf = new char[_INFOBUF_SIZE];

		#if defined(_WIN32)
		DWORD fullversion,majorv,minorv,buildv=0;

		fullversion = GetVersion();
		majorv = (DWORD) (LOBYTE(LOWORD(fullversion)));
		minorv = (DWORD) (HIBYTE(LOWORD(fullversion)));
		if (fullversion < 0x80000000)
		buildv = (DWORD) (HIWORD(fullversion));

		SYSTEM_INFO si;
		GetSystemInfo(&si);

		const char *machine;
		switch (si.wProcessorArchitecture) {
		case PROCESSOR_ARCHITECTURE_AMD64:
		machine = (const char *) "x86_64";
		break;
		case PROCESSOR_ARCHITECTURE_ARM:
		machine = (const char *) "arm";
		break;
		case PROCESSOR_ARCHITECTURE_IA64:
		machine = (const char *) "ia64";
		break;
		case PROCESSOR_ARCHITECTURE_INTEL:
		machine = (const char *) "i386";
		break;
		default:
		machine = (const char *) "(unknown)";
		}
		snprintf(buf,_INFOBUF_SIZE,"Windows %d.%d (%d) on %s",
		majorv,minorv,buildv,machine);
		#else
		struct utsname ut;
		uname(&ut);
		snprintf(buf,_INFOBUF_SIZE,"%s %s on %s",
		ut.sysname, ut.release, ut.machine);
		#endif
		return buf;
		}

		char *Info::get_compiler_info()
		{
		char *buf = new char[_INFOBUF_SIZE];
		#if __clang__
		snprintf(buf,_INFOBUF_SIZE,"Clang C++ %s", __VERSION__);
		#elif __INTEL_COMPILER
		snprintf(buf,_INFOBUF_SIZE,"Intel C++ %s", __VERSION__);
		#elif __GNUC__
		snprintf(buf,_INFOBUF_SIZE,"GNU C++ %s", __VERSION__);
		#else
		snprintf(buf,_INFOBUF_SIZE,"(Unknown)");
		#endif
		return buf;
		}

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

		char **Info::get_variable_names(int &num) {

src/info.h

+3 −0

Original line number	Diff line number	Diff line
		@@ -40,6 +40,9 @@ class Info : protected Pointers {
		static bool has_exceptions();
		static bool has_package(const char * package_name);

		static char *get_os_info();
		static char *get_compiler_info();

		char **get_variable_names(int &num);

		private:

src/lammps.cpp

+36 −28

Original line number	Diff line number	Diff line
		@@ -415,7 +415,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
		}
		}

		if (universe->me == 0) {
		if ((universe->me == 0) && !helpflag) {
		if (screen) fprintf(screen,"LAMMPS (%s)\n",universe->version);
		if (logfile) fprintf(logfile,"LAMMPS (%s)\n",universe->version);
		}
		@@ -489,7 +489,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :

		// screen and logfile messages for universe and world

		if (universe->me == 0) {
		if ((universe->me == 0) && (!helpflag)) {
		if (universe->uscreen) {
		fprintf(universe->uscreen,"LAMMPS (%s)\n",universe->version);
		fprintf(universe->uscreen,"Running on %d partitions of processors\n",
		@@ -502,7 +502,7 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
		}
		}

		if (me == 0) {
		if ((me == 0) && (!helpflag)) {
		if (screen) {
		fprintf(screen,"LAMMPS (%s)\n",universe->version);
		fprintf(screen,"Processor partition = %d\n",universe->iworld);
		@@ -587,16 +587,15 @@ LAMMPS::LAMMPS(int narg, char **arg, MPI_Comm communicator) :
		memory->destroy(plast);
		}

		// allocate top-level classes

		create();
		post_create();

		// if helpflag set, print help and quit with "success" status
		// otherwise allocate top level classes.

		if (helpflag) {
		if (universe->me == 0 && screen) help();
		error->done(0);
		} else {
		create();
		post_create();
		}

		// if either restart conversion option was used, invoke 2 commands and quit
		@@ -762,7 +761,7 @@ void LAMMPS::post_create()
		// check that KOKKOS package classes were instantiated
		// check that GPU, INTEL, USER-OMP fixes were compiled with LAMMPS

		if (!suffix_enable) return;
		if (suffix_enable) {

		if (strcmp(suffix,"gpu") == 0 && !modify->check_package("GPU"))
		error->all(FLERR,"Using suffix gpu without GPU package installed");
		@@ -783,6 +782,7 @@ void LAMMPS::post_create()
		if (strcmp(suffix2,"intel") == 0) input->one("package intel 1");
		if (strcmp(suffix2,"omp") == 0) input->one("package omp 0");
		}
		}

		// invoke any command-line package commands

		@@ -1082,6 +1082,14 @@ void LAMMPS::print_config(FILE *fp)
		const char *pkg;
		int ncword, ncline = 0;

		char *infobuf = Info::get_os_info();
		fprintf(fp,"OS: %s\n\n",infobuf);
		delete[] infobuf;

		infobuf = Info::get_compiler_info();
		fprintf(fp,"Compiler: %s\n\n",infobuf);
		delete[] infobuf;

		fputs("Active compile time flags:\n\n",fp);
		if (Info::has_gzip_support()) fputs("-DLAMMPS_GZIP\n",fp);
		if (Info::has_png_support()) fputs("-DLAMMPS_PNG\n",fp);

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