(b698d94d) · Commits · 郑智淋 / lammps

README

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Original line number	Diff line number	Diff line
		This is the LAMMPS (6 Jan 2009) software package.
		This is the LAMMPS (9 Jan 2009) software package.

		LAMMPS stands for Large-scale Atomic/Molecular Massively Parallel
		Simulator.
		@@ -20,7 +20,7 @@ The primary author of the code is Steve Plimpton, who can be emailed
		at sjplimp@sandia.gov. The LAMMPS WWW Site at lammps.sandia.gov has
		more information about the code and its uses.

		The LAMMPS (6 Jan 2009) distribution includes the following files
		The LAMMPS (9 Jan 2009) distribution includes the following files
		and directories:

		README this file

doc/Section_errors.txt

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		@@ -1801,14 +1801,26 @@ The time window for pressure relaxation must be > 0 :dd

		The time window for temperature or pressure relaxation must be > 0 :dd

		{Fix npt/asphere requires atom attributes quat, angmom, torque, shape} :dt

		An atom style that specifies these quantities is needed. :dd

		{Fix npt/sphere requires atom attribute shape} :dt

		An atom style that specifies atom shape is needed. :dd

		{Fix npt/sphere requires atom attributes omega, torque} :dt

		An atom style that specifies these quantities is needed. :dd

		{Fix npt/sphere requires spherical particle shapes} :dt

		Self-explanatory. :dd

		{Fix nve/asphere requires atom attributes quat, angmom, torque, shape} :dt

		An atom style that specifies these quantities is needed. :dd

		{Fix nve/sphere requires atom attribute mu} :dt

		An atom style with this attribute is needed. :dd
		@@ -1833,6 +1845,10 @@ Self-explanatory. :dd

		The time window for temperature relaxation must be > 0 :dd

		{Fix nvt/asphere requires atom attributes quat, angmom, torque, shape} :dt

		An atom style that specifies these quantities is needed. :dd

		{Fix nvt/sphere requires atom attribute shape} :dt

		An atom style with this attribute is needed. :dd
		@@ -3115,6 +3131,10 @@ Style in pair coeff must have been listed in pair_style command. :dd
		One or more pairwise cutoffs are too short to use with the specified
		rRESPA cutoffs. :dd

		{Pair dipole/cut requires atom attributes q, mu, torque, dipole} :dt

		An atom style that specifies these quantities is needed. :dd

		{Pair distance < table inner cutoff} :dt

		Two atoms are closer together than the pairwise table allows. :dd
		@@ -4039,6 +4059,24 @@ restriction. :dd
		Other fixes may change the position of the center-of-mass, so
		fix recenter should come last. :dd

		{Fix thermal/conductivity comes before fix ave/spatial} :dt

		The order of these 2 fixes in your input script is such that fix
		thermal/conductivity comes first. If you are using fix ave/spatial to
		measure the temperature profile induced by fix viscosity, then this
		may cause a glitch in the profile since you are averaging immediately
		after swaps have occurred. Flipping the order of the 2 fixes
		typically helps. :dd

		{Fix viscosity comes before fix ave/spatial} :dt

		The order of these 2 fixes in your input script is such that
		fix viscosity comes first. If you are using fix ave/spatial
		to measure the velocity profile induced by fix viscosity, then
		this may cause a glitch in the profile since you are averaging
		immediately after swaps have occurred. Flipping the order
		of the 2 fixes typically helps. :dd

		{Group for fix_modify temp != fix group} :dt

		The fix_modify command is specifying a temperature computation that

src/fix_npt_sphere.cpp

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		@@ -36,7 +36,7 @@ FixNPTSphere::FixNPTSphere(LAMMPS lmp, int narg, char *arg) :
		FixNPT(lmp, narg, arg)
		{
		if (!atom->omega_flag \|\| !atom->torque_flag)
		error->all("Fix nvt/sphere requires atom attributes omega, torque");
		error->all("Fix npt/sphere requires atom attributes omega, torque");

		dttype = new double[atom->ntypes+1];
		}

src/fix_thermal_conductivity.cpp

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		@@ -19,6 +19,7 @@
		#include "atom.h"
		#include "force.h"
		#include "domain.h"
		#include "modify.h"
		#include "error.h"

		using namespace LAMMPS_NS;
		@@ -103,6 +104,16 @@ int FixThermalConductivity::setmask()

		void FixThermalConductivity::init()
		{
		// warn if any fix ave/spatial comes after this fix
		// can cause glitch in averaging since ave will happen after swap

		int foundme = 0;
		for (int i = 0; i < modify->nfix; i++) {
		if (modify->fix[i] == this) foundme = 1;
		if (foundme && strcmp(modify->fix[i]->style,"ave/spatial") == 0 && me == 0)
		error->warning("Fix thermal/conductivity comes before fix ave/spatial");
		}

		// set bounds of 2 slabs in edim
		// only necessary for static box, else re-computed in end_of_step()
		// lo bin is always bottom bin

src/fix_viscosity.cpp

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		@@ -18,6 +18,7 @@
		#include "fix_viscosity.h"
		#include "atom.h"
		#include "domain.h"
		#include "modify.h"
		#include "error.h"

		using namespace LAMMPS_NS;
		@@ -113,6 +114,16 @@ int FixViscosity::setmask()

		void FixViscosity::init()
		{
		// warn if any fix ave/spatial comes after this fix
		// can cause glitch in averaging since ave will happen after swap

		int foundme = 0;
		for (int i = 0; i < modify->nfix; i++) {
		if (modify->fix[i] == this) foundme = 1;
		if (foundme && strcmp(modify->fix[i]->style,"ave/spatial") == 0 && me == 0)
		error->warning("Fix viscosity comes before fix ave/spatial");
		}

		// set bounds of 2 slabs in pdim
		// only necessary for static box, else re-computed in end_of_step()
		// lo bin is always bottom bin

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