Merge pull request #2227 from akohlmey/collected-small-fixes (284b1618) · Commits · 郑智淋 / lammps

doc/utils/check-styles.py

+7 −4

Original line number	Diff line number	Diff line
		@@ -52,6 +52,7 @@ minimize = {}
		pair = {}
		reader = {}
		region = {}
		total = 0

		upper = re.compile("[A-Z]+")
		gpu = re.compile("(.+)/gpu$")
		@@ -60,7 +61,7 @@ kokkos = re.compile("(.+)/kk$")
		kokkos_skip = re.compile("(.+)/kk/(host\|device)$")
		omp = re.compile("(.+)/omp$")
		opt = re.compile("(.+)/opt$")
		removed = re.compile("(.+)Deprecated$")
		removed = re.compile("(.*)Deprecated$")

		def register_style(list,style,info):
		if style in list.keys():
		@@ -119,6 +120,7 @@ for h in headers:

		# skip over internal styles w/o explicit documentation
		style = m[1]
		total += 1
		if upper.match(style):
		continue

		@@ -197,12 +199,13 @@ print("""Parsed style names w/o suffixes from C++ tree in %s:
		Fix styles: %3d Improper styles: %3d
		Integrate styles: %3d Kspace styles: %3d
		Minimize styles: %3d Pair styles: %3d
		Reader styles: %3d Region styles: %3d""" \
		Reader styles: %3d Region styles: %3d
		----------------------------------------------------
		Total number of styles (including suffixes): %d""" \
		% (src, len(angle), len(atom), len(body), len(bond), \
		len(command), len(compute), len(dihedral), len(dump), \
		len(fix), len(improper), len(integrate), len(kspace), \
		len(minimize), len(pair), len(reader), len(region)))

		len(minimize), len(pair), len(reader), len(region), total))

		counter = 0

0 → 120000

+1 −0

Original line number	Diff line number	Diff line
		../../potentials/CdTeZnSeHgS0.sw
		No newline at end of file

+6 −0

Original line number	Diff line number	Diff line
		@@ -204,6 +204,12 @@ class lammps(object):
		self.lib.lammps_neighlist_element_neighbors.argtypes = [c_void_p, c_int, c_int, POINTER(c_int), POINTER(c_int), POINTER(POINTER(c_int))]
		self.lib.lammps_neighlist_element_neighbors.restype = None

		self.lib.lammps_has_error.argtypes = [c_void_p]
		self.lib.lammps_has_error.restype = c_bool

		self.lib.lammps_get_last_error_message.argtypes = [c_void_p, c_char_p, c_int]
		self.lib.lammps_get_last_error_message.restype = c_int

		# if no ptr provided, create an instance of LAMMPS
		# don't know how to pass an MPI communicator from PyPar
		# but we can pass an MPI communicator from mpi4py v2.0.0 and later

+7 −0

Original line number	Diff line number	Diff line
		@@ -285,6 +285,13 @@ void PairKIM::allocate()

		void PairKIM::settings(int narg, char **arg)
		{
		// some of the code below needs to know the number of atom types,
		// but that is not set until the simulation box is created.

		if (domain->box_exist == 0)
		error->all(FLERR,"May not use 'pair_style kim' command before "
		"simulation box is defined");

		// This is called when "pair_style kim ..." is read from input
		// may be called multiple times
		++settings_call_count;

+8 −3

Original line number	Diff line number	Diff line
		@@ -139,14 +139,16 @@ void EwaldDisp::init()
		nsums += n[k];
		}

		if (!gewaldflag) g_ewald = g_ewald_6 = 1.0;
		if (!gewaldflag) g_ewald = 1.0;
		if (!gewaldflag_6) g_ewald_6 = 1.0;
		pair->init(); // so B is defined
		init_coeffs();
		init_coeff_sums();
		if (function[0]) qsum_qsq();
		else qsqsum = qsum = 0.0;
		natoms_original = atom->natoms;
		if (!gewaldflag) g_ewald = g_ewald_6 = 0.0;
		if (!gewaldflag) g_ewald = 0.0;
		if (!gewaldflag_6) g_ewald_6 = 0.0;

		// turn off coulombic if no charge

		@@ -231,7 +233,9 @@ void EwaldDisp::init()
		utils::logmesg(lmp,fmt::format(" G vector = {:.8g}, accuracy = {:.8g}\n",
		g_ewald,accuracy));

		g_ewald_6 = g_ewald;
		// apply coulomb g_ewald to dispersion unless it is explicitly set

		if (!gewaldflag_6) g_ewald_6 = g_ewald;
		deallocate_peratom();
		peratom_allocate_flag = 0;
		}
		@@ -507,6 +511,7 @@ void EwaldDisp::init_coeffs()
		if (function[2]) { // arithmetic 1/r^6
		double epsilon = (double ) force->pair->extract("epsilon",tmp);
		double sigma = (double ) force->pair->extract("sigma",tmp);
		delete [] B;
		double eps_i, sigma_i, sigma_n, bi = B = new double[7n+7];
		double c[7] = {
		1.0, sqrt(6.0), sqrt(15.0), sqrt(20.0), sqrt(15.0), sqrt(6.0), 1.0};