Merge branch 'master' into resetids (a19e8fb2) · Commits · 郑智淋 / lammps

doc/src/compute_displace_atom.txt

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		@@ -15,8 +15,9 @@ compute ID group-ID displace/atom :pre
		ID, group-ID are documented in "compute"_compute.html command :ulb,l
		displace/atom = style name of this compute command :l
		zero or more keyword/arg pairs may be appended :l
		keyword = {refresh} :l
		{replace} arg = per-atom variable ID :pre
		keyword = {refresh} :
		{replace} arg = name of per-atom variable :pre

		:ule

		[Examples:]

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		@@ -121,7 +121,7 @@ See the "dump_modify every"_dump_modify.html command.

		Only information for atoms in the specified group is dumped. The
		"dump_modify thresh and region and refresh"_dump_modify.html commands
		can also alter what atoms are included. Not all styles support all
		can also alter what atoms are included. Not all styles support
		these options; see details on the "dump_modify"_dump_modify.html doc
		page.

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		# Solvated 5-mer peptide
		# Demonstrating temper_npt
		units real
		atom_style full

		pair_style lj/charmm/coul/long 8.0 10.0 10.0
		bond_style harmonic
		angle_style charmm
		dihedral_style charmm
		improper_style harmonic
		kspace_style pppm 0.0001

		read_data data.peptide

		neighbor 2.0 bin
		neigh_modify delay 5

		timestep 2.0

		thermo_style custom step temp epair emol etotal press density
		thermo 50

		variable temper_T world 275 280 285 290 295 300 305 310
		variable rep world 0 1 2 3 4 5 6 7
		fix myfix all npt temp ${temper_T} ${temper_T} 100.0 iso 1 1 1000
		run 500
		temper_npt 2000 100 ${temper_T} myfix 0 58728 1
		fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
		group peptide type <= 12

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		@@ -264,12 +264,21 @@ void FixSRP::setup_pre_force(int zz)
		rmax = sqrt(rsqmax);
		double cutneighmax_srp = neighbor->cutneighmax + 0.51*rmax;

		// find smallest cutghost
		double cutghostmin = comm->cutghost[0];
		if (cutghostmin > comm->cutghost[1])
		cutghostmin = comm->cutghost[1];
		if (cutghostmin > comm->cutghost[2])
		cutghostmin = comm->cutghost[2];
		double length0,length1,length2;
		if (domain->triclinic) {
		double *h_inv = domain->h_inv;
		length0 = sqrt(h_inv[0]h_inv[0] + h_inv[5]h_inv[5] + h_inv[4]*h_inv[4]);
		length1 = sqrt(h_inv[1]h_inv[1] + h_inv[3]h_inv[3]);
		length2 = h_inv[2];
		} else length0 = length1 = length2 = 1.0;

		// find smallest cutghost.
		// comm->cutghost is stored in fractional coordinates for triclinic
		double cutghostmin = comm->cutghost[0]/length0;
		if (cutghostmin > comm->cutghost[1]/length1)
		cutghostmin = comm->cutghost[1]/length1;
		if (cutghostmin > comm->cutghost[2]/length2)
		cutghostmin = comm->cutghost[2]/length2;

		// stop if cutghost is insufficient
		if (cutneighmax_srp > cutghostmin){