Merge pull request #268 from arielzn/born_dsf (bfea3dce) · Commits · 郑智淋 / lammps

doc/src/pair_born.txt

+22 −5

Original line number	Diff line number	Diff line
		@@ -19,6 +19,8 @@ pair_style born/coul/msm/omp command :h3
		pair_style born/coul/wolf command :h3
		pair_style born/coul/wolf/gpu command :h3
		pair_style born/coul/wolf/omp command :h3
		pair_style born/coul/dsf command :h3
		pair_style born/coul/dsf/cs command :h3

		[Syntax:]

		@@ -37,7 +39,11 @@ args = list of arguments for a particular style :ul
		{born/coul/wolf} args = alpha cutoff (cutoff2)
		alpha = damping parameter (inverse distance units)
		cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
		cutoff2 = global cutoff for Coulombic (optional) (distance units) :pre
		cutoff2 = global cutoff for Coulombic (optional) (distance units)
		{born/coul/dsf} or {born/coul/dsf/cs} args = alpha cutoff (cutoff2)
		alpha = damping parameter (inverse distance units)
		cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
		cutoff2 = global cutoff for Coulombic (distance units) :pre

		[Examples:]

		@@ -62,6 +68,11 @@ pair_style born/coul/wolf 0.25 10.0 9.0
		pair_coeff * * 6.08 0.317 2.340 24.18 11.51
		pair_coeff 1 1 6.08 0.317 2.340 24.18 11.51 :pre

		pair_style born/coul/dsf 0.1 10.0 12.0
		pair_coeff * * 0.0 1.00 0.00 0.00 0.00
		pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre


		[Description:]

		The {born} style computes the Born-Mayer-Huggins or Tosi/Fumi
		@@ -90,10 +101,15 @@ term.
		The {born/coul/wolf} style adds a Coulombic term as described for the
		Wolf potential in the "coul/wolf"_pair_coul.html pair style.

		The {born/coul/dsf} style computes the Coulomb contribution
		with the damped shifted force model as in the
		"coul/dsf"_pair_coul.html style.

		Style {born/coul/long/cs} is identical to {born/coul/long} except that
		a term is added for the "core/shell model"_Section_howto.html#howto_25
		to allow charges on core and shell particles to be separated by r =
		0.0.
		0.0. The same correction is introduced for {born/coul/dsf/cs} style
		which is identical to {born/coul/dsf}.

		Note that these potentials are related to the "Buckingham
		potential"_pair_buck.html.
		@@ -116,9 +132,10 @@ The second coefficient, rho, must be greater than zero.
		The last coefficient is optional. If not specified, the global A,C,D
		cutoff specified in the pair_style command is used.

		For {born/coul/long} and {born/coul/wolf} no Coulombic cutoff can be
		specified for an individual I,J type pair. All type pairs use the
		same global Coulombic cutoff specified in the pair_style command.
		For {born/coul/long}, {born/coul/wolf} and {born/coul/dsf} no
		Coulombic cutoff can be specified for an individual I,J type pair.
		All type pairs use the same global Coulombic cutoff specified in
		the pair_style command.

		:line

doc/src/pair_cs.txt

+20 −3

Original line number	Diff line number	Diff line
		@@ -8,19 +8,24 @@

		pair_style born/coul/long/cs command :h3
		pair_style buck/coul/long/cs command :h3
		pair_style born/coul/dsf/cs command :h3

		[Syntax:]

		pair_style style args :pre

		style = {born/coul/long/cs} or {buck/coul/long/cs}
		style = {born/coul/long/cs} or {buck/coul/long/cs} or {born/coul/dsf/cs}
		args = list of arguments for a particular style :ul
		{born/coul/long/cs} args = cutoff (cutoff2)
		cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
		cutoff2 = global cutoff for Coulombic (optional) (distance units)
		{buck/coul/long/cs} args = cutoff (cutoff2)
		cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
		cutoff2 = global cutoff for Coulombic (optional) (distance units) :pre
		cutoff2 = global cutoff for Coulombic (optional) (distance units)
		{born/coul/dsf/cs} args = alpha cutoff (cutoff2)
		alpha = damping parameter (inverse distance units)
		cutoff = global cutoff for non-Coulombic (and Coulombic if only 1 arg) (distance units)
		cutoff2 = global cutoff for Coulombic (distance units) :pre

		[Examples:]

		@@ -32,6 +37,10 @@ pair_style buck/coul/long/cs 10.0 8.0
		pair_coeff * * 100.0 1.5 200.0
		pair_coeff 1 1 100.0 1.5 200.0 9.0 :pre

		pair_style born/coul/dsf/cs 0.1 10.0 12.0
		pair_coeff * * 0.0 1.00 0.00 0.00 0.00
		pair_coeff 1 1 480.0 0.25 0.00 1.05 0.50 :pre

		[Description:]

		These pair styles are designed to be used with the adiabatic
		@@ -39,7 +48,7 @@ core/shell model of "(Mitchell and Finchham)"_#MitchellFinchham. See
		"Section 6.25"_Section_howto.html#howto_25 of the manual for an
		overview of the model as implemented in LAMMPS.

		These pair styles are identical to the "pair_style
		The styles with a {coul/long} term are identical to the "pair_style
		born/coul/long"_pair_born.html and "pair_style
		buck/coul/long"_pair_buck.html styles, except they correctly treat the
		special case where the distance between two charged core and shell
		@@ -63,6 +72,14 @@ where C is an energy-conversion constant, Qi and Qj are the charges on
		the core and shell, epsilon is the dielectric constant and r_min is the
		minimal distance.

		The pair style {born/coul/dsf/cs} is identical to the
		"pair_style born/coul/dsf"_pair_born.html style, which uses the
		the damped shifted force model as in "coul/dsf"_pair_coul.html
		to compute the Coulomb contribution. This approach does not require
		a long-range solver, thus the only correction is the addition of a
		minimal distance to avoid the possible r = 0.0 case for a
		core/shell pair.

		[Restrictions:]

		These pair styles are part of the CORESHELL package. They are only

examples/coreshell/in.coreshell.dsf

0 → 100644

+71 −0

Original line number	Diff line number	Diff line
		# Testsystem for core-shell model compared to Mitchel and Finchham
		# Hendrik Heenen, June 2014

		# ------------------------ INITIALIZATION ----------------------------

		units metal
		dimension 3
		boundary p p p
		atom_style full

		# ----------------------- ATOM DEFINITION ----------------------------

		fix csinfo all property/atom i_CSID
		read_data data.coreshell fix csinfo NULL CS-Info

		group cores type 1 2
		group shells type 3 4

		neighbor 2.0 bin
		comm_modify vel yes

		# ------------------------ FORCE FIELDS ------------------------------

		pair_style born/coul/dsf/cs 0.1 20.0 20.0 # A, rho, sigma=0, C, D
		pair_coeff * * 0.0 1.000 0.00 0.00 0.00
		pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na
		pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl
		pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl

		bond_style harmonic
		bond_coeff 1 63.014 0.0
		bond_coeff 2 25.724 0.0

		# ------------------------ Equilibration Run -------------------------------

		reset_timestep 0

		thermo 50
		thermo_style custom step etotal pe ke temp press &
		epair evdwl ecoul elong ebond fnorm fmax vol

		compute CSequ all temp/cs cores shells

		# output via chunk method

		#compute prop all property/atom i_CSID
		#compute cs_chunk all chunk/atom c_prop
		#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0
		#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector

		thermo_modify temp CSequ

		# velocity bias option

		velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ
		velocity all scale 1427 temp CSequ

		fix thermoberendsen all temp/berendsen 1427 1427 0.4
		fix nve all nve
		fix_modify thermoberendsen temp CSequ

		# 2 fmsec timestep

		timestep 0.002
		run 500

		unfix thermoberendsen

		# ------------------------ Dynamic Run -------------------------------

		run 1000

examples/coreshell/log.8Nov16.coreshell.dsf.1

0 → 100644

+185 −0

Original line number	Diff line number	Diff line
		LAMMPS (27 Oct 2016)
		# Testsystem for core-shell model compared to Mitchel and Finchham
		# Hendrik Heenen, June 2014

		# ------------------------ INITIALIZATION ----------------------------

		units metal
		dimension 3
		boundary p p p
		atom_style full

		# ----------------------- ATOM DEFINITION ----------------------------

		fix csinfo all property/atom i_CSID
		read_data data.coreshell fix csinfo NULL CS-Info
		orthogonal box = (0 0 0) to (24.096 24.096 24.096)
		1 by 1 by 1 MPI processor grid
		reading atoms ...
		432 atoms
		scanning bonds ...
		1 = max bonds/atom
		reading bonds ...
		216 bonds
		1 = max # of 1-2 neighbors
		0 = max # of 1-3 neighbors
		0 = max # of 1-4 neighbors
		1 = max # of special neighbors

		group cores type 1 2
		216 atoms in group cores
		group shells type 3 4
		216 atoms in group shells

		neighbor 2.0 bin
		comm_modify vel yes

		# ------------------------ FORCE FIELDS ------------------------------

		pair_style born/coul/dsf/cs 0.1 20.0 20.0 # A, rho, sigma=0, C, D
		pair_coeff * * 0.0 1.000 0.00 0.00 0.00
		pair_coeff 3 3 487.0 0.23768 0.00 1.05 0.50 #Na-Na
		pair_coeff 3 4 145134.0 0.23768 0.00 6.99 8.70 #Na-Cl
		pair_coeff 4 4 405774.0 0.23768 0.00 72.40 145.40 #Cl-Cl

		bond_style harmonic
		bond_coeff 1 63.014 0.0
		bond_coeff 2 25.724 0.0

		# ------------------------ Equilibration Run -------------------------------

		reset_timestep 0

		thermo 50
		thermo_style custom step etotal pe ke temp press epair evdwl ecoul elong ebond fnorm fmax vol

		compute CSequ all temp/cs cores shells

		# output via chunk method

		#compute prop all property/atom i_CSID
		#compute cs_chunk all chunk/atom c_prop
		#compute cstherm all temp/chunk cs_chunk temp internal com yes cdof 3.0
		#fix ave_chunk all ave/time 100 1 100 c_cstherm file chunk.dump mode vector

		thermo_modify temp CSequ

		# velocity bias option

		velocity all create 1427 134 dist gaussian mom yes rot no bias yes temp CSequ
		Neighbor list info ...
		1 neighbor list requests
		update every 1 steps, delay 10 steps, check yes
		max neighbors/atom: 2000, page size: 100000
		master list distance cutoff = 22
		ghost atom cutoff = 22
		binsize = 11 -> bins = 3 3 3
		velocity all scale 1427 temp CSequ

		fix thermoberendsen all temp/berendsen 1427 1427 0.4
		fix nve all nve
		fix_modify thermoberendsen temp CSequ

		# 2 fmsec timestep

		timestep 0.002
		run 500
		Memory usage per processor = 7.04355 Mbytes
		Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
		0 -635.80596 -675.46362 39.657659 1427 -21302.622 -675.46362 1.6320365 -677.09565 0 0 1.3517686e-14 2.942091e-15 13990.5
		50 -633.9898 -666.02679 32.03699 1152.7858 -4578.5681 -668.50431 37.800204 -706.30452 0 2.4775226 14.568073 4.3012389 13990.5
		100 -631.89604 -661.96148 30.065442 1081.8436 -3536.6738 -664.61798 39.18583 -703.80381 0 2.6564973 14.677968 3.9051029 13990.5
		150 -630.08723 -662.95879 32.871559 1182.816 -109.19506 -665.76772 46.247821 -712.01554 0 2.8089226 15.270039 2.9328953 13990.5
		200 -628.55895 -663.97376 35.414806 1274.3296 -1748.35 -666.58439 41.738552 -708.32294 0 2.6106349 14.148282 3.1047826 13990.5
		250 -627.28761 -661.92274 34.635123 1246.2743 -1280.4899 -664.917 43.045475 -707.96247 0 2.9942594 14.248617 2.4694705 13990.5
		300 -626.6163 -663.65651 37.040209 1332.8164 -1887.9043 -666.35215 40.84964 -707.20179 0 2.6956373 13.142643 1.9263242 13990.5
		350 -625.76781 -664.66441 38.896607 1399.6151 -1839.482 -667.47659 40.999206 -708.47579 0 2.8121749 13.601238 1.9262698 13990.5
		400 -625.02586 -661.46042 36.434568 1311.0236 -868.2031 -664.40231 43.21398 -707.61629 0 2.9418875 14.945389 2.7493413 13990.5
		450 -624.3278 -660.50844 36.180639 1301.8865 -2203.3944 -663.49896 40.008669 -703.50763 0 2.9905179 14.158866 1.7299899 13990.5
		500 -623.56254 -661.33839 37.775849 1359.2869 -810.50736 -664.11652 42.993999 -707.11052 0 2.7781274 13.68709 2.9115277 13990.5
		Loop time of 10.7162 on 1 procs for 500 steps with 432 atoms

		Performance: 8.063 ns/day, 2.977 hours/ns, 46.658 timesteps/s
		99.9% CPU use with 1 MPI tasks x no OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 10.478 \| 10.478 \| 10.478 \| 0.0 \| 97.78
		Bond \| 0.0029511 \| 0.0029511 \| 0.0029511 \| 0.0 \| 0.03
		Neigh \| 0.14159 \| 0.14159 \| 0.14159 \| 0.0 \| 1.32
		Comm \| 0.074382 \| 0.074382 \| 0.074382 \| 0.0 \| 0.69
		Output \| 0.00054097 \| 0.00054097 \| 0.00054097 \| 0.0 \| 0.01
		Modify \| 0.010588 \| 0.010588 \| 0.010588 \| 0.0 \| 0.10
		Other \| \| 0.007748 \| \| \| 0.07

		Nlocal: 432 ave 432 max 432 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Nghost: 9280 ave 9280 max 9280 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Neighs: 297636 ave 297636 max 297636 min
		Histogram: 1 0 0 0 0 0 0 0 0 0

		Total # of neighbors = 297636
		Ave neighs/atom = 688.972
		Ave special neighs/atom = 1
		Neighbor list builds = 20
		Dangerous builds = 0

		unfix thermoberendsen

		# ------------------------ Dynamic Run -------------------------------

		run 1000
		Memory usage per processor = 7.04355 Mbytes
		Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
		500 -623.56254 -661.33839 37.775849 1359.2869 -810.50736 -664.11652 42.993999 -707.11052 0 2.7781274 13.68709 2.9115277 13990.5
		550 -623.5004 -660.74472 37.244326 1340.1611 -1413.4326 -663.99669 41.875014 -705.8717 0 3.2519651 15.097948 2.278405 13990.5
		600 -623.46963 -659.61729 36.147655 1300.6997 -521.50578 -662.54994 43.956071 -706.50601 0 2.9326492 14.99649 2.6334959 13990.5
		650 -623.49291 -661.50698 38.014069 1367.8588 -1230.0925 -664.21074 42.027844 -706.23859 0 2.7037578 13.982308 1.6247207 13990.5
		700 -623.4913 -660.11564 36.62434 1317.8522 -727.89052 -663.24921 43.413397 -706.66261 0 3.1335699 15.009937 2.0563966 13990.5
		750 -623.50292 -657.95982 34.4569 1239.8613 636.46644 -661.16971 46.539267 -707.70898 0 3.2098934 15.25993 2.1864622 13990.5
		800 -623.5176 -659.92032 36.402711 1309.8773 -912.75799 -662.84989 42.668309 -705.5182 0 2.9295708 13.577516 2.0006099 13990.5
		850 -623.44098 -660.92727 37.486295 1348.8679 -550.40358 -664.08308 43.667245 -707.75033 0 3.1558098 14.836208 2.279198 13990.5
		900 -623.46361 -661.21737 37.753765 1358.4923 1267.8647 -664.52195 47.67284 -712.19479 0 3.3045765 15.058502 1.886141 13990.5
		950 -623.50114 -660.58464 37.083492 1334.3739 1754.7359 -663.48186 48.70363 -712.18549 0 2.897226 15.519042 2.2654928 13990.5
		1000 -623.50161 -660.02915 36.527539 1314.369 228.76104 -663.31152 45.374099 -708.68562 0 3.2823685 14.783709 2.4201134 13990.5
		1050 -623.45985 -660.57417 37.114321 1335.4832 -1490.604 -663.75391 41.258878 -705.01279 0 3.1797391 14.250262 2.3153255 13990.5
		1100 -623.51051 -661.20338 37.692871 1356.3011 1791.7899 -664.01042 48.626451 -712.63687 0 2.807039 15.559872 3.184101 13990.5
		1150 -623.51067 -663.19545 39.684776 1427.9758 1023.0584 -666.07723 46.5628 -712.64003 0 2.8817804 13.895322 2.3950292 13990.5
		1200 -623.49625 -659.6715 36.175253 1301.6927 1600.2805 -662.62259 48.522365 -711.14495 0 2.9510854 15.567834 2.1677651 13990.5
		1250 -623.48282 -660.56735 37.084533 1334.4113 -871.67341 -663.86673 42.560699 -706.42743 0 3.2993759 14.569539 2.0093709 13990.5
		1300 -623.47744 -663.63125 40.153811 1444.853 1343.7147 -666.39564 47.104842 -713.50048 0 2.7643857 14.186019 1.4599359 13990.5
		1350 -623.49121 -661.42731 37.936096 1365.0531 589.73669 -664.46099 45.947687 -710.40867 0 3.0336821 14.801223 2.7486556 13990.5
		1400 -623.50803 -660.03912 36.53109 1314.4968 362.97431 -663.24909 45.772904 -709.02199 0 3.2099708 14.566488 1.9170714 13990.5
		1450 -623.51243 -659.65548 36.143052 1300.534 2853.0755 -663.0534 51.355353 -714.40875 0 3.3979157 15.890282 2.5251359 13990.5
		1500 -623.51621 -661.87741 38.361201 1380.3496 740.04973 -665.00896 46.208742 -711.2177 0 3.1315492 15.168927 2.4710846 13990.5
		Loop time of 22.2766 on 1 procs for 1000 steps with 432 atoms

		Performance: 7.757 ns/day, 3.094 hours/ns, 44.890 timesteps/s
		99.9% CPU use with 1 MPI tasks x no OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 21.8 \| 21.8 \| 21.8 \| 0.0 \| 97.86
		Bond \| 0.005852 \| 0.005852 \| 0.005852 \| 0.0 \| 0.03
		Neigh \| 0.30423 \| 0.30423 \| 0.30423 \| 0.0 \| 1.37
		Comm \| 0.14388 \| 0.14388 \| 0.14388 \| 0.0 \| 0.65
		Output \| 0.0010855 \| 0.0010855 \| 0.0010855 \| 0.0 \| 0.00
		Modify \| 0.0064189 \| 0.0064189 \| 0.0064189 \| 0.0 \| 0.03
		Other \| \| 0.01527 \| \| \| 0.07

		Nlocal: 432 ave 432 max 432 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Nghost: 9318 ave 9318 max 9318 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Neighs: 297131 ave 297131 max 297131 min
		Histogram: 1 0 0 0 0 0 0 0 0 0

		Total # of neighbors = 297131
		Ave neighs/atom = 687.803
		Ave special neighs/atom = 1
		Neighbor list builds = 44
		Dangerous builds = 0
		Total wall time: 0:00:33

examples/coreshell/log.8Nov16.coreshell.dsf.2

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