added some documentation and reference example (e284545c) · Commits · 郑智淋 / lammps

doc/src/pair_cs.txt

+19 −2

Original line number	Diff line number	Diff line
		@@ -9,12 +9,13 @@
		pair_style born/coul/long/cs command :h3
		pair_style buck/coul/long/cs command :h3
		pair_style born/coul/dsf/cs command :h3
		pair_style born/coul/wolf/cs command :h3

		[Syntax:]

		pair_style style args :pre

		style = {born/coul/long/cs} or {buck/coul/long/cs} or {born/coul/dsf/cs}
		style = {born/coul/long/cs} or {buck/coul/long/cs} or {born/coul/dsf/cs} or {born/coul/wolf/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)
		@@ -26,6 +27,10 @@ args = list of arguments for a particular style :ul
		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
		{born/coul/wolf/cs} args = alpha cutoff (cutoff2)
		alpha = damping parameter (inverse distance units)
		cutoff = global cutoff for Buckingham (and Coulombic if only 1 arg) (distance units)
		cutoff2 = global cutoff for Coulombic (optional) (distance units)

		[Examples:]

		@@ -41,6 +46,10 @@ 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

		pair_style born/coul/wolf/cs 0.25 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
		@@ -73,13 +82,21 @@ 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
		"pair_style born/coul/dsf"_pair_born.html style, which uses
		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.

		The pair style {born/coul/wolf/cs} is identical to the
		"pair_style born/coul/wolf"_pair_born.html style, which uses
		the Wolf summation as in "coul/wolf"_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.wolf

0 → 100644

+71 −0

Original line number	Diff line number	Diff line
		# Testsystem for core-shell model compared to Mitchel and Finchham
		# Shamelessly copied from in.coreshell.dsf but this script uses Wolf summation.

		# ------------------------ 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/wolf/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.22Sep17.coreshell.wolf.g++.1

0 → 100644

+190 −0

Original line number	Diff line number	Diff line
		LAMMPS (22 Sep 2017)
		# Testsystem for core-shell model compared to Mitchel and Finchham
		# Shamelessly copied from in.coreshell.dsf but this script uses Wolf summation.

		# ------------------------ 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/wolf/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 ...
		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
		1 neighbor lists, perpetual/occasional/extra = 1 0 0
		(1) pair born/coul/wolf/cs, perpetual
		attributes: half, newton on
		pair build: half/bin/newton
		stencil: half/bin/3d/newton
		bin: standard
		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
		Per MPI rank memory allocation (min/avg/max) = 8.59 \| 8.59 \| 8.59 Mbytes
		Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
		0 -637.41039 -677.06805 39.657659 1427 -21302.622 -677.06805 1.6320365 -678.70009 0 0 1.2935454e-14 3.3306691e-15 13990.5
		50 -635.62711 -667.67134 32.044236 1153.0465 -4533.0717 -669.45724 37.76997 -707.22721 0 1.7858939 9.6844521 2.2001656 13990.5
		100 -632.76337 -662.83035 30.066977 1081.8989 -3492.8736 -664.98454 39.197093 -704.18164 0 2.1541967 11.063962 2.1543406 13990.5
		150 -630.82538 -663.70056 32.875182 1182.9464 -74.330324 -666.12202 46.263665 -712.38569 0 2.4214607 11.739683 2.7558416 13990.5
		200 -629.1541 -664.54637 35.39227 1273.5187 -1707.5508 -666.87772 41.796197 -708.67391 0 2.3313445 10.594804 3.0025376 13990.5
		250 -627.86587 -662.60879 34.742918 1250.1531 -1258.7537 -665.21416 43.017024 -708.23118 0 2.6053655 10.576999 1.8400986 13990.5
		300 -627.10755 -664.12897 37.021419 1332.1403 -1891.3466 -666.39618 40.769593 -707.16577 0 2.2672094 9.412943 1.2434258 13990.5
		350 -626.27558 -665.04303 38.767448 1394.9676 -1436.8514 -667.47081 41.854746 -709.32556 0 2.4277827 10.304721 1.977594 13990.5
		400 -625.55098 -661.86388 36.312896 1306.6455 -331.92076 -664.4632 44.426542 -708.88975 0 2.599325 11.081635 2.1734468 13990.5
		450 -624.88626 -661.07359 36.187328 1302.1272 -2325.834 -663.6031 39.662697 -703.26579 0 2.5295037 9.9810051 1.3068929 13990.5
		500 -623.87093 -660.24145 36.370525 1308.7192 410.85324 -662.86944 45.869201 -708.73864 0 2.6279856 10.592785 1.8162326 13990.5
		Loop time of 11.7065 on 1 procs for 500 steps with 432 atoms

		Performance: 7.381 ns/day, 3.252 hours/ns, 42.711 timesteps/s
		100.0% CPU use with 1 MPI tasks x no OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 11.535 \| 11.535 \| 11.535 \| 0.0 \| 98.54
		Bond \| 0.001443 \| 0.001443 \| 0.001443 \| 0.0 \| 0.01
		Neigh \| 0.10952 \| 0.10952 \| 0.10952 \| 0.0 \| 0.94
		Comm \| 0.048796 \| 0.048796 \| 0.048796 \| 0.0 \| 0.42
		Output \| 0.00038695 \| 0.00038695 \| 0.00038695 \| 0.0 \| 0.00
		Modify \| 0.0067511 \| 0.0067511 \| 0.0067511 \| 0.0 \| 0.06
		Other \| \| 0.004243 \| \| \| 0.04

		Nlocal: 432 ave 432 max 432 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Nghost: 9328 ave 9328 max 9328 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Neighs: 297280 ave 297280 max 297280 min
		Histogram: 1 0 0 0 0 0 0 0 0 0

		Total # of neighbors = 297280
		Ave neighs/atom = 688.148
		Ave special neighs/atom = 1
		Neighbor list builds = 21
		Dangerous builds = 0

		unfix thermoberendsen

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

		run 1000
		Per MPI rank memory allocation (min/avg/max) = 8.59 \| 8.59 \| 8.59 Mbytes
		Step TotEng PotEng KinEng Temp Press E_pair E_vdwl E_coul E_long E_bond Fnorm Fmax Volume
		500 -623.87093 -660.24145 36.370525 1308.7192 410.85324 -662.86944 45.869201 -708.73864 0 2.6279856 10.592785 1.8162326 13990.5
		550 -623.95762 -659.99899 36.041371 1296.8752 -442.62446 -662.68699 44.004419 -706.69141 0 2.6879934 10.936057 1.7358509 13990.5
		600 -624.04214 -661.21748 37.175332 1337.6785 47.615854 -663.76133 45.009742 -708.77107 0 2.5438549 11.431366 2.1185464 13990.5
		650 -623.98279 -661.85255 37.86976 1362.6661 -1708.3823 -664.31138 40.933446 -705.24482 0 2.4588298 9.7960191 1.4159904 13990.5
		700 -624.02941 -661.57484 37.54543 1350.9958 -124.09512 -663.95322 44.666402 -708.61962 0 2.3783801 10.518712 2.0854584 13990.5
		750 -624.03935 -661.11619 37.076837 1334.1344 -1163.2721 -663.82553 42.1219 -705.94743 0 2.7093404 10.634859 1.9381654 13990.5
		800 -623.98709 -659.43647 35.44938 1275.5737 -285.65702 -662.23782 44.650233 -706.88805 0 2.8013482 11.83459 3.4506407 13990.5
		850 -623.96081 -661.77923 37.818422 1360.8188 -814.33212 -664.38161 42.860208 -707.24181 0 2.6023728 10.766451 2.9211132 13990.5
		900 -623.96136 -662.98419 39.022831 1404.157 308.13105 -665.65877 45.053188 -710.71195 0 2.6745786 11.028799 1.8494322 13990.5
		950 -623.91048 -660.63828 36.7278 1321.575 -445.31526 -663.79806 43.94833 -707.74639 0 3.1597729 11.852051 1.8238458 13990.5
		1000 -623.90541 -661.03474 37.129332 1336.0233 522.57958 -663.50212 45.863261 -709.36538 0 2.4673781 10.949291 1.8614095 13990.5
		1050 -624.01134 -660.99076 36.979422 1330.6291 -1710.2829 -663.67762 41.056102 -704.73372 0 2.6868521 10.86533 2.2154165 13990.5
		1100 -624.02639 -660.86661 36.840225 1325.6204 1151.0236 -663.5066 47.207185 -710.71378 0 2.6399847 11.298044 1.8900703 13990.5
		1150 -624.04418 -661.29819 37.254006 1340.5094 161.09847 -663.73735 45.222561 -708.95991 0 2.4391651 11.261119 2.2245673 13990.5
		1200 -624.08628 -662.39932 38.313043 1378.6168 -1405.0927 -664.93121 41.728112 -706.65933 0 2.5318927 10.458041 2.1153159 13990.5
		1250 -624.03036 -661.25661 37.226248 1339.5106 63.407721 -663.72719 45.086961 -708.81415 0 2.4705832 11.766021 2.2297809 13990.5
		1300 -623.97475 -661.55998 37.585229 1352.4278 -763.66781 -663.80645 42.870244 -706.6767 0 2.2464703 10.098322 1.7614596 13990.5
		1350 -623.93123 -660.30786 36.376631 1308.9389 -2389.8052 -663.04725 39.749029 -702.79628 0 2.7393936 10.879364 2.6622521 13990.5
		1400 -623.86468 -658.44644 34.581765 1244.3543 2262.7586 -660.95368 50.10608 -711.05976 0 2.5072434 11.528291 1.7861906 13990.5
		1450 -623.85494 -661.47216 37.617217 1353.5789 -1435.0174 -664.13587 41.701767 -705.83764 0 2.6637191 11.297444 2.0038345 13990.5
		1500 -623.79928 -659.70124 35.901959 1291.8588 -198.39562 -662.57415 44.358482 -706.93263 0 2.872907 11.075746 2.2821286 13990.5
		Loop time of 23.4119 on 1 procs for 1000 steps with 432 atoms

		Performance: 7.381 ns/day, 3.252 hours/ns, 42.713 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 \| 23.069 \| 23.069 \| 23.069 \| 0.0 \| 98.54
		Bond \| 0.0029275 \| 0.0029275 \| 0.0029275 \| 0.0 \| 0.01
		Neigh \| 0.22821 \| 0.22821 \| 0.22821 \| 0.0 \| 0.97
		Comm \| 0.097941 \| 0.097941 \| 0.097941 \| 0.0 \| 0.42
		Output \| 0.00074033 \| 0.00074033 \| 0.00074033 \| 0.0 \| 0.00
		Modify \| 0.0042015 \| 0.0042015 \| 0.0042015 \| 0.0 \| 0.02
		Other \| \| 0.00865 \| \| \| 0.04

		Nlocal: 432 ave 432 max 432 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Nghost: 9388 ave 9388 max 9388 min
		Histogram: 1 0 0 0 0 0 0 0 0 0
		Neighs: 297212 ave 297212 max 297212 min
		Histogram: 1 0 0 0 0 0 0 0 0 0

		Total # of neighbors = 297212
		Ave neighs/atom = 687.991
		Ave special neighs/atom = 1
		Neighbor list builds = 45
		Dangerous builds = 0
		Total wall time: 0:00:35

examples/coreshell/log.22Sep17.coreshell.wolf.g++.4

0 → 100644

+190 −0

File added.

Preview size limit exceeded, changes collapsed.

src/CORESHELL/pair_born_coul_wolf_cs.cpp

+4 −5

Original line number	Diff line number	Diff line
		@@ -70,8 +70,7 @@ void PairBornCoulWolfCS::compute(int eflag, int vflag)

		e_self = v_sh = 0.0;
		e_shift = erfc(alf*cut_coul)/cut_coul;
		f_shift = -(e_shift+ 2.0alf/MY_PIS exp(-alfalfcut_coul*cut_coul)) /
		cut_coul;
		f_shift = -(e_shift+ 2.0alf/MY_PIS exp(-alfalfcut_coul*cut_coul)) / cut_coul;

		inum = list->inum;
		ilist = list->ilist;

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