Added fix_charge_regulation source code and documentation.
This commit is contained in:
tc387
7
examples/USER/misc/charge_regulation/README
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7
examples/USER/misc/charge_regulation/README
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This directory has two input scripts that illustrates how to use fix charge_regulation in LAMMPS to perform coarse-grained molecular dynamics (MD) simulations with incorporation of charge regulation effects. The charge regulation is implemented via Monte Carlo (MC) sampling following the reaction ensemble MC approach, producing a MC/MD hybrid tool for modeling charge regulation in solvated systems.
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The script `in_acid.chreg` sets up a simple weak acid electrolyte (pH=7,pKa=6,pI=3). Four different types of MC moves are implemented: acid protonation & de-protonation, and monovalent ion pair insertion and deletion. Note here we have grouped all free monovalent ions into a single type, a physically natural choice on the level of coarse-grained primitive electrolyte models, which increases the calculation performance but has no effects on thermodynamic observables. The variables such as pH, pKa, pI, and lb at the top of the input script can be adjusted to play with various simulation parameters. The cumulative MC attempted moves and cumulative number of accepted moves, as well as, current number of neutral and charged acid particles, neutral and charged base particles (in this example always 0), and the current number of free cations and anions in the system are printed in the `log_acid.lammps`.
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The script `in_polymer.chreg` sets up a weak polyelectrolyte chain of N=80 beads. Each bead is a weak acid with pKa=5 and solution has pH=7 and salt pI=3. In this example, we choose to treat salt ions, protons, and hydroxyl ions separately, which results in 5 types of MC moves: acid [type 1] protonation & de-protonation (with protons [type 4] insertion & deletion), acid [type 1] protonation & de-protonation (with salt cation [type 2] insertion & deletion), water self-ionization (insertion and deletion of proton [type4] and hydroxyl ion [type 5] pair), insertion and deletion of monovalent salt pair [type 2 and type 3] , insertion and deletion
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Of a proton [type4] and salt anion [type 3]. The current number of neutral and charged acid particles, the current number of free salt cations and anions, and the current number of protons and hydroxyl ions are printed in the `log_polymer.lammps`.
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235
examples/USER/misc/charge_regulation/data_acid.chreg
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235
examples/USER/misc/charge_regulation/data_acid.chreg
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LAMMPS data file generated by get_input.py
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219 atoms
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3 atom types
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-2.5000000000000000e+01 2.5000000000000000e+01 xlo xhi
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-2.5000000000000000e+01 2.5000000000000000e+01 ylo yhi
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-2.5000000000000000e+01 2.5000000000000000e+01 zlo zhi
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Masses
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1 1
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2 1
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3 1
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Atoms
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||||
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|
||||
186 2 1 7.05280226857041 6.658154377550723 17.993436860997946
|
||||
187 2 1 20.98391844656716 -3.7711929542825544 -22.37222924252256
|
||||
188 2 1 -8.856382807041598 -16.421301042649826 -7.682473719905396
|
||||
189 2 1 -14.381919492441797 -7.667674808763277 -10.178028203828621
|
||||
190 2 1 -22.93472549116592 10.072854607637751 3.756868463885592
|
||||
191 2 1 9.458987867260412 17.23200182595278 -0.03503381482496337
|
||||
192 2 1 11.013603635791974 19.842184408029837 -5.83598462187852
|
||||
193 2 1 23.28897987479008 2.835578651649044 -20.512845011389647
|
||||
194 2 1 -18.86161127148128 8.956542530565656 14.193388541103026
|
||||
195 2 1 13.688477473034126 -15.973205475346514 10.952445409682397
|
||||
196 2 1 2.1058159557459497 2.740725960214597 -23.72037436968614
|
||||
197 2 1 20.982351847235442 7.072739454450108 -24.07322254392252
|
||||
198 2 1 5.962360707177609 -19.424513569281604 22.469955103109243
|
||||
199 2 1 -17.13607356062674 20.038457022813326 12.94227215395123
|
||||
200 2 1 11.592617137491743 22.283887092702138 2.339699650677858
|
||||
201 2 1 -1.3864952037065237 19.199632510575505 -7.684210221911414
|
||||
202 2 1 -22.44476570586083 -19.66385674506424 -8.981660607669522
|
||||
203 2 1 0.36547911522815824 -7.628556098996082 16.326944822668068
|
||||
204 2 1 -9.766164330974753 24.38435844399602 -14.352553497163
|
||||
205 2 1 -0.6310792726759544 -5.625399375968325 13.665993163571486
|
||||
206 2 1 2.6795300975636103 -0.37097710463575595 15.575183407667495
|
||||
207 2 1 10.68508361399715 24.638181487800373 -17.538711281692827
|
||||
208 2 1 18.30809729940504 18.39121662193474 18.285926328751984
|
||||
209 2 1 -11.52561870836783 -11.871004571782223 12.890674390475048
|
||||
210 3 -1 16.038097437687007 -0.8308290507120688 9.140710202344948
|
||||
211 3 -1 -12.071581865552927 23.77532123232212 -6.250109721970887
|
||||
212 3 -1 24.179073767023887 19.6390206210449 22.20321951706368
|
||||
213 3 -1 22.899159789805424 8.918385700451317 -1.1269016129923664
|
||||
214 3 -1 -10.48576153865241 5.691510884812594 21.955276995406933
|
||||
215 3 -1 6.272776670877239 10.035821052072265 22.22030412319301
|
||||
216 3 -1 14.689947575936934 -7.785907120217196 0.5033983092114553
|
||||
217 3 -1 23.173937996535116 -21.041572031861037 -21.057283440516468
|
||||
218 3 -1 -6.015120142466472 6.3962924962024985 21.58241945230285
|
||||
219 3 -1 -0.77667042466472 0.3962848125024985 1.582473830285
|
||||
264
examples/USER/misc/charge_regulation/data_polymer.chreg
Normal file
264
examples/USER/misc/charge_regulation/data_polymer.chreg
Normal file
@ -0,0 +1,264 @@
|
||||
##A Weak PE Chain of N=80
|
||||
|
||||
160 atoms
|
||||
79 bonds
|
||||
|
||||
5 atom types
|
||||
1 bond types
|
||||
|
||||
-50 50 xlo xhi
|
||||
-50 50 ylo yhi
|
||||
-50 50 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 1.0
|
||||
2 1.0
|
||||
3 1.0
|
||||
4 1.0
|
||||
5 1.0
|
||||
|
||||
Atoms
|
||||
# atom_id molecule_id atom_type charge x y z
|
||||
1 1 1 -1 0 0 -48.37753795169063
|
||||
2 1 1 -1 0 0 -47.255075903381254
|
||||
3 1 1 -1 0 0 -46.13261385507188
|
||||
4 1 1 -1 0 0 -45.01015180676251
|
||||
5 1 1 -1 0 0 -43.887689758453135
|
||||
6 1 1 -1 0 0 -42.76522771014376
|
||||
7 1 1 -1 0 0 -41.64276566183439
|
||||
8 1 1 -1 0 0 -40.520303613525016
|
||||
9 1 1 -1 0 0 -39.39784156521564
|
||||
10 1 1 -1 0 0 -38.27537951690627
|
||||
11 1 1 -1 0 0 -37.1529174685969
|
||||
12 1 1 -1 0 0 -36.030455420287524
|
||||
13 1 1 -1 0 0 -34.90799337197815
|
||||
14 1 1 -1 0 0 -33.78553132366878
|
||||
15 1 1 -1 0 0 -32.663069275359405
|
||||
16 1 1 -1 0 0 -31.54060722705003
|
||||
17 1 1 -1 0 0 -30.41814517874066
|
||||
18 1 1 -1 0 0 -29.295683130431286
|
||||
19 1 1 -1 0 0 -28.173221082121913
|
||||
20 1 1 -1 0 0 -27.05075903381254
|
||||
21 1 1 -1 0 0 -25.928296985503167
|
||||
22 1 1 -1 0 0 -24.805834937193794
|
||||
23 1 1 -1 0 0 -23.68337288888442
|
||||
24 1 1 -1 0 0 -22.560910840575048
|
||||
25 1 1 -1 0 0 -21.438448792265675
|
||||
26 1 1 -1 0 0 -20.3159867439563
|
||||
27 1 1 -1 0 0 -19.19352469564693
|
||||
28 1 1 -1 0 0 -18.071062647337556
|
||||
29 1 1 -1 0 0 -16.948600599028183
|
||||
30 1 1 -1 0 0 -15.82613855071881
|
||||
31 1 1 -1 0 0 -14.703676502409436
|
||||
32 1 1 -1 0 0 -13.581214454100063
|
||||
33 1 1 -1 0 0 -12.45875240579069
|
||||
34 1 1 -1 0 0 -11.336290357481317
|
||||
35 1 1 -1 0 0 -10.213828309171944
|
||||
36 1 1 -1 0 0 -9.091366260862571
|
||||
37 1 1 -1 0 0 -7.968904212553198
|
||||
38 1 1 -1 0 0 -6.846442164243825
|
||||
39 1 1 -1 0 0 -5.723980115934452
|
||||
40 1 1 -1 0 0 -4.601518067625079
|
||||
41 1 1 -1 0 0 -3.4790560193157063
|
||||
42 1 1 -1 0 0 -2.3565939710063333
|
||||
43 1 1 -1 0 0 -1.2341319226969603
|
||||
44 1 1 -1 0 0 -0.11166987438758724
|
||||
45 1 1 -1 0 0 1.0107921739217858
|
||||
46 1 1 -1 0 0 2.133254222231159
|
||||
47 1 1 -1 0 0 3.255716270540532
|
||||
48 1 1 -1 0 0 4.378178318849905
|
||||
49 1 1 -1 0 0 5.500640367159278
|
||||
50 1 1 -1 0 0 6.623102415468651
|
||||
51 1 1 -1 0 0 7.745564463778024
|
||||
52 1 1 -1 0 0 8.868026512087397
|
||||
53 1 1 -1 0 0 9.99048856039677
|
||||
54 1 1 -1 0 0 11.112950608706143
|
||||
55 1 1 -1 0 0 12.235412657015516
|
||||
56 1 1 -1 0 0 13.357874705324889
|
||||
57 1 1 -1 0 0 14.480336753634262
|
||||
58 1 1 -1 0 0 15.602798801943635
|
||||
59 1 1 -1 0 0 16.725260850253008
|
||||
60 1 1 -1 0 0 17.84772289856238
|
||||
61 1 1 -1 0 0 18.970184946871754
|
||||
62 1 1 -1 0 0 20.092646995181127
|
||||
63 1 1 -1 0 0 21.2151090434905
|
||||
64 1 1 -1 0 0 22.337571091799873
|
||||
65 1 1 -1 0 0 23.460033140109246
|
||||
66 1 1 -1 0 0 24.58249518841862
|
||||
67 1 1 -1 0 0 25.704957236727992
|
||||
68 1 1 -1 0 0 26.827419285037365
|
||||
69 1 1 -1 0 0 27.949881333346738
|
||||
70 1 1 -1 0 0 29.07234338165611
|
||||
71 1 1 -1 0 0 30.194805429965484
|
||||
72 1 1 -1 0 0 31.317267478274857
|
||||
73 1 1 -1 0 0 32.43972952658423
|
||||
74 1 1 -1 0 0 33.5621915748936
|
||||
75 1 1 -1 0 0 34.684653623202976
|
||||
76 1 1 -1 0 0 35.80711567151235
|
||||
77 1 1 -1 0 0 36.92957771982172
|
||||
78 1 1 -1 0 0 38.052039768131095
|
||||
79 1 1 -1 0 0 39.17450181644047
|
||||
80 1 1 -1 0 0 40.29696386474984
|
||||
81 0 2 1 -27.886422274724097 27.72001798427955 38.68169635811057
|
||||
82 0 2 1 29.812255760623188 17.871838747003693 -29.094648426460257
|
||||
83 0 2 1 -13.23881351410531 13.28123966828678 -24.422176415560116
|
||||
84 0 2 1 4.9465650593939685 -37.7521903558826 -15.115417767729575
|
||||
85 0 2 1 34.82527943387106 29.457664434004897 -25.565595338061254
|
||||
86 0 2 1 46.35660570786446 -7.161776614070412 -20.2471250527001
|
||||
87 0 2 1 39.20854546781531 34.96815569014278 13.893531822586723
|
||||
88 0 2 1 -7.797240698180197 0.07861219105048889 48.686453603015224
|
||||
89 0 2 1 43.92391845355516 -39.42362941705827 22.448930565867585
|
||||
90 0 2 1 -40.371744364329984 -17.743039071967246 -15.08153047835009
|
||||
91 0 2 1 -21.573165497710058 -0.5844447399891948 -45.73596994149077
|
||||
92 0 2 1 -19.882394451769102 -7.392447895357577 30.733607063808876
|
||||
93 0 2 1 -17.393031309514107 26.882975097407467 -47.64059480000892
|
||||
94 0 2 1 25.652222561671735 1.0229206994719107 -14.959030208952043
|
||||
95 0 2 1 26.075045766879313 19.902341017250052 46.70284805469666
|
||||
96 0 2 1 39.91980369168496 0.753749460187592 -26.203575929573407
|
||||
97 0 2 1 13.777613371273958 7.112171629839359 -33.5270487721399
|
||||
98 0 2 1 18.944534687271826 20.090215089875286 -34.381335468790574
|
||||
99 0 2 1 -23.801856387842435 -42.275962146864586 -8.322936238250279
|
||||
100 0 2 1 -31.386991395893826 29.83894468611787 8.937114269513422
|
||||
101 0 2 1 -41.07090001085809 49.59339931450579 6.666864232174753
|
||||
102 0 2 1 -46.58911504232167 -32.46068937927039 19.40424197066872
|
||||
103 0 2 1 -39.94659416571965 -36.28203465180086 5.841020764632312
|
||||
104 0 2 1 -26.027467090120137 -41.05522015175137 -1.1145958296128313
|
||||
105 0 2 1 37.09602855959457 23.76087951027276 45.09142423198867
|
||||
106 0 2 1 -27.78138413517528 -48.97344929918942 45.91491289356401
|
||||
107 0 2 1 4.468912883622387 -5.217782298407556 6.381420595433383
|
||||
108 0 2 1 36.758686966564525 48.425582881586166 -25.909273336802997
|
||||
109 0 2 1 -27.045102667146036 -19.713951008254117 4.339232870380627
|
||||
110 0 2 1 -5.984280016624311 -49.45311479123866 36.35727783065221
|
||||
111 0 2 1 27.833389147163018 -47.80144978082761 -47.71458334276804
|
||||
112 0 2 1 -23.628507668044364 -30.353876765128685 36.174277933133254
|
||||
113 0 2 1 -40.93360714431151 40.1336490864843 -27.035347797435495
|
||||
114 0 2 1 6.3523980881104976 -28.636485436097082 -10.671354350535445
|
||||
115 0 2 1 42.765716958607086 -32.85779663523676 -1.9682360265562124
|
||||
116 0 2 1 -33.68069757415453 16.800769050458484 -6.273374390373085
|
||||
117 0 2 1 13.909148568042937 4.921040289518388 12.111069913598996
|
||||
118 0 2 1 6.728324076730296 -48.44092815223126 -35.92436883370601
|
||||
119 0 2 1 -18.121173967321912 -15.76903395165283 2.2495451015454933
|
||||
120 0 2 1 -11.75253233489407 -45.82569982175387 -12.477142440015896
|
||||
121 0 2 1 1.9713864197144133 17.961034900064007 32.97992150691711
|
||||
122 0 2 1 -3.993384770632943 -47.63120435620297 27.75490859098018
|
||||
123 0 2 1 -0.32208279553454844 -47.30616152402566 -22.751109302380367
|
||||
124 0 2 1 -0.135777029397957 23.88599790464609 -31.87440560354473
|
||||
125 0 2 1 -6.123924906817393 -2.038519565120424 45.4809181974626
|
||||
126 0 2 1 -29.622588299895046 42.40404115712096 6.640479709229595
|
||||
127 0 2 1 -11.694512971272673 19.983258641775762 -38.152427411711145
|
||||
128 0 2 1 -20.93721440637313 39.46397829322392 -45.52708262202337
|
||||
129 0 2 1 34.13340147809369 36.14268504987945 -23.978137043267044
|
||||
130 0 2 1 -37.422309952611485 29.181841318883087 27.55677757161692
|
||||
131 0 2 1 30.11314373799594 18.721794400471353 1.5553303682670574
|
||||
132 0 2 1 -7.3563467211571805 46.84253369205935 -39.84708490437832
|
||||
133 0 2 1 -3.695927445484358 2.494403998274727 -7.634369981832755
|
||||
134 0 2 1 44.09701173592077 17.717328437831043 31.54108326477207
|
||||
135 0 2 1 48.070189931616795 10.601166369398662 -28.28574863896286
|
||||
136 0 2 1 -7.044858382811761 -42.080663380241766 -1.4369925734636553
|
||||
137 0 2 1 -12.485032488076918 23.87106169116919 6.178803347562642
|
||||
138 0 2 1 -15.613232443702309 10.103630885941392 -20.447182948810916
|
||||
139 0 2 1 28.610332347774147 37.08335835592116 -19.90280831362493
|
||||
140 0 2 1 25.853920233242505 -27.768648181803655 24.971357611943475
|
||||
141 0 2 1 9.256159541363296 -23.562096053197934 -4.722701100419371
|
||||
142 0 2 1 39.96929397877305 -11.88228547846326 -28.70638149104603
|
||||
143 0 2 1 -37.98545134633291 -23.50528193202669 -10.939982626098441
|
||||
144 0 2 1 25.40017763114089 -47.49220127581256 15.1783064865064
|
||||
145 0 2 1 28.073596076651768 3.6631266774864386 31.54355751177208
|
||||
146 0 2 1 -19.596457173068703 46.79824882013442 -12.302655772327597
|
||||
147 0 2 1 -36.46192411958321 -2.785830672302666 -25.1901381125736
|
||||
148 0 2 1 -27.377389198969894 11.295792272951147 39.32842550184691
|
||||
149 0 2 1 32.24967019136358 -20.517755791016402 31.20590722085157
|
||||
150 0 2 1 47.70698618147787 9.75462874031868 -28.267447889542563
|
||||
151 0 2 1 17.157803106328345 -27.48141290657965 7.7670687016760525
|
||||
152 0 2 1 15.089833959419678 5.342811012118396 27.35336620165029
|
||||
153 0 2 1 9.836963929211372 -11.047378229392443 -20.960811370690678
|
||||
154 0 2 1 44.66600586278604 14.949733274456321 -29.328965994323575
|
||||
155 0 2 1 -21.006260382140685 8.492712712433658 -46.31580169190271
|
||||
156 0 2 1 -29.970979487850748 -36.46250489415931 26.914372830947457
|
||||
157 0 2 1 -1.0821372755756329 -8.453379951300242 -19.95665062432509
|
||||
158 0 2 1 -24.033653425909772 -39.51330620205049 20.067656167683793
|
||||
159 0 2 1 27.747287624384626 -21.904990435351312 -10.819345241055956
|
||||
160 0 2 1 -40.86737066410612 -25.609300376714796 -21.128139356809783
|
||||
|
||||
Bonds
|
||||
# bond_id bond_type atom1_id atom2_id
|
||||
1 1 1 2
|
||||
2 1 2 3
|
||||
3 1 3 4
|
||||
4 1 4 5
|
||||
5 1 5 6
|
||||
6 1 6 7
|
||||
7 1 7 8
|
||||
8 1 8 9
|
||||
9 1 9 10
|
||||
10 1 10 11
|
||||
11 1 11 12
|
||||
12 1 12 13
|
||||
13 1 13 14
|
||||
14 1 14 15
|
||||
15 1 15 16
|
||||
16 1 16 17
|
||||
17 1 17 18
|
||||
18 1 18 19
|
||||
19 1 19 20
|
||||
20 1 20 21
|
||||
21 1 21 22
|
||||
22 1 22 23
|
||||
23 1 23 24
|
||||
24 1 24 25
|
||||
25 1 25 26
|
||||
26 1 26 27
|
||||
27 1 27 28
|
||||
28 1 28 29
|
||||
29 1 29 30
|
||||
30 1 30 31
|
||||
31 1 31 32
|
||||
32 1 32 33
|
||||
33 1 33 34
|
||||
34 1 34 35
|
||||
35 1 35 36
|
||||
36 1 36 37
|
||||
37 1 37 38
|
||||
38 1 38 39
|
||||
39 1 39 40
|
||||
40 1 40 41
|
||||
41 1 41 42
|
||||
42 1 42 43
|
||||
43 1 43 44
|
||||
44 1 44 45
|
||||
45 1 45 46
|
||||
46 1 46 47
|
||||
47 1 47 48
|
||||
48 1 48 49
|
||||
49 1 49 50
|
||||
50 1 50 51
|
||||
51 1 51 52
|
||||
52 1 52 53
|
||||
53 1 53 54
|
||||
54 1 54 55
|
||||
55 1 55 56
|
||||
56 1 56 57
|
||||
57 1 57 58
|
||||
58 1 58 59
|
||||
59 1 59 60
|
||||
60 1 60 61
|
||||
61 1 61 62
|
||||
62 1 62 63
|
||||
63 1 63 64
|
||||
64 1 64 65
|
||||
65 1 65 66
|
||||
66 1 66 67
|
||||
67 1 67 68
|
||||
68 1 68 69
|
||||
69 1 69 70
|
||||
70 1 70 71
|
||||
71 1 71 72
|
||||
72 1 72 73
|
||||
73 1 73 74
|
||||
74 1 74 75
|
||||
75 1 75 76
|
||||
76 1 76 77
|
||||
77 1 77 78
|
||||
78 1 78 79
|
||||
79 1 79 80
|
||||
40
examples/USER/misc/charge_regulation/in_acid.chreg
Normal file
40
examples/USER/misc/charge_regulation/in_acid.chreg
Normal file
@ -0,0 +1,40 @@
|
||||
# Charge regulation lammps for simple weak electrolyte
|
||||
|
||||
units lj
|
||||
atom_style charge
|
||||
dimension 3
|
||||
boundary p p p
|
||||
processors * * *
|
||||
neighbor 3.0 bin
|
||||
read_data data_acid.chreg
|
||||
|
||||
variable cut_long equal 12.5
|
||||
variable nevery equal 100
|
||||
variable nmc equal 100
|
||||
variable pH equal 7.0
|
||||
variable pKa equal 6.0
|
||||
variable pIm equal 3.0
|
||||
variable pIp equal 3.0
|
||||
|
||||
variable cut_lj equal 2^(1.0/6.0)
|
||||
variable lunit_nm equal 0.72 # in the units of nm
|
||||
velocity all create 1.0 8008 loop geom
|
||||
|
||||
pair_style lj/cut/coul/long ${cut_lj} ${cut_long}
|
||||
pair_coeff * * 1.0 1.0 ${cut_lj} # charges
|
||||
kspace_style ewald 1.0e-3
|
||||
dielectric 1.0
|
||||
pair_modify shift no
|
||||
|
||||
######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ###########
|
||||
fix fnve all nve
|
||||
compute dtemp all temp
|
||||
compute_modify dtemp dynamic yes
|
||||
fix fT all langevin 1.0 1.0 1.0 123
|
||||
fix_modify fT temp dtemp
|
||||
|
||||
fix chareg all charge_regulation 2 3 acid_type 1 pH ${pH} pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm ${lunit_nm} nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
||||
thermo 100
|
||||
thermo_style custom step pe c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8]
|
||||
timestep 0.005
|
||||
run 10000
|
||||
35
examples/USER/misc/charge_regulation/in_polymer.chreg
Normal file
35
examples/USER/misc/charge_regulation/in_polymer.chreg
Normal file
@ -0,0 +1,35 @@
|
||||
# Charge regulation lammps for a polymer chain
|
||||
units lj
|
||||
atom_style full
|
||||
dimension 3
|
||||
boundary p p p
|
||||
processors * * *
|
||||
neighbor 3.0 bin
|
||||
read_data data_polymer.chreg
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 100 1.122462 # K R0
|
||||
velocity all create 1.0 8008 loop geom
|
||||
|
||||
pair_style lj/cut/coul/long 1.122462 20
|
||||
pair_coeff * * 1.0 1.0 1.122462 # charges
|
||||
kspace_style pppm 1.0e-3
|
||||
pair_modify shift no
|
||||
dielectric 1.0
|
||||
|
||||
######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ###########
|
||||
fix fnve all nve
|
||||
compute dtemp all temp
|
||||
compute_modify dtemp dynamic yes
|
||||
fix fT all langevin 1.0 1.0 1.0 123
|
||||
fix_modify fT temp dtemp
|
||||
|
||||
fix chareg1 all charge_regulation 2 3 acid_type 1 pH 7.0 pKa 6.5 pIp 3.0 pIm 3.0 temp 1.0 nmc 40
|
||||
fix chareg2 all charge_regulation 4 5 acid_type 1 pH 7.0 pKa 6.5 pIp 7.0 pIm 7.0 temp 1.0 nmc 40
|
||||
fix chareg3 all charge_regulation 4 3 pIp 7.0 pIm 3.0 temp 1.0 nmc 20
|
||||
|
||||
thermo 100
|
||||
# print: step, potential energy, temperature, neutral acids, charged acids, salt cations, salt anions, H+ ions, OH- ions
|
||||
thermo_style custom step pe c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8]
|
||||
timestep 0.005
|
||||
run 10000
|
||||
163
examples/USER/misc/charge_regulation/log_acid.lammps
Normal file
163
examples/USER/misc/charge_regulation/log_acid.lammps
Normal file
@ -0,0 +1,163 @@
|
||||
LAMMPS (24 Dec 2020)
|
||||
Reading data file ...
|
||||
orthogonal box = (-25.000000 -25.000000 -25.000000) to (25.000000 25.000000 25.000000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
219 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
Ewald initialization ...
|
||||
using 12-bit tables for long-range coulomb (../kspace.cpp:339)
|
||||
G vector (1/distance) = 0.14221027
|
||||
estimated absolute RMS force accuracy = 0.0010128126
|
||||
estimated relative force accuracy = 0.0010128126
|
||||
KSpace vectors: actual max1d max3d = 257 5 665
|
||||
kxmax kymax kzmax = 5 5 5
|
||||
0 atoms in group Fix_CR:exclusion_group:chareg
|
||||
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:486)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 15.5
|
||||
ghost atom cutoff = 15.5
|
||||
binsize = 7.75, bins = 7 7 7
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : lj
|
||||
Current step : 0
|
||||
Time step : 0.005
|
||||
Per MPI rank memory allocation (min/avg/max) = 11.91 | 11.91 | 11.91 Mbytes
|
||||
Step PotEng c_dtemp f_chareg[1] f_chareg[2] f_chareg[3] f_chareg[4] f_chareg[5] f_chareg[6] f_chareg[7] f_chareg[8]
|
||||
0 -0.054228269 1 0 0 1 99 0 0 109 10
|
||||
100 -0.058672881 0.99159291 100 71 16 84 0 0 92 8
|
||||
200 -0.05399313 0.92006523 200 154 26 74 0 0 85 11
|
||||
300 -0.047035343 0.92728143 300 240 22 78 0 0 85 7
|
||||
400 -0.049597809 1.0617937 400 319 16 84 0 0 92 8
|
||||
500 -0.052409835 1.0006148 500 404 12 88 0 0 97 9
|
||||
600 -0.056012172 0.98059344 600 481 15 85 0 0 92 7
|
||||
700 -0.053639989 0.99572709 700 561 16 84 0 0 94 10
|
||||
800 -0.060026132 0.95764632 800 639 22 78 0 0 84 6
|
||||
900 -0.050785422 0.98399084 900 719 28 72 0 0 82 10
|
||||
1000 -0.062294743 0.97200068 1000 797 26 74 0 0 82 8
|
||||
1100 -0.051269402 1.0064376 1100 877 25 75 0 0 84 9
|
||||
1200 -0.077744839 1.0159098 1200 955 23 77 0 0 88 11
|
||||
1300 -0.084889696 1.1230485 1300 1037 20 80 0 0 90 10
|
||||
1400 -0.059361445 0.96735845 1400 1120 18 82 0 0 93 11
|
||||
1500 -0.052926174 0.95579188 1500 1199 24 76 0 0 86 10
|
||||
1600 -0.052376649 0.99376378 1600 1284 22 78 0 0 89 11
|
||||
1700 -0.052480188 0.96085964 1700 1361 27 73 0 0 84 11
|
||||
1800 -0.065884306 0.96747971 1800 1441 21 79 0 0 84 5
|
||||
1900 -0.054315859 0.95873145 1900 1521 23 77 0 0 84 7
|
||||
2000 -0.037161802 0.93562039 2000 1604 27 73 0 0 79 6
|
||||
2100 -0.034977265 0.97177103 2100 1684 26 74 0 0 85 11
|
||||
2200 -0.047434868 0.97897613 2200 1762 17 83 0 0 93 10
|
||||
2300 -0.047392634 0.96570672 2300 1837 18 82 0 0 92 10
|
||||
2400 -0.044879306 0.98620033 2400 1910 19 81 0 0 89 8
|
||||
2500 -0.069690496 1.0690505 2500 1988 16 84 0 0 91 7
|
||||
2600 -0.081588407 0.97711054 2600 2067 17 83 0 0 92 9
|
||||
2700 -0.06341681 1.0386711 2700 2146 20 80 0 0 85 5
|
||||
2800 -0.045290012 1.0402055 2800 2230 18 82 0 0 91 9
|
||||
2900 -0.046875012 1.0609775 2900 2317 24 76 0 0 86 10
|
||||
3000 -0.031258722 0.93861202 3000 2400 24 76 0 0 85 9
|
||||
3100 -0.04673342 0.90800583 3100 2485 25 75 0 0 90 15
|
||||
3200 -0.054354227 0.94493881 3200 2567 16 84 0 0 94 10
|
||||
3300 -0.053647746 0.92321446 3300 2641 17 83 0 0 94 11
|
||||
3400 -0.031751732 0.93735127 3400 2725 22 78 0 0 92 14
|
||||
3500 -0.053806113 0.98798136 3500 2795 28 72 0 0 84 12
|
||||
3600 -0.040751349 0.84291639 3600 2873 28 72 0 0 84 12
|
||||
3700 -0.051747138 1.072448 3700 2951 24 76 0 0 92 16
|
||||
3800 -0.043420594 1.0076309 3800 3030 26 74 0 0 79 5
|
||||
3900 -0.050845848 1.0250023 3900 3103 29 71 0 0 76 5
|
||||
4000 -0.039837847 1.064111 4000 3182 29 71 0 0 83 12
|
||||
4100 -0.045638995 1.1249685 4100 3262 28 72 0 0 81 9
|
||||
4200 -0.047956491 0.92255907 4200 3348 26 74 0 0 87 13
|
||||
4300 -0.054052822 1.006239 4300 3423 19 81 0 0 90 9
|
||||
4400 -0.053148034 1.0028887 4400 3506 24 76 0 0 83 7
|
||||
4500 -0.062132076 1.0317847 4500 3587 23 77 0 0 82 5
|
||||
4600 -0.04616043 0.99066453 4600 3673 28 72 0 0 82 10
|
||||
4700 -0.066990889 1.0242064 4700 3755 18 82 0 0 90 8
|
||||
4800 -0.0564736 0.91765628 4800 3832 22 78 0 0 91 13
|
||||
4900 -0.052301294 0.95348659 4900 3912 28 72 0 0 81 9
|
||||
5000 -0.062630677 1.0336579 5000 3989 18 82 0 0 92 10
|
||||
5100 -0.053645908 1.0314613 5100 4062 20 80 0 0 85 5
|
||||
5200 -0.062189568 1.0504732 5200 4133 23 77 0 0 84 7
|
||||
5300 -0.049092746 1.0310832 5300 4217 24 76 0 0 82 6
|
||||
5400 -0.051859257 0.99600428 5400 4299 27 73 0 0 80 7
|
||||
5500 -0.065540815 0.98012128 5500 4381 19 81 0 0 92 11
|
||||
5600 -0.071018582 0.9252814 5600 4455 23 77 0 0 84 7
|
||||
5700 -0.066954185 1.0325214 5700 4535 26 74 0 0 82 8
|
||||
5800 -0.064847249 1.0313536 5800 4617 21 79 0 0 90 11
|
||||
5900 -0.063173056 0.95455853 5900 4703 18 82 0 0 92 10
|
||||
6000 -0.064807837 0.97182222 6000 4790 21 79 0 0 91 12
|
||||
6100 -0.07067683 0.91775921 6100 4875 16 84 0 0 94 10
|
||||
6200 -0.071400842 1.0162225 6200 4952 17 83 0 0 87 4
|
||||
6300 -0.078479449 1.0106706 6300 5033 21 79 0 0 84 5
|
||||
6400 -0.083167651 1.0246584 6400 5111 18 82 0 0 90 8
|
||||
6500 -0.092611537 1.0766467 6500 5195 20 80 0 0 88 8
|
||||
6600 -0.096710071 1.0246648 6600 5274 15 85 0 0 91 6
|
||||
6700 -0.073399857 0.94939392 6700 5351 17 83 0 0 92 9
|
||||
6800 -0.062479375 0.9393967 6800 5434 18 82 0 0 93 11
|
||||
6900 -0.065391043 0.93475954 6900 5514 22 78 0 0 89 11
|
||||
7000 -0.045655499 0.98688239 7000 5601 21 79 0 0 90 11
|
||||
7100 -0.061186309 1.0309063 7100 5684 22 78 0 0 87 9
|
||||
7200 -0.074737514 1.0516593 7200 5769 25 75 0 0 80 5
|
||||
7300 -0.075228979 1.0167704 7300 5847 21 79 0 0 86 7
|
||||
7400 -0.06660147 1.0947107 7400 5930 25 75 0 0 87 12
|
||||
7500 -0.071915247 1.10542 7500 6009 24 76 0 0 84 8
|
||||
7600 -0.029974303 0.99202697 7600 6095 28 72 0 0 80 8
|
||||
7700 -0.029024004 1.0390995 7700 6182 28 72 0 0 83 11
|
||||
7800 -0.056250746 0.96393961 7800 6260 18 82 0 0 91 9
|
||||
7900 -0.072178944 0.9833919 7900 6339 21 79 0 0 86 7
|
||||
8000 -0.070377248 1.021342 8000 6419 23 77 0 0 88 11
|
||||
8100 -0.07753283 0.96194312 8100 6493 26 74 0 0 86 12
|
||||
8200 -0.075617309 0.9715344 8200 6576 25 75 0 0 89 14
|
||||
8300 -0.077480013 0.99106705 8300 6662 20 80 0 0 91 11
|
||||
8400 -0.079901928 0.89855112 8400 6744 23 77 0 0 91 14
|
||||
8500 -0.069192745 1.0606791 8500 6822 19 81 0 0 91 10
|
||||
8600 -0.058657202 1.1270217 8600 6898 15 85 0 0 95 10
|
||||
8700 -0.044985397 1.0367419 8700 6979 27 73 0 0 84 11
|
||||
8800 -0.064266376 0.91557003 8800 7060 21 79 0 0 89 10
|
||||
8900 -0.068680533 0.95963643 8900 7133 19 81 0 0 88 7
|
||||
9000 -0.051736144 1.0398547 9000 7213 13 87 0 0 94 7
|
||||
9100 -0.058381436 0.98047663 9100 7290 17 83 0 0 89 6
|
||||
9200 -0.05531014 0.92541631 9200 7368 22 78 0 0 85 7
|
||||
9300 -0.04386907 0.9339658 9300 7454 22 78 0 0 89 11
|
||||
9400 -0.052293168 0.94314034 9400 7539 22 78 0 0 86 8
|
||||
9500 -0.050362046 1.0489028 9500 7617 18 82 0 0 90 8
|
||||
9600 -0.054272227 1.0879161 9600 7697 11 89 0 0 96 7
|
||||
9700 -0.042514179 1.0051505 9700 7771 22 78 0 0 84 6
|
||||
9800 -0.045365018 0.95363669 9800 7850 25 75 0 0 77 2
|
||||
9900 -0.064287274 0.91994667 9900 7928 27 73 0 0 81 8
|
||||
10000 -0.05689162 0.99963208 10000 8011 22 78 0 0 84 6
|
||||
Loop time of 19.4452 on 1 procs for 10000 steps with 190 atoms
|
||||
|
||||
Performance: 222162.510 tau/day, 514.265 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 | 0.68864 | 0.68864 | 0.68864 | 0.0 | 3.54
|
||||
Kspace | 6.7893 | 6.7893 | 6.7893 | 0.0 | 34.92
|
||||
Neigh | 0.060782 | 0.060782 | 0.060782 | 0.0 | 0.31
|
||||
Comm | 0.047035 | 0.047035 | 0.047035 | 0.0 | 0.24
|
||||
Output | 0.0027227 | 0.0027227 | 0.0027227 | 0.0 | 0.01
|
||||
Modify | 11.838 | 11.838 | 11.838 | 0.0 | 60.88
|
||||
Other | | 0.01878 | | | 0.10
|
||||
|
||||
Nlocal: 190.000 ave 190 max 190 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 592.000 ave 592 max 592 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2194.00 ave 2194 max 2194 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2194
|
||||
Ave neighs/atom = 11.547368
|
||||
Neighbor list builds = 10287
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:19
|
||||
181
examples/USER/misc/charge_regulation/log_polymer.lammps
Normal file
181
examples/USER/misc/charge_regulation/log_polymer.lammps
Normal file
@ -0,0 +1,181 @@
|
||||
LAMMPS (24 Dec 2020)
|
||||
Reading data file ...
|
||||
orthogonal box = (-50.000000 -50.000000 -50.000000) to (50.000000 50.000000 50.000000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
160 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
reading bonds ...
|
||||
79 bonds
|
||||
Finding 1-2 1-3 1-4 neighbors ...
|
||||
special bond factors lj: 0 0 0
|
||||
special bond factors coul: 0 0 0
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of 1-3 neighbors
|
||||
4 = max # of 1-4 neighbors
|
||||
6 = max # of special neighbors
|
||||
special bonds CPU = 0.000 seconds
|
||||
read_data CPU = 0.004 seconds
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (../kspace.cpp:339)
|
||||
G vector (1/distance) = 0.077106934
|
||||
grid = 8 8 8
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00074388331
|
||||
estimated relative force accuracy = 0.00074388331
|
||||
using double precision KISS FFT
|
||||
3d grid and FFT values/proc = 2197 512
|
||||
0 atoms in group Fix_CR:exclusion_group:chareg1
|
||||
0 atoms in group Fix_CR:exclusion_group:chareg2
|
||||
0 atoms in group Fix_CR:exclusion_group:chareg3
|
||||
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (../neighbor.cpp:486)
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 10 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 23
|
||||
ghost atom cutoff = 23
|
||||
binsize = 11.5, bins = 9 9 9
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Setting up Verlet run ...
|
||||
Unit style : lj
|
||||
Current step : 0
|
||||
Time step : 0.005
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.962 | 6.962 | 6.962 Mbytes
|
||||
Step PotEng c_dtemp f_chareg1[3] f_chareg1[4] f_chareg1[7] f_chareg1[8] f_chareg2[7] f_chareg2[8]
|
||||
0 0.49903297 1 0 80 80 0 0 0
|
||||
100 0.63380666 0.87307225 8 72 77 6 1 0
|
||||
200 0.5865464 1.0048645 16 64 81 16 0 1
|
||||
300 0.55802913 1.0499142 19 61 91 29 0 1
|
||||
400 0.44734087 1.0838048 24 56 98 41 0 1
|
||||
500 0.47010775 1.005226 23 57 106 48 0 1
|
||||
600 0.3452105 0.97814306 28 52 109 56 0 1
|
||||
700 0.29208955 0.99766419 32 48 115 67 0 0
|
||||
800 0.27821915 1.0091641 31 49 128 80 1 0
|
||||
900 0.28943788 0.93619239 26 54 145 91 0 0
|
||||
1000 0.22963142 1.0162138 27 53 150 97 0 0
|
||||
1100 0.24238916 0.99146577 31 49 149 100 0 0
|
||||
1200 0.17029095 1.0406453 38 42 144 102 0 0
|
||||
1300 0.15830969 0.94661447 34 46 155 109 0 0
|
||||
1400 0.16698712 1.0116563 35 45 159 114 0 0
|
||||
1500 0.15432936 0.95600941 36 44 162 118 0 0
|
||||
1600 0.16973501 0.98326602 31 49 171 122 0 0
|
||||
1700 0.19725116 0.9915273 33 47 175 128 0 0
|
||||
1800 0.15278999 1.0304873 29 51 193 142 0 0
|
||||
1900 0.17418479 0.99490216 30 50 194 144 0 0
|
||||
2000 0.14238391 0.9638301 32 48 189 141 0 0
|
||||
2100 0.13054378 0.97164976 32 48 192 144 0 0
|
||||
2200 0.092083069 1.0112059 40 40 191 151 0 0
|
||||
2300 0.085175091 1.0070667 39 41 200 159 0 0
|
||||
2400 0.083367076 0.9934796 35 45 208 163 0 0
|
||||
2500 0.11494744 0.97650855 31 49 220 172 1 0
|
||||
2600 0.10796032 0.97047046 34 46 221 175 0 0
|
||||
2700 0.11080141 0.93570013 36 44 223 179 0 0
|
||||
2800 0.096699277 0.97702627 35 45 223 178 0 0
|
||||
2900 0.079403783 1.0870961 32 48 229 181 0 0
|
||||
3000 0.08288836 1.0642515 35 45 231 186 0 0
|
||||
3100 0.094000833 1.0241111 38 42 229 187 0 0
|
||||
3200 0.10011052 1.043594 34 46 235 189 0 0
|
||||
3300 0.096782103 0.99549134 34 46 234 188 0 0
|
||||
3400 0.057703946 1.00292 34 46 236 190 0 0
|
||||
3500 0.074345642 0.95064523 36 44 234 190 0 0
|
||||
3600 0.085872341 0.9759514 35 45 238 192 0 1
|
||||
3700 0.086427565 0.99843063 35 45 240 194 0 1
|
||||
3800 0.076091357 0.98516844 32 48 252 203 0 1
|
||||
3900 0.047187813 1.0063336 37 43 247 204 0 0
|
||||
4000 0.068269223 1.0390369 35 45 248 203 0 0
|
||||
4100 0.074209582 0.99912762 36 44 249 205 0 0
|
||||
4200 0.087016078 1.050265 36 44 246 202 0 0
|
||||
4300 0.081325479 1.0417103 35 45 245 200 0 0
|
||||
4400 0.047345973 0.96517298 39 41 243 202 0 0
|
||||
4500 0.041856955 0.94569673 38 42 245 203 0 0
|
||||
4600 0.049588267 0.99046371 42 38 249 211 0 0
|
||||
4700 0.043079897 1.0098538 43 37 245 208 0 0
|
||||
4800 0.049122913 1.0229995 41 39 247 208 0 0
|
||||
4900 0.059151797 1.0236679 36 44 249 205 0 0
|
||||
5000 0.053806841 1.0308397 42 38 243 205 0 0
|
||||
5100 0.053623833 1.0638841 39 41 246 205 0 0
|
||||
5200 0.086215806 1.0027613 37 43 243 200 0 0
|
||||
5300 0.031422797 1.0338154 38 42 245 203 0 0
|
||||
5400 0.051341116 0.92205149 34 46 246 200 0 0
|
||||
5500 0.039292708 0.97530704 32 48 251 203 0 0
|
||||
5600 0.035215415 1.023123 33 47 246 199 0 0
|
||||
5700 0.054553598 0.95833063 30 50 253 203 0 0
|
||||
5800 0.035699456 1.0721613 37 43 248 205 0 0
|
||||
5900 0.062426908 1.0612245 38 42 252 210 0 0
|
||||
6000 0.056362902 1.0002968 36 44 248 204 0 0
|
||||
6100 0.061550208 0.97270904 38 42 245 203 0 0
|
||||
6200 0.051825485 0.98187623 36 44 253 209 0 0
|
||||
6300 0.052137885 0.98906723 36 44 253 210 1 0
|
||||
6400 0.068218075 1.0511584 36 44 256 212 0 0
|
||||
6500 0.080167413 0.97270144 36 44 252 208 0 0
|
||||
6600 0.052169204 1.0160108 41 39 249 210 0 0
|
||||
6700 0.057313326 0.98033894 38 42 251 209 0 0
|
||||
6800 0.073008094 0.96239565 35 45 256 211 0 0
|
||||
6900 0.060159599 1.0063892 37 43 264 221 0 0
|
||||
7000 0.061738744 1.0031443 39 41 259 218 0 0
|
||||
7100 0.043263424 1.0425248 44 36 255 219 0 0
|
||||
7200 0.052179167 0.99512151 39 41 261 220 0 0
|
||||
7300 0.053258707 1.0171204 43 37 256 219 0 0
|
||||
7400 0.026037532 0.93786837 45 35 259 224 0 0
|
||||
7500 0.029731213 1.0172281 46 34 250 216 0 0
|
||||
7600 0.023118288 0.95628439 42 38 262 224 0 0
|
||||
7700 0.037021854 0.99991854 42 38 263 225 0 0
|
||||
7800 0.050404736 1.0130826 40 40 260 220 0 0
|
||||
7900 0.035658921 0.95772506 40 40 259 219 0 0
|
||||
8000 0.034426806 1.0028052 40 40 254 214 0 0
|
||||
8100 0.041427611 1.0347682 40 40 256 216 0 0
|
||||
8200 0.05986843 0.9804614 38 42 262 220 0 0
|
||||
8300 0.041419023 1.0613186 37 43 264 221 0 0
|
||||
8400 0.065701758 1.0511531 40 40 256 216 0 0
|
||||
8500 0.091954526 0.97190676 37 43 257 214 0 0
|
||||
8600 0.056982532 1.017813 35 45 252 207 0 0
|
||||
8700 0.075615111 1.0148527 29 51 263 212 0 0
|
||||
8800 0.066070082 1.0259454 33 47 260 213 0 0
|
||||
8900 0.055054194 1.0183535 37 43 247 204 0 0
|
||||
9000 0.063070816 1.0266115 39 41 244 203 0 0
|
||||
9100 0.10174156 0.99457684 34 46 246 200 0 0
|
||||
9200 0.071667261 1.033159 33 47 249 202 0 0
|
||||
9300 0.05520096 0.99821492 38 42 243 201 0 0
|
||||
9400 0.050355422 0.99148522 37 43 243 200 0 0
|
||||
9500 0.062314961 1.0042937 36 44 252 208 0 0
|
||||
9600 0.061148899 1.0052132 37 43 254 211 0 0
|
||||
9700 0.078695273 1.0175164 37 43 252 209 0 0
|
||||
9800 0.067487202 1.0110138 35 45 258 213 0 0
|
||||
9900 0.070340779 0.99640142 31 49 263 214 0 0
|
||||
10000 0.037252172 0.99863894 32 48 259 211 0 0
|
||||
Loop time of 23.0419 on 1 procs for 10000 steps with 550 atoms
|
||||
|
||||
Performance: 187484.206 tau/day, 433.991 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 | 2.5444 | 2.5444 | 2.5444 | 0.0 | 11.04
|
||||
Bond | 0.025075 | 0.025075 | 0.025075 | 0.0 | 0.11
|
||||
Kspace | 4.7385 | 4.7385 | 4.7385 | 0.0 | 20.56
|
||||
Neigh | 0.2058 | 0.2058 | 0.2058 | 0.0 | 0.89
|
||||
Comm | 0.073087 | 0.073087 | 0.073087 | 0.0 | 0.32
|
||||
Output | 0.003464 | 0.003464 | 0.003464 | 0.0 | 0.02
|
||||
Modify | 15.417 | 15.417 | 15.417 | 0.0 | 66.91
|
||||
Other | | 0.03479 | | | 0.15
|
||||
|
||||
Nlocal: 550.000 ave 550 max 550 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1023.00 ave 1023 max 1023 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 9644.00 ave 9644 max 9644 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 9644
|
||||
Ave neighs/atom = 17.534545
|
||||
Ave special neighs/atom = 0.85090909
|
||||
Neighbor list builds = 7576
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:23
|
||||
Reference in New Issue
Block a user