Added an example using real units.
This commit is contained in:
tc387
235
examples/USER/misc/charge_regulation/data.chreg-acid-real
Normal file
235
examples/USER/misc/charge_regulation/data.chreg-acid-real
Normal file
@ -0,0 +1,235 @@
|
||||
LAMMPS data file generated by get_input.py
|
||||
|
||||
219 atoms
|
||||
3 atom types
|
||||
-180 180 xlo xhi
|
||||
-180 180 ylo yhi
|
||||
-180 180 zlo zhi
|
||||
|
||||
Masses
|
||||
|
||||
1 20
|
||||
2 20
|
||||
3 20
|
||||
|
||||
Atoms
|
||||
|
||||
1 1 0 18.70795854 -60.24998141 144.0092784
|
||||
2 1 -1 -130.9166548 -58.17450505 59.42690807
|
||||
3 1 -1 -125.5489258 58.46696329 77.38308245
|
||||
4 1 -1 46.8178314 -169.1807517 143.6272062
|
||||
5 1 -1 -162.2028908 -135.2407217 -129.3455357
|
||||
6 1 -1 -69.93717134 136.6009615 -140.3684699
|
||||
7 1 -1 -92.39022725 0.88313303 -156.091658
|
||||
8 1 -1 150.5452585 -15.59052452 3.326246397
|
||||
9 1 -1 171.8072626 172.9794849 75.84528386
|
||||
10 1 -1 -3.808294794 171.5056017 -19.13183671
|
||||
11 1 -1 68.90552852 86.21187482 24.628687
|
||||
12 1 -1 -73.4512319 54.41387468 86.90435812
|
||||
13 1 -1 35.26889793 14.52239846 -149.5100547
|
||||
14 1 -1 -173.4235696 31.85993966 -30.27092231
|
||||
15 1 -1 26.52275652 -34.29527864 -91.86288894
|
||||
16 1 -1 -87.96846598 -127.5856503 -97.6057498
|
||||
17 1 -1 -154.4848498 -53.45277349 -49.99665917
|
||||
18 1 -1 98.62055171 61.22620607 58.21550969
|
||||
19 1 -1 -41.50240351 82.79211492 -36.80199381
|
||||
20 1 -1 28.75979595 121.8830702 -107.1045784
|
||||
21 1 -1 32.46858199 119.7785312 -159.9729476
|
||||
22 1 -1 159.2306995 -136.6051631 -172.6738992
|
||||
23 1 -1 102.0172393 -120.2283106 99.20908244
|
||||
24 1 -1 123.7452923 63.55770833 165.9991324
|
||||
25 1 -1 21.47248943 -121.2255157 -153.2060898
|
||||
26 1 -1 119.9343938 -11.67643844 -81.47418783
|
||||
27 1 -1 138.3518387 -111.6909718 52.34478391
|
||||
28 1 -1 -63.98455793 -173.4943975 28.8937153
|
||||
29 1 -1 151.1941205 32.1957053 2.770016951
|
||||
30 1 -1 9.678451862 40.32965827 -107.4138803
|
||||
31 1 -1 -50.13343476 147.3853225 -117.9277823
|
||||
32 1 -1 -71.89428479 68.56083346 -179.8533411
|
||||
33 1 -1 -124.7615264 41.48173515 41.18558752
|
||||
34 1 -1 37.21218965 -170.6314486 18.86382891
|
||||
35 1 -1 136.6419056 46.16558949 45.50222572
|
||||
36 1 -1 -117.9745136 -106.7487877 29.70172113
|
||||
37 1 -1 57.41607893 -135.959946 79.2519303
|
||||
38 1 -1 99.2146782 13.37903953 65.55038181
|
||||
39 1 -1 -172.1483566 -24.09752036 -73.64723741
|
||||
40 1 -1 155.6386288 60.79647905 -137.6687854
|
||||
41 1 -1 -63.53265172 104.1203088 115.6442718
|
||||
42 1 -1 -17.57295284 90.38545929 148.3687022
|
||||
43 1 -1 -132.9077114 109.8788504 152.5487953
|
||||
44 1 -1 16.09488244 -168.1200949 81.85901273
|
||||
45 1 -1 112.2904059 -47.57448978 39.12664557
|
||||
46 1 -1 -126.2033528 29.5901835 -10.20047838
|
||||
47 1 -1 15.56623544 -118.8796306 -87.74057744
|
||||
48 1 -1 -62.53683723 -50.93540139 -8.324528194
|
||||
49 1 -1 112.4826277 -47.2269151 148.0087872
|
||||
50 1 -1 -50.1494905 -103.3112513 -103.8344246
|
||||
51 1 -1 -87.11540287 -177.3205662 -114.041712
|
||||
52 1 -1 48.0517504 56.41745572 -69.94172272
|
||||
53 1 -1 -125.3768674 89.18463079 -121.5525657
|
||||
54 1 -1 157.6559442 89.89879164 -104.7846361
|
||||
55 1 -1 -60.30935405 -178.4439001 53.67216823
|
||||
56 1 -1 101.3842749 -156.3782696 -125.6200241
|
||||
57 1 -1 33.71034745 14.19807232 -56.33090362
|
||||
58 1 -1 31.34283781 114.2588441 177.621698
|
||||
59 1 -1 167.8681492 -33.73721495 17.70943601
|
||||
60 1 -1 50.73906277 165.7201913 -94.6041936
|
||||
61 1 -1 84.42400278 -113.8271268 -11.73087326
|
||||
62 1 -1 -146.6200007 -87.0115127 -164.2802459
|
||||
63 1 -1 -17.94345563 -5.266117623 -114.4770608
|
||||
64 1 -1 -161.6618755 -81.21577064 -68.78715057
|
||||
65 1 -1 178.3275787 144.9284223 75.80861878
|
||||
66 1 -1 81.54873843 -83.6941478 -69.75163018
|
||||
67 1 -1 -41.13190239 113.6079886 -6.669536125
|
||||
68 1 -1 -108.5270482 -89.08499627 -39.32427247
|
||||
69 1 -1 -41.97432027 -32.96246695 65.11935497
|
||||
70 1 -1 -39.09020679 10.47027922 -53.26049629
|
||||
71 1 -1 -168.3760012 -85.85704062 27.51501191
|
||||
72 1 -1 -7.699755475 21.59960856 26.43069039
|
||||
73 1 -1 87.36704757 14.21816794 -107.2504322
|
||||
74 1 -1 153.4284087 136.6052131 -126.1502487
|
||||
75 1 -1 -175.3682642 25.88313064 123.6455547
|
||||
76 1 -1 90.96648194 175.4891969 32.84622917
|
||||
77 1 -1 -77.3297511 139.285477 -24.02526586
|
||||
78 1 -1 -21.80051132 76.35556687 53.9496888
|
||||
79 1 -1 36.00388293 84.74463507 124.0379428
|
||||
80 1 -1 8.341344194 -176.0991953 -90.11296078
|
||||
81 1 -1 13.79742378 -101.263178 81.37760753
|
||||
82 1 -1 -150.1706978 153.3081009 125.261789
|
||||
83 1 -1 -176.434078 -91.73850736 -13.91415701
|
||||
84 1 -1 19.14212656 -8.014482902 53.93954558
|
||||
85 1 -1 -133.3111329 174.2862517 104.1616036
|
||||
86 1 -1 141.4028288 71.58712061 62.57853826
|
||||
87 1 -1 -55.41310448 84.69012271 -53.69230074
|
||||
88 1 -1 7.57030387 -82.51421069 121.7019339
|
||||
89 1 -1 6.593627122 170.3286085 -47.07783075
|
||||
90 1 -1 167.9772199 -52.51603119 -77.32359634
|
||||
91 1 -1 9.68753279 2.580696533 63.63273049
|
||||
92 1 -1 -157.900078 -78.41001295 -74.97298362
|
||||
93 1 -1 157.7779932 -77.61759639 83.11626672
|
||||
94 1 -1 8.735687555 -51.63741526 149.2886008
|
||||
95 1 -1 166.3370649 158.0395191 2.108272744
|
||||
96 1 -1 -136.2080224 -0.233620925 170.1641304
|
||||
97 1 -1 54.59763504 77.34086464 -34.97254442
|
||||
98 1 -1 -53.93524806 -102.0122253 -46.27109402
|
||||
99 1 -1 -148.8398471 -62.976886 79.28200649
|
||||
100 1 -1 -134.367229 -153.7685306 -62.89913905
|
||||
101 2 1 85.68701047 47.45902631 136.9309939
|
||||
102 2 1 -168.7218611 -136.4862888 34.82926874
|
||||
103 2 1 -85.14342147 -27.50852705 22.44064244
|
||||
104 2 1 -125.9841936 -166.432033 69.22175254
|
||||
105 2 1 78.40196016 32.48784706 134.5355212
|
||||
106 2 1 -158.7356866 172.6075363 -168.6081077
|
||||
107 2 1 -97.70696089 125.0552693 152.541151
|
||||
108 2 1 47.42532862 117.2059839 -26.2001494
|
||||
109 2 1 58.97843054 49.16794046 -45.70255405
|
||||
110 2 1 -113.2077086 -147.4896474 -109.0593944
|
||||
111 2 1 133.7818478 137.2370883 -74.12887346
|
||||
112 2 1 -151.8619681 -55.72321046 39.00697883
|
||||
113 2 1 -101.5491513 -113.5421107 -135.9492067
|
||||
114 2 1 -105.4410412 63.66017268 62.00391546
|
||||
115 2 1 -84.37716183 -35.78408568 -7.089644848
|
||||
116 2 1 140.387382 -75.00992841 -159.2710691
|
||||
117 2 1 157.3753205 145.1311104 -98.29723102
|
||||
118 2 1 -126.8885841 157.4914592 -47.04455377
|
||||
119 2 1 52.06885202 -100.2669325 38.59257737
|
||||
120 2 1 -54.06789629 137.7750035 -116.8953091
|
||||
121 2 1 -29.14739431 94.50860741 -51.527097
|
||||
122 2 1 -145.9322739 154.5384232 112.3421798
|
||||
123 2 1 -32.24342538 -22.90490626 -133.4101075
|
||||
124 2 1 155.0953371 97.30799449 -13.02231424
|
||||
125 2 1 -109.6079033 -42.89844953 -51.80376701
|
||||
126 2 1 -150.2770445 -55.20818421 147.7312972
|
||||
127 2 1 -26.96028917 151.3053234 51.82429115
|
||||
128 2 1 -42.51040448 55.12547194 -10.01649745
|
||||
129 2 1 -154.7332138 -166.4922488 75.56066422
|
||||
130 2 1 179.3252381 50.98353603 -103.842222
|
||||
131 2 1 -87.64561442 -167.4026399 -37.04977996
|
||||
132 2 1 -141.7543098 32.23109989 44.99445113
|
||||
133 2 1 121.3596596 -6.092779973 129.6856923
|
||||
134 2 1 124.4836766 -86.35531223 85.50625099
|
||||
135 2 1 140.6305506 -165.9843021 -35.3966949
|
||||
136 2 1 -89.51258901 36.2123163 54.25434215
|
||||
137 2 1 107.5306105 58.22419926 141.7457531
|
||||
138 2 1 -51.03564423 -166.277591 119.3103596
|
||||
139 2 1 106.3738063 153.673561 100.7747233
|
||||
140 2 1 -105.1662471 -49.88388187 -163.5658795
|
||||
141 2 1 -123.4063552 104.6405545 -157.1806703
|
||||
142 2 1 30.68517662 111.7365757 -128.0988407
|
||||
143 2 1 -70.66650991 -36.87088431 101.1920697
|
||||
144 2 1 59.85584345 28.56015074 -148.8751279
|
||||
145 2 1 76.34296857 -18.88899045 11.99663247
|
||||
146 2 1 -127.898772 9.029786744 -155.2067979
|
||||
147 2 1 -61.47407783 106.6906337 -32.24644961
|
||||
148 2 1 -41.82882356 105.2048819 95.67134776
|
||||
149 2 1 64.70518204 -125.5606981 -130.2221179
|
||||
150 2 1 -95.86998176 64.01110464 -62.69889224
|
||||
151 2 1 -3.893149866 -170.4938796 -173.9425756
|
||||
152 2 1 -142.5571999 -115.9852755 -42.33527796
|
||||
153 2 1 -170.1094774 67.22933296 -69.41406448
|
||||
154 2 1 -135.7002446 -117.3853245 -77.66219554
|
||||
155 2 1 97.68794466 -176.3481416 64.0577303
|
||||
156 2 1 98.30084322 -179.1048324 157.6098802
|
||||
157 2 1 -61.74657154 71.45180441 36.21267022
|
||||
158 2 1 148.9924395 8.130617629 2.580809806
|
||||
159 2 1 -7.179797893 131.8852645 48.92705878
|
||||
160 2 1 166.7210737 111.3028256 122.5151765
|
||||
161 2 1 160.4061661 105.4292149 147.9164951
|
||||
162 2 1 70.35573238 -156.217711 -37.86968306
|
||||
163 2 1 37.82167168 128.9612675 113.5371453
|
||||
164 2 1 -149.4650805 40.2544478 -89.16446826
|
||||
165 2 1 23.15794976 -35.62998186 -128.5225995
|
||||
166 2 1 148.5909499 65.59167763 44.47571026
|
||||
167 2 1 38.20567747 91.06090259 167.2556933
|
||||
168 2 1 -173.8935359 124.3001041 -123.4154022
|
||||
169 2 1 -113.0780192 -112.7185827 -75.51909042
|
||||
170 2 1 -47.52814398 -162.0232543 -40.84518679
|
||||
171 2 1 164.6580923 96.26106544 -67.52475023
|
||||
172 2 1 -166.687599 -28.28821753 -80.04284273
|
||||
173 2 1 9.786487166 -133.5748603 -110.4924395
|
||||
174 2 1 73.69685916 -130.6229707 -12.1566579
|
||||
175 2 1 90.69039384 -12.53964183 -156.8650452
|
||||
176 2 1 -1.065055548 123.2458955 9.207883208
|
||||
177 2 1 175.3144942 -62.38332615 89.50309521
|
||||
178 2 1 -135.5554643 -135.3786299 -12.22599884
|
||||
179 2 1 -65.15130962 -12.87802388 -85.25728639
|
||||
180 2 1 -161.9760397 -159.2069523 72.10033228
|
||||
181 2 1 -116.5200037 9.430944126 5.8294178
|
||||
182 2 1 -28.85454266 -176.0245493 -141.7245957
|
||||
183 2 1 63.2968571 -114.4145268 -168.891953
|
||||
184 2 1 -61.61686575 -158.2947391 162.9099557
|
||||
185 2 1 51.43661765 119.3411567 4.253266919
|
||||
186 2 1 50.78017633 47.93871152 129.5527454
|
||||
187 2 1 151.0842128 -27.15258927 -161.0800505
|
||||
188 2 1 -63.76595621 -118.2333675 -55.31381078
|
||||
189 2 1 -103.5498203 -55.20725862 -73.28180307
|
||||
190 2 1 -165.1300235 72.52455317 27.04945294
|
||||
191 2 1 68.10471264 124.0704131 -0.252243467
|
||||
192 2 1 79.29794618 142.8637277 -42.01908928
|
||||
193 2 1 167.6806551 20.41616629 -147.6924841
|
||||
194 2 1 -135.8036012 64.48710622 102.1923975
|
||||
195 2 1 98.55703781 -115.0070794 78.85760695
|
||||
196 2 1 15.16187488 19.73322691 -170.7866955
|
||||
197 2 1 151.0729333 50.92372407 -173.3272023
|
||||
198 2 1 42.92899709 -139.8564977 161.7836767
|
||||
199 2 1 -123.3797296 144.2768906 93.18435951
|
||||
200 2 1 83.46684339 160.4439871 16.84583748
|
||||
201 2 1 -9.982765467 138.2373541 -55.3263136
|
||||
202 2 1 -161.6023131 -141.5797686 -64.66795638
|
||||
203 2 1 2.63144963 -54.92560391 117.5540027
|
||||
204 2 1 -70.31638318 175.5673808 -103.3383852
|
||||
205 2 1 -4.543770763 -40.50287551 98.39515078
|
||||
206 2 1 19.2926167 -2.671035153 112.1413205
|
||||
207 2 1 76.93260202 177.3949067 -126.2787212
|
||||
208 2 1 131.8183006 132.4167597 131.6586696
|
||||
209 2 1 -82.9844547 -85.47123292 92.81285561
|
||||
210 3 -1 115.4743016 -5.981969165 65.81311346
|
||||
211 3 -1 -86.91538943 171.1823129 -45.00079
|
||||
212 3 -1 174.0893311 141.4009485 159.8631805
|
||||
213 3 -1 164.8739505 64.21237704 -8.113691614
|
||||
214 3 -1 -75.49748308 40.97887837 158.0779944
|
||||
215 3 -1 45.16399203 72.25791157 159.9861897
|
||||
216 3 -1 105.7676225 -56.05853127 3.624467826
|
||||
217 3 -1 166.8523536 -151.4993186 -151.6124408
|
||||
218 3 -1 -43.30886503 46.05330597 155.3934201
|
||||
219 3 -1 -5.592027058 2.85325065 11.39381158
|
||||
44
examples/USER/misc/charge_regulation/in.chreg-acid-real
Normal file
44
examples/USER/misc/charge_regulation/in.chreg-acid-real
Normal file
@ -0,0 +1,44 @@
|
||||
# Charge regulation lammps for simple weak electrolyte
|
||||
|
||||
units real
|
||||
atom_style charge
|
||||
neighbor 3.0 bin
|
||||
read_data data.chreg-acid-real
|
||||
|
||||
#real units
|
||||
variable sigma equal 7.2 # particle diameter 0.72 nm
|
||||
variable temperature equal 298 # temperature 298 K
|
||||
variable kb index 0.0019872067 # kB in Kcal/mol/K
|
||||
variable epsilon equal ${kb}*${temperature}
|
||||
variable tunit equal 2000 # time unit is 2000 fs
|
||||
variable timestep equal 0.005*${tunit}
|
||||
|
||||
variable cut_long equal 12.5*${sigma}
|
||||
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)*${sigma}
|
||||
velocity all create ${temperature} 8008 loop geom
|
||||
|
||||
pair_style lj/cut/coul/long ${cut_lj} ${cut_long}
|
||||
pair_coeff * * ${epsilon} ${sigma}
|
||||
kspace_style pppm 1.0e-3
|
||||
dielectric 78
|
||||
pair_modify shift yes
|
||||
|
||||
######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ###########
|
||||
fix fnve all nve
|
||||
compute dtemp all temp
|
||||
compute_modify dtemp dynamic yes
|
||||
fix fT all langevin $(v_temperature) $(v_temperature) $(v_tunit) 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 0.1 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 ${timestep}
|
||||
run 2000
|
||||
@ -0,0 +1,145 @@
|
||||
LAMMPS (10 Feb 2021)
|
||||
# Charge regulation lammps for simple weak electrolyte
|
||||
|
||||
units real
|
||||
atom_style charge
|
||||
neighbor 3.0 bin
|
||||
read_data data.chreg-acid-real
|
||||
Reading data file ...
|
||||
orthogonal box = (-180.00000 -180.00000 -180.00000) to (180.00000 180.00000 180.00000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
219 atoms
|
||||
read_data CPU = 0.002 seconds
|
||||
|
||||
#real units
|
||||
variable sigma equal 7.2 # particle diameter 0.72 nm
|
||||
variable temperature equal 298 # temperature 298 K
|
||||
variable kb index 0.0019872067 # kB in Kcal/mol/K
|
||||
variable epsilon equal ${kb}*${temperature}
|
||||
variable epsilon equal 0.0019872067*${temperature}
|
||||
variable epsilon equal 0.0019872067*298
|
||||
variable tunit equal 2000 # time unit is 2000 fs
|
||||
variable timestep equal 0.005*${tunit}
|
||||
variable timestep equal 0.005*2000
|
||||
|
||||
variable cut_long equal 12.5*${sigma}
|
||||
variable cut_long equal 12.5*7.2
|
||||
variable nevery equal 100
|
||||
variable nmc equal 100
|
||||
variable pH equal 7.0
|
||||
variable pKa equal 6.0
|
||||
variable pIm equal 3.0
|
||||
variable pIp equal 3.0
|
||||
|
||||
variable cut_lj equal 2^(1.0/6.0)*${sigma}
|
||||
variable cut_lj equal 2^(1.0/6.0)*7.2
|
||||
velocity all create ${temperature} 8008 loop geom
|
||||
velocity all create 298 8008 loop geom
|
||||
|
||||
pair_style lj/cut/coul/long ${cut_lj} ${cut_long}
|
||||
pair_style lj/cut/coul/long 8.08172674782749 ${cut_long}
|
||||
pair_style lj/cut/coul/long 8.08172674782749 90
|
||||
pair_coeff * * ${epsilon} ${sigma}
|
||||
pair_coeff * * 0.5921875966 ${sigma}
|
||||
pair_coeff * * 0.5921875966 7.2
|
||||
kspace_style pppm 1.0e-3
|
||||
dielectric 78
|
||||
pair_modify shift yes
|
||||
|
||||
######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ###########
|
||||
fix fnve all nve
|
||||
compute dtemp all temp
|
||||
compute_modify dtemp dynamic yes
|
||||
fix fT all langevin $(v_temperature) $(v_temperature) $(v_tunit) 123
|
||||
fix fT all langevin 298 $(v_temperature) $(v_tunit) 123
|
||||
fix fT all langevin 298 298 $(v_tunit) 123
|
||||
fix fT all langevin 298 298 2000 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 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.1 nevery 100 nmc ${nmc} seed 2345 tempfixid fT
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.1 nevery 100 nmc 100 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 ${timestep}
|
||||
timestep 10
|
||||
run 2000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (../kspace.cpp:339)
|
||||
G vector (1/distance) = 0.019408615
|
||||
grid = 8 8 8
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00012527706
|
||||
estimated relative force accuracy = 3.7726815e-07
|
||||
using double precision KISS FFT
|
||||
3d grid and FFT values/proc = 2197 512
|
||||
0 atoms in group FixChargeRegulation: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 = 93
|
||||
ghost atom cutoff = 93
|
||||
binsize = 46.5, bins = 8 8 8
|
||||
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
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.707 | 3.707 | 3.707 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 -6.4798431 298 0 0 1 99 0 0 109 10
|
||||
100 -6.9219668 306.44177 100 77 15 85 0 0 94 9
|
||||
200 -6.8175255 306.64254 200 164 23 77 0 0 87 10
|
||||
300 -5.2482381 331.67831 300 248 21 79 0 0 85 6
|
||||
400 -7.4531538 285.3495 400 326 17 83 0 0 89 6
|
||||
500 -6.9662528 286.2123 500 408 14 86 0 0 95 9
|
||||
600 -6.528214 291.41762 600 492 14 86 0 0 95 9
|
||||
700 -6.290871 271.50948 700 567 14 86 0 0 96 10
|
||||
800 -6.4944741 300.66261 800 650 23 77 0 0 83 6
|
||||
900 -8.0414672 305.6179 900 731 25 75 0 0 84 9
|
||||
1000 -8.5694583 297.69733 1000 810 25 75 0 0 83 8
|
||||
1100 -8.9364878 292.52429 1100 891 22 78 0 0 88 10
|
||||
1200 -8.733737 316.79814 1200 963 21 79 0 0 88 9
|
||||
1300 -8.0946506 350.85016 1300 1043 21 79 0 0 88 9
|
||||
1400 -7.1835794 283.90836 1400 1128 17 83 0 0 93 10
|
||||
1500 -6.5673667 306.70066 1500 1208 23 77 0 0 87 10
|
||||
1600 -7.0819412 272.07245 1600 1288 21 79 0 0 89 10
|
||||
1700 -5.8907481 301.00694 1700 1365 28 72 0 0 84 12
|
||||
1800 -4.9932405 282.95729 1800 1447 24 76 0 0 82 6
|
||||
1900 -4.3273176 296.96436 1900 1527 22 78 0 0 86 8
|
||||
2000 -4.4859306 299.76741 2000 1600 26 74 0 0 81 7
|
||||
Loop time of 1.15911 on 1 procs for 2000 steps with 188 atoms
|
||||
|
||||
Performance: 1490.798 ns/day, 0.016 hours/ns, 1725.460 timesteps/s
|
||||
99.5% CPU use with 1 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.036171 | 0.036171 | 0.036171 | 0.0 | 3.12
|
||||
Kspace | 0.37716 | 0.37716 | 0.37716 | 0.0 | 32.54
|
||||
Neigh | 0.022399 | 0.022399 | 0.022399 | 0.0 | 1.93
|
||||
Comm | 0.005311 | 0.005311 | 0.005311 | 0.0 | 0.46
|
||||
Output | 0.000745 | 0.000745 | 0.000745 | 0.0 | 0.06
|
||||
Modify | 0.71566 | 0.71566 | 0.71566 | 0.0 | 61.74
|
||||
Other | | 0.001663 | | | 0.14
|
||||
|
||||
Nlocal: 188.000 ave 188 max 188 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 411.000 ave 411 max 411 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1268.00 ave 1268 max 1268 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1268
|
||||
Ave neighs/atom = 6.7446809
|
||||
Neighbor list builds = 2195
|
||||
Dangerous builds = 15
|
||||
Total wall time: 0:00:01
|
||||
@ -0,0 +1,145 @@
|
||||
LAMMPS (10 Feb 2021)
|
||||
# Charge regulation lammps for simple weak electrolyte
|
||||
|
||||
units real
|
||||
atom_style charge
|
||||
neighbor 3.0 bin
|
||||
read_data data.chreg-acid-real
|
||||
Reading data file ...
|
||||
orthogonal box = (-180.00000 -180.00000 -180.00000) to (180.00000 180.00000 180.00000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
219 atoms
|
||||
read_data CPU = 0.002 seconds
|
||||
|
||||
#real units
|
||||
variable sigma equal 7.2 # particle diameter 0.72 nm
|
||||
variable temperature equal 298 # temperature 298 K
|
||||
variable kb index 0.0019872067 # kB in Kcal/mol/K
|
||||
variable epsilon equal ${kb}*${temperature}
|
||||
variable epsilon equal 0.0019872067*${temperature}
|
||||
variable epsilon equal 0.0019872067*298
|
||||
variable tunit equal 2000 # time unit is 2000 fs
|
||||
variable timestep equal 0.005*${tunit}
|
||||
variable timestep equal 0.005*2000
|
||||
|
||||
variable cut_long equal 12.5*${sigma}
|
||||
variable cut_long equal 12.5*7.2
|
||||
variable nevery equal 100
|
||||
variable nmc equal 100
|
||||
variable pH equal 7.0
|
||||
variable pKa equal 6.0
|
||||
variable pIm equal 3.0
|
||||
variable pIp equal 3.0
|
||||
|
||||
variable cut_lj equal 2^(1.0/6.0)*${sigma}
|
||||
variable cut_lj equal 2^(1.0/6.0)*7.2
|
||||
velocity all create ${temperature} 8008 loop geom
|
||||
velocity all create 298 8008 loop geom
|
||||
|
||||
pair_style lj/cut/coul/long ${cut_lj} ${cut_long}
|
||||
pair_style lj/cut/coul/long 8.08172674782749 ${cut_long}
|
||||
pair_style lj/cut/coul/long 8.08172674782749 90
|
||||
pair_coeff * * ${epsilon} ${sigma}
|
||||
pair_coeff * * 0.5921875966 ${sigma}
|
||||
pair_coeff * * 0.5921875966 7.2
|
||||
kspace_style pppm 1.0e-3
|
||||
dielectric 78
|
||||
pair_modify shift yes
|
||||
|
||||
######### VERLET INTEGRATION WITH LANGEVIN THERMOSTAT ###########
|
||||
fix fnve all nve
|
||||
compute dtemp all temp
|
||||
compute_modify dtemp dynamic yes
|
||||
fix fT all langevin $(v_temperature) $(v_temperature) $(v_tunit) 123
|
||||
fix fT all langevin 298 $(v_temperature) $(v_tunit) 123
|
||||
fix fT all langevin 298 298 $(v_tunit) 123
|
||||
fix fT all langevin 298 298 2000 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 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa ${pKa} pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp ${pIp} pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm ${pIm} lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.1 nevery ${nevery} nmc ${nmc} seed 2345 tempfixid fT
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.1 nevery 100 nmc ${nmc} seed 2345 tempfixid fT
|
||||
fix chareg all charge/regulation 2 3 acid_type 1 pH 7 pKa 6 pIp 3 pIm 3 lunit_nm 0.1 nevery 100 nmc 100 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 ${timestep}
|
||||
timestep 10
|
||||
run 2000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (../kspace.cpp:339)
|
||||
G vector (1/distance) = 0.019408615
|
||||
grid = 8 8 8
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.00012527706
|
||||
estimated relative force accuracy = 3.7726815e-07
|
||||
using double precision KISS FFT
|
||||
3d grid and FFT values/proc = 1053 128
|
||||
0 atoms in group FixChargeRegulation: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 = 93
|
||||
ghost atom cutoff = 93
|
||||
binsize = 46.5, bins = 8 8 8
|
||||
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
|
||||
Per MPI rank memory allocation (min/avg/max) = 3.624 | 3.624 | 3.624 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 -6.4798431 298 0 0 1 99 0 0 109 10
|
||||
100 -7.9144028 317.49717 100 73 15 85 0 0 94 9
|
||||
200 -5.9183735 315.31348 200 157 24 76 0 0 86 10
|
||||
300 -6.7851544 295.82718 300 243 21 79 0 0 86 7
|
||||
400 -6.3777493 297.53619 400 316 16 84 0 0 91 7
|
||||
500 -6.0281518 287.62012 500 398 15 85 0 0 93 8
|
||||
600 -8.4403907 301.30302 600 483 14 86 0 0 94 8
|
||||
700 -9.6450828 305.33793 700 563 15 85 0 0 96 11
|
||||
800 -6.1034312 307.18396 800 646 20 80 0 0 85 5
|
||||
900 -7.3098915 295.21039 900 729 24 76 0 0 86 10
|
||||
1000 -6.721795 316.34459 1000 803 25 75 0 0 84 9
|
||||
1100 -7.389073 326.53025 1100 882 23 77 0 0 87 10
|
||||
1200 -9.6721231 327.15878 1200 958 20 80 0 0 89 9
|
||||
1300 -7.4738885 295.09338 1300 1045 20 80 0 0 88 8
|
||||
1400 -7.8136191 297.62074 1400 1127 18 82 0 0 92 10
|
||||
1500 -7.6522652 284.20977 1500 1204 24 76 0 0 85 9
|
||||
1600 -8.473883 293.37704 1600 1283 22 78 0 0 92 14
|
||||
1700 -5.7030629 327.53233 1700 1366 26 74 0 0 83 9
|
||||
1800 -6.1817998 278.22073 1800 1447 21 79 0 0 84 5
|
||||
1900 -5.3113964 293.69193 1900 1526 24 76 0 0 85 9
|
||||
2000 -5.5827334 307.91424 2000 1599 26 74 0 0 80 6
|
||||
Loop time of 0.547632 on 4 procs for 2000 steps with 186 atoms
|
||||
|
||||
Performance: 3155.407 ns/day, 0.008 hours/ns, 3652.091 timesteps/s
|
||||
99.5% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.008417 | 0.01004 | 0.010817 | 1.0 | 1.83
|
||||
Kspace | 0.17103 | 0.17157 | 0.17208 | 0.1 | 31.33
|
||||
Neigh | 0.004536 | 0.0052815 | 0.005857 | 0.7 | 0.96
|
||||
Comm | 0.023141 | 0.02398 | 0.02617 | 0.8 | 4.38
|
||||
Output | 0.000556 | 0.00063325 | 0.000864 | 0.0 | 0.12
|
||||
Modify | 0.33403 | 0.33441 | 0.33471 | 0.1 | 61.07
|
||||
Other | | 0.001711 | | | 0.31
|
||||
|
||||
Nlocal: 46.5000 ave 48 max 44 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
Nghost: 241.500 ave 244 max 238 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 1 1
|
||||
Neighs: 303.750 ave 333 max 286 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 1215
|
||||
Ave neighs/atom = 6.5322581
|
||||
Neighbor list builds = 2196
|
||||
Dangerous builds = 12
|
||||
Total wall time: 0:00:00
|
||||
Reference in New Issue
Block a user