From d81f03706cb8783020c990f6701933036c05e16f Mon Sep 17 00:00:00 2001 From: tc387 Date: Mon, 12 Apr 2021 01:30:36 -0500 Subject: [PATCH] Added an example using real units. --- .../charge_regulation/data.chreg-acid-real | 235 ++++++++++++++++++ .../misc/charge_regulation/in.chreg-acid-real | 44 ++++ .../log.11Apr21.chreg-acid-real.g++.1 | 145 +++++++++++ .../log.11Apr21.chreg-acid-real.g++.4 | 145 +++++++++++ 4 files changed, 569 insertions(+) create mode 100644 examples/USER/misc/charge_regulation/data.chreg-acid-real create mode 100644 examples/USER/misc/charge_regulation/in.chreg-acid-real create mode 100644 examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.1 create mode 100644 examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.4 diff --git a/examples/USER/misc/charge_regulation/data.chreg-acid-real b/examples/USER/misc/charge_regulation/data.chreg-acid-real new file mode 100644 index 0000000000..1f005a155b --- /dev/null +++ b/examples/USER/misc/charge_regulation/data.chreg-acid-real @@ -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 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-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 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-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 \ No newline at end of file diff --git a/examples/USER/misc/charge_regulation/in.chreg-acid-real b/examples/USER/misc/charge_regulation/in.chreg-acid-real new file mode 100644 index 0000000000..195b163d96 --- /dev/null +++ b/examples/USER/misc/charge_regulation/in.chreg-acid-real @@ -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 diff --git a/examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.1 b/examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.1 new file mode 100644 index 0000000000..3b766d662d --- /dev/null +++ b/examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.1 @@ -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 diff --git a/examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.4 b/examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.4 new file mode 100644 index 0000000000..7ab22c1f36 --- /dev/null +++ b/examples/USER/misc/charge_regulation/log.11Apr21.chreg-acid-real.g++.4 @@ -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