From 81293b0fdab4fa032f37dec8fbd66cb5eced237a Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Sat, 5 May 2018 10:21:11 -0400
Subject: [PATCH] changes to integrate USER-BOCS into LAMMPS and to closer
follow the LAMMPS programming/documentation style
---
doc/src/Section_packages.txt | 38 +
{src/USER-BOCS/doc => doc/src}/fix_bocs.txt | 4 +
doc/src/fixes.txt | 1 +
doc/src/lammps.book | 1 +
.../USER/bocs/{methanol.lmp => in.methanol} | 0
src/Makefile | 2 +-
src/USER-BOCS/README | 14 +-
src/USER-BOCS/bocs/README | 6 -
src/USER-BOCS/bocs/lammps_nb_MET-MET.table | 2505 -----------------
src/USER-BOCS/bocs/methanol.data | 991 -------
src/USER-BOCS/bocs/methanol.lmp | 69 -
src/USER-BOCS/compute_pressure_bocs.cpp | 106 +-
src/USER-BOCS/compute_pressure_bocs.h | 19 +-
src/USER-BOCS/fix_bocs.cpp | 141 +-
src/USER-BOCS/fix_bocs.h | 59 +-
15 files changed, 201 insertions(+), 3755 deletions(-)
rename {src/USER-BOCS/doc => doc/src}/fix_bocs.txt (95%)
rename examples/USER/bocs/{methanol.lmp => in.methanol} (100%)
delete mode 100644 src/USER-BOCS/bocs/README
delete mode 100644 src/USER-BOCS/bocs/lammps_nb_MET-MET.table
delete mode 100644 src/USER-BOCS/bocs/methanol.data
delete mode 100644 src/USER-BOCS/bocs/methanol.lmp
diff --git a/doc/src/Section_packages.txt b/doc/src/Section_packages.txt
index ade75c588f..e9387fe35f 100644
--- a/doc/src/Section_packages.txt
+++ b/doc/src/Section_packages.txt
@@ -122,6 +122,7 @@ Package, Description, Doc page, Example, Library
Package, Description, Doc page, Example, Library
"USER-ATC"_#USER-ATC, atom-to-continuum coupling, "fix atc"_fix_atc.html, USER/atc, int
"USER-AWPMD"_#USER-AWPMD, wave-packet MD, "pair_style awpmd/cut"_pair_awpmd.html, USER/awpmd, int
+"USER-BOCS"_#USER-BOCS, BOCS bottom up coarse graining, "fix bocs"_fix_bocs.html, USER/bocs, -
"USER-CGDNA"_#USER-CGDNA, coarse-grained DNA force fields, src/USER-CGDNA/README, USER/cgdna, -
"USER-CGSDK"_#USER-CGSDK, SDK coarse-graining model, "pair_style lj/sdk"_pair_sdk.html, USER/cgsdk, -
"USER-COLVARS"_#USER-COLVARS, collective variables library, "fix colvars"_fix_colvars.html, USER/colvars, int
@@ -1625,6 +1626,43 @@ examples/USER/awpmd :ul
:line
+USER-BOCS package :link(USER-BOCS),h4
+
+[Contents:]
+
+This package provides "fix bocs"_fix_bocs.html, a modified version
+of "fix npt"_fix_nh.html which includes the pressure correction to
+the barostat as outlined in:
+
+N. J. H. Dunn and W. G. Noid, "Bottom-up coarse-grained models that
+accurately describe the structure, pressure, and compressibility of
+molecular liquids," J. Chem. Phys. 143, 243148 (2015).
+
+[Authors:] Nicholas J. H. Dunn and Michael R. DeLyser (The Pennsylvania State University)
+
+[Install or un-install:]
+
+make yes-user-bocs
+make machine :pre
+
+make no-user-bocs
+make machine :pre
+
+[Supporting info:]
+
+The USER-BOCS user package for LAMMPS is part of the BOCS software package:
+"https://github.com/noid-group/BOCS"_https://github.com/noid-group/BOCS
+
+See the following reference for information about the entire package:
+
+Dunn, NJH; Lebold, KM; DeLyser, MR; Rudzinski, JF; Noid, WG.
+"BOCS: Bottom-Up Open-Source Coarse-Graining Software."
+J. Phys. Chem. B. 122, 13, 3363-3377 (2018).
+
+Example inputs are in the examples/USER/bocs folder.
+
+:line
+
USER-CGDNA package :link(USER-CGDNA),h4
[Contents:]
diff --git a/src/USER-BOCS/doc/fix_bocs.txt b/doc/src/fix_bocs.txt
similarity index 95%
rename from src/USER-BOCS/doc/fix_bocs.txt
rename to doc/src/fix_bocs.txt
index 8824893d65..f53b7c785c 100644
--- a/src/USER-BOCS/doc/fix_bocs.txt
+++ b/doc/src/fix_bocs.txt
@@ -84,6 +84,10 @@ the examples. For the last argument in the command, you should put
XXXX_press, where XXXX is the ID given to the fix bocs command (in the
example, the ID of the fix bocs command is 1 ).
+This fix is part of the USER-BOCS package. It is only enabled if
+LAMMPS was built with that package. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info.
+
[Related:]
For more details about the pressure correction and the entire BOCS software
diff --git a/doc/src/fixes.txt b/doc/src/fixes.txt
index c3fcc06bf1..8384270085 100644
--- a/doc/src/fixes.txt
+++ b/doc/src/fixes.txt
@@ -20,6 +20,7 @@ Fixes :h1
fix_ave_time
fix_aveforce
fix_balance
+ fix_bocs
fix_bond_break
fix_bond_create
fix_bond_swap
diff --git a/doc/src/lammps.book b/doc/src/lammps.book
index ec34f41872..0fd2156084 100644
--- a/doc/src/lammps.book
+++ b/doc/src/lammps.book
@@ -135,6 +135,7 @@ fix_ave_histo.html
fix_ave_time.html
fix_aveforce.html
fix_balance.html
+fix_bocs.html
fix_bond_break.html
fix_bond_create.html
fix_bond_swap.html
diff --git a/examples/USER/bocs/methanol.lmp b/examples/USER/bocs/in.methanol
similarity index 100%
rename from examples/USER/bocs/methanol.lmp
rename to examples/USER/bocs/in.methanol
diff --git a/src/Makefile b/src/Makefile
index 03f4072132..55e6326954 100644
--- a/src/Makefile
+++ b/src/Makefile
@@ -57,7 +57,7 @@ PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \
molecule mpiio mscg opt peri poems \
python qeq reax replica rigid shock snap srd voronoi
-PACKUSER = user-atc user-awpmd user-cgdna user-cgsdk user-colvars \
+PACKUSER = user-atc user-awpmd user-bocs user-cgdna user-cgsdk user-colvars \
user-diffraction user-dpd user-drude user-eff user-fep user-h5md \
user-intel user-lb user-manifold user-meamc user-meso \
user-mgpt user-misc user-molfile \
diff --git a/src/USER-BOCS/README b/src/USER-BOCS/README
index 001cb94d55..adeb34c387 100644
--- a/src/USER-BOCS/README
+++ b/src/USER-BOCS/README
@@ -16,16 +16,4 @@ Dunn, NJH; Lebold, KM; DeLyser, MR; Rudzinski, JF; Noid, WG.
"BOCS: Bottom-Up Open-Source Coarse-Graining Software."
J. Phys. Chem. B. 122, 13, 3363-3377 (2018).
-Along with the source code files, the following files have been included
- (in the /bocs/ directory):
-methanol.lmp
-methanol.data
-lammps_nb_MET-MET.table
-
-methanol.lmp is the input file for LAMMPS.
-methanol.data contains the positions of 968 CG methanol molecules. It is
- read in by methanol.lmp
-lammps_nb_MET-MET.table contains the pairwise nonbonded force calculated
- via the Multi-Scale Coarse-Graining method.
-
-
+Example inputs are in the examples/USER/bocs folder.
diff --git a/src/USER-BOCS/bocs/README b/src/USER-BOCS/bocs/README
deleted file mode 100644
index ae1739f8c0..0000000000
--- a/src/USER-BOCS/bocs/README
+++ /dev/null
@@ -1,6 +0,0 @@
-This folder contains the files to run a NPT simulation of 1 site CG methanol
-while employing a correction to the barostat.
-The pair force was computed via the Multi-Scale Coarse-Graining method.
-The resulting model was then iteratively pressure matched.
-The model accurately reproduces both structural (RDF) and thermodynamic
-(Pressure-Volume EoS) properties of the underlying OPLS-AA model of methanol.
diff --git a/src/USER-BOCS/bocs/lammps_nb_MET-MET.table b/src/USER-BOCS/bocs/lammps_nb_MET-MET.table
deleted file mode 100644
index c6d9fc6ca2..0000000000
--- a/src/USER-BOCS/bocs/lammps_nb_MET-MET.table
+++ /dev/null
@@ -1,2505 +0,0 @@
-#Converted from table.xvg
-
-nb_METMET
-N 2500
-
-1 0.010000 573.151769 380.122371
-2 0.020000 569.356836 378.855163
-3 0.030000 565.574570 377.588193
-4 0.040000 561.805210 376.320985
-5 0.050000 558.048279 375.053776
-6 0.060000 554.304015 373.786807
-7 0.070000 550.572419 372.519598
-8 0.080000 546.853728 371.252390
-9 0.090000 543.147467 369.985421
-10 0.100000 539.453872 368.718212
-11 0.110000 535.773184 367.451004
-12 0.120000 532.104924 366.184034
-13 0.130000 528.449331 364.916826
-14 0.140000 524.806644 363.649618
-15 0.150000 521.176386 362.382648
-16 0.160000 517.559034 361.115440
-17 0.170000 513.954111 359.848231
-18 0.180000 510.361855 358.581262
-19 0.190000 506.782505 357.314054
-20 0.200000 503.215583 356.046845
-21 0.210000 499.661568 354.779876
-22 0.220000 496.119981 353.512667
-23 0.230000 492.591300 352.245459
-24 0.240000 489.075287 350.978489
-25 0.250000 485.571702 349.711281
-26 0.260000 482.081023 348.444073
-27 0.270000 478.602772 347.177103
-28 0.280000 475.137428 345.909895
-29 0.290000 471.684751 344.642686
-30 0.300000 468.244503 343.375717
-31 0.310000 464.817161 342.108509
-32 0.320000 461.402486 340.841300
-33 0.330000 458.000239 339.574331
-34 0.340000 454.610899 338.307122
-35 0.350000 451.234226 337.039914
-36 0.360000 447.870220 335.772945
-37 0.370000 444.518642 334.505736
-38 0.380000 441.179971 333.238528
-39 0.390000 437.853967 331.971558
-40 0.400000 434.540631 330.704350
-41 0.410000 431.239962 329.437141
-42 0.420000 427.951721 328.170172
-43 0.430000 424.676386 326.902964
-44 0.440000 421.413719 325.635755
-45 0.450000 418.163719 324.368786
-46 0.460000 414.926386 323.101577
-47 0.470000 411.701721 321.834369
-48 0.480000 408.489723 320.567400
-49 0.490000 405.290392 319.300191
-50 0.500000 402.103728 318.032983
-51 0.510000 398.929732 316.766013
-52 0.520000 395.768403 315.498805
-53 0.530000 392.619742 314.231597
-54 0.540000 389.483748 312.964627
-55 0.550000 386.360421 311.697419
-56 0.560000 383.249761 310.430210
-57 0.570000 380.151769 309.163241
-58 0.580000 377.066444 307.896033
-59 0.590000 373.993786 306.628824
-60 0.600000 370.934034 305.361855
-61 0.610000 367.886711 304.094646
-62 0.620000 364.852055 302.827438
-63 0.630000 361.830067 301.560468
-64 0.640000 358.820746 300.293260
-65 0.650000 355.824331 299.026052
-66 0.660000 352.840344 297.759082
-67 0.670000 349.869025 296.491874
-68 0.680000 346.910373 295.224904
-69 0.690000 343.964627 293.957696
-70 0.700000 341.031310 292.690488
-71 0.710000 338.110660 291.423518
-72 0.720000 335.202916 290.156310
-73 0.730000 332.307600 288.889101
-74 0.740000 329.425191 287.622132
-75 0.750000 326.555210 286.354924
-76 0.760000 323.697897 285.087715
-77 0.770000 320.853489 283.820746
-78 0.780000 318.021511 282.553537
-79 0.790000 315.202438 281.286329
-80 0.800000 312.395793 280.019359
-81 0.810000 309.602055 278.752151
-82 0.820000 306.820746 277.484943
-83 0.830000 304.052342 276.217973
-84 0.840000 301.296367 274.950765
-85 0.850000 298.553298 273.683556
-86 0.860000 295.822658 272.416587
-87 0.870000 293.104924 271.149379
-88 0.880000 290.399857 269.882170
-89 0.890000 287.707218 268.615201
-90 0.900000 285.027486 267.347992
-91 0.910000 282.360421 266.080784
-92 0.920000 279.705784 264.813815
-93 0.930000 277.064054 263.546606
-94 0.940000 274.434990 262.279398
-95 0.950000 271.818356 261.012428
-96 0.960000 269.214627 259.745220
-97 0.970000 266.623566 258.478011
-98 0.980000 264.045172 257.211042
-99 0.990000 261.479446 255.943834
-100 1.000000 258.926147 254.676625
-101 1.010000 256.385755 253.409656
-102 1.020000 253.858031 252.142447
-103 1.030000 251.342973 250.875239
-104 1.040000 248.840583 249.608270
-105 1.050000 246.350860 248.341061
-106 1.060000 243.873805 247.073853
-107 1.070000 241.409417 245.806883
-108 1.080000 238.957600 244.539675
-109 1.090000 236.518523 243.272467
-110 1.100000 234.092137 242.005497
-111 1.110000 231.678418 240.738289
-112 1.120000 229.277366 239.471080
-113 1.130000 226.889006 238.204039
-114 1.140000 224.513289 236.936926
-115 1.150000 222.150263 235.669790
-116 1.160000 219.799904 234.402653
-117 1.170000 217.462213 233.135540
-118 1.180000 215.137189 231.868403
-119 1.190000 212.824833 230.601267
-120 1.200000 210.525167 229.334154
-121 1.210000 208.238145 228.067017
-122 1.220000 205.963815 226.799904
-123 1.230000 203.702151 225.532768
-124 1.240000 201.453155 224.265631
-125 1.250000 199.216850 222.998518
-126 1.260000 196.993188 221.731381
-127 1.270000 194.782218 220.464269
-128 1.280000 192.583915 219.197132
-129 1.290000 190.398279 217.929995
-130 1.300000 188.225311 216.662882
-131 1.310000 186.065010 215.395746
-132 1.320000 183.917400 214.128609
-133 1.330000 181.782433 212.861496
-134 1.340000 179.660158 211.594359
-135 1.350000 177.550550 210.327247
-136 1.360000 175.453609 209.060110
-137 1.370000 173.369359 207.792973
-138 1.380000 171.297753 206.525860
-139 1.390000 169.238838 205.258724
-140 1.400000 167.192591 203.991587
-141 1.410000 165.159011 202.724474
-142 1.420000 163.138098 201.457337
-143 1.430000 161.129852 200.190225
-144 1.440000 159.134297 198.923088
-145 1.450000 157.151386 197.655951
-146 1.460000 155.181166 196.388838
-147 1.470000 153.223614 195.121702
-148 1.480000 151.278728 193.854565
-149 1.490000 149.346534 192.587452
-150 1.500000 147.426984 191.320315
-151 1.510000 145.520124 190.053203
-152 1.520000 143.625932 188.786066
-153 1.530000 141.744407 187.518929
-154 1.540000 139.875550 186.251816
-155 1.550000 138.019359 184.984680
-156 1.560000 136.175860 183.717567
-157 1.570000 134.345005 182.450430
-158 1.580000 132.526840 181.183293
-159 1.590000 130.721343 179.916181
-160 1.600000 128.928513 178.649044
-161 1.610000 127.148375 177.381907
-162 1.620000 125.380880 176.114794
-163 1.630000 123.626076 174.847658
-164 1.640000 121.883939 173.580545
-165 1.650000 120.154469 172.313408
-166 1.660000 118.437667 171.046272
-167 1.670000 116.733533 169.779159
-168 1.680000 115.042089 168.512022
-169 1.690000 113.363289 167.244885
-170 1.700000 111.697180 165.977772
-171 1.710000 110.043738 164.710636
-172 1.720000 108.402964 163.443523
-173 1.730000 106.774857 162.176386
-174 1.740000 105.159441 160.909250
-175 1.750000 103.556692 159.642137
-176 1.760000 101.966587 158.375000
-177 1.770000 100.389173 157.107887
-178 1.780000 98.824450 155.840750
-179 1.790000 97.272371 154.573614
-180 1.800000 95.732959 153.306501
-181 1.810000 94.206238 152.039364
-182 1.820000 92.692185 150.772228
-183 1.830000 91.190798 149.505115
-184 1.840000 89.702079 148.237978
-185 1.850000 88.226028 146.970865
-186 1.860000 86.762667 145.703728
-187 1.870000 85.311950 144.436592
-188 1.880000 83.873924 143.169479
-189 1.890000 82.448566 141.902342
-190 1.900000 81.035875 140.635206
-191 1.910000 79.635875 139.368093
-192 1.920000 78.248518 138.100956
-193 1.930000 76.873853 136.833843
-194 1.940000 75.511831 135.566707
-195 1.950000 74.162500 134.299570
-196 1.960000 72.825860 133.032457
-197 1.970000 71.501864 131.765320
-198 1.980000 70.190535 130.498184
-199 1.990000 68.891898 129.231071
-200 2.000000 67.605927 127.963934
-201 2.010000 66.332624 126.696821
-202 2.020000 65.071989 125.429685
-203 2.030000 63.824020 124.162548
-204 2.040000 62.588743 122.895435
-205 2.050000 61.366109 121.628298
-206 2.060000 60.156166 120.361185
-207 2.070000 58.958891 119.094049
-208 2.080000 57.774283 117.826912
-209 2.090000 56.602366 116.559799
-210 2.100000 55.443093 115.292663
-211 2.110000 54.296511 114.025526
-212 2.120000 53.162572 112.758413
-213 2.130000 52.041324 111.491276
-214 2.140000 50.932768 110.224163
-215 2.150000 49.836855 108.957027
-216 2.160000 48.753609 107.689890
-217 2.170000 47.683054 106.422777
-218 2.180000 46.625167 105.155641
-219 2.190000 45.579947 103.888504
-220 2.200000 44.547395 102.621391
-221 2.210000 43.527510 101.354254
-222 2.220000 42.520315 100.087141
-223 2.230000 41.525765 98.820005
-224 2.240000 40.543905 97.552868
-225 2.250000 39.574713 96.285755
-226 2.260000 38.618188 95.018619
-227 2.270000 37.674331 93.751506
-228 2.280000 36.743164 92.484369
-229 2.290000 35.824641 91.217232
-230 2.300000 34.918810 89.950120
-231 2.310000 34.025645 88.682983
-232 2.320000 33.145148 87.415846
-233 2.330000 32.277342 86.148733
-234 2.340000 31.422180 84.881597
-235 2.350000 30.579708 83.614484
-236 2.360000 29.749880 82.347347
-237 2.370000 28.932744 81.080210
-238 2.380000 28.128298 79.813098
-239 2.390000 27.336496 78.545961
-240 2.400000 26.557361 77.278824
-241 2.410000 25.790918 76.011711
-242 2.420000 25.037141 74.744575
-243 2.430000 24.296033 73.477462
-244 2.440000 23.567584 72.210325
-245 2.450000 22.851816 70.943188
-246 2.460000 22.148721 69.676076
-247 2.470000 21.458296 68.408939
-248 2.480000 20.780543 67.141802
-249 2.490000 20.115459 65.874689
-250 2.500000 19.463047 64.607553
-251 2.510000 18.823308 63.340440
-252 2.520000 18.196240 62.073303
-253 2.530000 17.581843 60.806166
-254 2.540000 16.980117 59.539054
-255 2.550000 16.391061 58.271917
-256 2.560000 15.814677 57.004804
-257 2.570000 15.250966 55.737667
-258 2.580000 14.699924 54.470531
-259 2.590000 14.161554 53.203418
-260 2.600000 13.635856 51.936281
-261 2.610000 13.122830 50.669144
-262 2.620000 12.622474 49.402032
-263 2.630000 12.134787 48.134895
-264 2.640000 11.659775 46.867782
-265 2.650000 11.197433 45.600645
-266 2.660000 10.747763 44.333509
-267 2.670000 10.310762 43.066396
-268 2.680000 9.886434 41.799259
-269 2.690000 9.474778 40.532122
-270 2.700000 9.075791 39.265010
-271 2.710000 8.689477 37.997873
-272 2.720000 8.315834 36.730760
-273 2.730000 7.954861 35.463623
-274 2.740000 7.606561 34.196487
-275 2.750000 7.270932 32.927892
-276 2.760000 6.948004 31.654852
-277 2.770000 6.637835 30.377510
-278 2.780000 6.340454 29.101769
-279 2.790000 6.055801 27.837620
-280 2.800000 5.783702 26.597945
-281 2.810000 5.523841 25.396726
-282 2.820000 5.275767 24.244336
-283 2.830000 5.038956 23.144804
-284 2.840000 4.812870 22.097438
-285 2.850000 4.597005 21.099622
-286 2.860000 4.390880 20.148458
-287 2.870000 4.194037 19.241052
-288 2.880000 4.006056 18.374520
-289 2.890000 3.826546 17.546083
-290 2.900000 3.655136 16.753186
-291 2.910000 3.491482 15.993602
-292 2.920000 3.335263 15.265425
-293 2.930000 3.186174 14.567077
-294 2.940000 3.043922 13.897208
-295 2.950000 2.908229 13.254567
-296 2.960000 2.778831 12.637918
-297 2.970000 2.655471 12.046023
-298 2.980000 2.537911 11.477648
-299 2.990000 2.425918 10.931613
-300 3.000000 2.319278 10.406840
-301 3.010000 2.217782 9.902409
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diff --git a/src/USER-BOCS/bocs/methanol.data b/src/USER-BOCS/bocs/methanol.data
deleted file mode 100644
index 01f66de6f6..0000000000
--- a/src/USER-BOCS/bocs/methanol.data
+++ /dev/null
@@ -1,991 +0,0 @@
-LAMMPS Description
-
- 968 atoms
- 0 bonds
- 0 angles
- 0 dihedrals
- 0 impropers
-
- 1 atom types
- 0 bond types
- 0 angle types
- 0 dihedral types
-
- 0 40.4635 xlo xhi
- 0 40.4635 ylo yhi
- 0 40.4635 zlo zhi
-
-Masses
-
- 1 32.0424
-
-Atoms
-
-1 1 36.39 8.05 27.55
-2 1 18.38 15.72 26.03
-3 1 3.52 1.77 23.57
-4 1 31.09 11.38 12.17
-5 1 13.3 34.8 2.89
-6 1 1.72 38.55 10.36
-7 1 38.6 23.16 6.19
-8 1 0.74 33.21 0.17
-9 1 26.97 9.53 11.24
-10 1 31.68 12.19 17.04
-11 1 15.19 9.06 0.2
-12 1 34.39 20.63 35.71
-13 1 21.79 4.93 6.49
-14 1 28.08 33.01 24.51
-15 1 37.03 20.52 32.9
-16 1 32.69 20 30.11
-17 1 23.77 38.59 18.79
-18 1 16.01 2.31 20.15
-19 1 5.65 15.5 28.5
-20 1 8.35 17.35 20.48
-21 1 31.24 24.68 27.4
-22 1 29.41 16.64 19.79
-23 1 37.42 31.93 26.68
-24 1 18.76 39.06 30.68
-25 1 22.97 35 20.81
-26 1 39.47 18.28 29.6
-27 1 34.37 19.4 0.17
-28 1 5.94 9.53 10.95
-29 1 11.45 38.44 14.64
-30 1 39.57 11.04 1.57
-31 1 25.91 20.97 12.79
-32 1 36.3 22.1 1.68
-33 1 21.87 22.49 3.43
-34 1 5.77 18.66 3.97
-35 1 7 7.59 18.42
-36 1 39.76 27.63 17.98
-37 1 10.26 23.18 5.11
-38 1 23.23 21.37 17.38
-39 1 7.47 37.37 5.57
-40 1 0.73 21.6 14.78
-41 1 2.27 30.22 14.93
-42 1 7.39 28.22 14.88
-43 1 27.48 1.11 25.02
-44 1 8.37 13.19 14.64
-45 1 7.11 33.57 0.65
-46 1 34.19 35.11 3.17
-47 1 7.52 3.2 20.33
-48 1 1.02 17.69 37.85
-49 1 8.59 6.21 10.26
-50 1 2.89 16.81 30.02
-51 1 27.05 9.07 32.8
-52 1 12.32 14.79 21.11
-53 1 26.63 22.69 16.75
-54 1 31.6 2.79 20.45
-55 1 35.11 0.74 12.16
-56 1 29.71 31.23 37.63
-57 1 38.22 19.02 18.12
-58 1 10.95 17.4 0.39
-59 1 1.65 19.87 6.67
-60 1 5.15 1.94 14.61
-61 1 8.2 31.43 15.72
-62 1 0.55 20.85 2.45
-63 1 15.27 31.74 0.33
-64 1 17.9 9.84 23.87
-65 1 1.46 8.39 19.24
-66 1 37.79 25.11 12.24
-67 1 14.11 27.19 30.7
-68 1 29.39 24.12 38.92
-69 1 39.15 20.32 39.86
-70 1 11.79 11.38 30.6
-71 1 29.87 30.18 32.5
-72 1 11.06 37.8 30.18
-73 1 20.11 4.59 35.57
-74 1 37.19 27.23 1.44
-75 1 18.83 26.13 35.26
-76 1 29.27 7.86 36.75
-77 1 34.83 29.59 37.82
-78 1 22.16 34.68 25.27
-79 1 5.95 14.65 25.55
-80 1 -0.04 3.48 29.91
-81 1 14.69 6.75 38.06
-82 1 16.8 23.69 3.14
-83 1 14.52 38.72 21.61
-84 1 37.36 15.13 27.98
-85 1 29.79 17.03 27.55
-86 1 21.01 0.39 0.9
-87 1 35.3 6.45 14.41
-88 1 13.74 34.69 10.01
-89 1 13.83 7.92 31.88
-90 1 26.88 37.81 22.36
-91 1 31.76 7.34 10.03
-92 1 11.98 37.49 19.61
-93 1 29.19 31.74 20.69
-94 1 39.15 10.97 21.06
-95 1 1.47 5 22.21
-96 1 -0.1 1.33 16.26
-97 1 34.74 34.78 30.66
-98 1 22.09 26.78 2.27
-99 1 36.58 34.8 16.19
-100 1 19.09 24.88 15.75
-101 1 2.21 31.42 38.32
-102 1 28.02 8.18 29.77
-103 1 15.99 16.78 17.61
-104 1 32.43 12.2 35.3
-105 1 26.54 38.8 30.88
-106 1 35.58 22.23 18.31
-107 1 28.3 30.81 2.96
-108 1 8.95 32.9 9.02
-109 1 28.51 30.02 29.39
-110 1 13 5.35 34.26
-111 1 37.9 36.79 1.37
-112 1 12.78 1.99 40.66
-113 1 21.19 34.55 17.45
-114 1 10.5 20 5.07
-115 1 16.19 21.64 18.49
-116 1 14.62 26.41 19.88
-117 1 27.97 2.89 28.03
-118 1 29.44 14.35 39.04
-119 1 2.29 24.16 33.8
-120 1 39.22 15.81 32.02
-121 1 7.31 19.66 18.18
-122 1 27.67 7.98 15.53
-123 1 31.23 4.04 33
-124 1 29.52 39.44 28.71
-125 1 30.86 20.28 15.84
-126 1 32.25 7.44 19.79
-127 1 34.68 15.68 1.18
-128 1 16.58 27.98 27.97
-129 1 32.27 24.24 15.82
-130 1 3.86 6.57 39.8
-131 1 9.1 2.88 13.12
-132 1 17.84 27.8 11.79
-133 1 4.77 10.88 6.75
-134 1 16.58 24.21 24.5
-135 1 10.17 19.31 38.32
-136 1 6.27 7.81 36.44
-137 1 34.76 37.89 29.76
-138 1 40.99 38.22 35.21
-139 1 25.04 21.79 36.88
-140 1 4.78 15.35 16.44
-141 1 19.24 5.77 40.18
-142 1 13.59 11.27 37.14
-143 1 1.61 23.83 39.61
-144 1 6.02 33.07 3.77
-145 1 0.85 7.4 35.42
-146 1 6.47 40.34 4.65
-147 1 16.45 36.52 15.44
-148 1 19.58 9.5 1.64
-149 1 1.36 1.72 35.53
-150 1 11.74 5.48 4.98
-151 1 25.45 40.36 15.44
-152 1 19.09 0.74 36.18
-153 1 31.78 37.98 1.84
-154 1 23.26 18.47 38.56
-155 1 7.29 22.87 25.86
-156 1 2.36 7.83 8.78
-157 1 39.61 25.94 21.12
-158 1 7.78 18.97 25.29
-159 1 36.56 19.61 26.7
-160 1 4.64 12.06 19.9
-161 1 21.05 33.08 0.87
-162 1 33.93 22.87 39.71
-163 1 33.62 29.48 20.83
-164 1 0.64 18.79 9.52
-165 1 27.53 16.7 22.51
-166 1 17.66 9.84 14.61
-167 1 31.23 22.44 24.98
-168 1 39.3 34.88 11.03
-169 1 24.01 10.56 0.09
-170 1 15.81 33.44 18.52
-171 1 19.92 30.61 19.25
-172 1 16.49 3.95 38.28
-173 1 18.6 38.87 24.98
-174 1 33.04 25.55 8.57
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-176 1 15.18 6.74 2.33
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-179 1 33.52 38.19 14.89
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-181 1 19.49 29.03 2.52
-182 1 26.97 18.55 38.45
-183 1 24.1 11.86 17.22
-184 1 12.02 0.55 10.39
-185 1 3.8 35.94 19.94
-186 1 8.31 14.31 37.4
-187 1 29.03 8.28 22.92
-188 1 18.92 0.22 27.87
-189 1 26.79 24.9 24.62
-190 1 36.59 18.86 21.13
-191 1 33.06 13.58 30.17
-192 1 32.37 2.02 39.69
-193 1 22.65 25.97 32.59
-194 1 21.81 38.04 33.85
-195 1 36.82 37.68 19.22
-196 1 32.48 31.43 33.66
-197 1 8.75 36.66 20.34
-198 1 14.88 15.11 28.76
-199 1 22.83 28.55 29.5
-200 1 2.98 12.06 2.88
-201 1 3.01 37 6.91
-202 1 14.79 16.69 3.66
-203 1 12.62 38.28 0.97
-204 1 40.07 21.27 25.25
-205 1 34.58 6.14 39.48
-206 1 11.51 30.52 33.53
-207 1 32.22 9.28 30.52
-208 1 0.7 4.01 38.87
-209 1 32.66 39.86 36.84
-210 1 27.34 34.57 21.76
-211 1 13.7 23.12 8.34
-212 1 28 9.71 6.29
-213 1 31.69 26.39 38.19
-214 1 2.04 20.93 36.95
-215 1 30.31 26.61 12.31
-216 1 25.37 20.63 9.4
-217 1 16.29 5.62 14.04
-218 1 1.36 1.95 4.97
-219 1 38.75 26.8 5.62
-220 1 40.28 29.89 12.27
-221 1 0.52 31.22 7.58
-222 1 15.64 21.64 14.71
-223 1 10.11 28.8 9.67
-224 1 19.03 37.3 38.87
-225 1 12.07 6.46 19.25
-226 1 36.22 21.11 15.02
-227 1 12.49 15.69 7.21
-228 1 25.2 30.8 19.71
-229 1 8.24 35.22 23.02
-230 1 9.94 4.1 1.86
-231 1 4.31 19.07 26.23
-232 1 22.03 19.99 14.19
-233 1 30.84 5.24 2.75
-234 1 35.51 30.52 32.3
-235 1 3.88 20.41 39.48
-236 1 30.86 0.39 31.56
-237 1 25.91 27.12 39.04
-238 1 33.39 5.37 4.51
-239 1 20.58 28.33 37.53
-240 1 11.83 21.81 39.11
-241 1 39.94 5.2 5.73
-242 1 29.89 33.21 15.44
-243 1 23.42 15.38 30.98
-244 1 28.66 11.56 16.13
-245 1 16.74 20.43 21.72
-246 1 9.31 0.26 22.42
-247 1 4.38 37.78 14.12
-248 1 13.86 4.65 16.99
-249 1 6.72 27.43 8.14
-250 1 33.45 18.74 19.98
-251 1 17.34 14.55 35.57
-252 1 14.21 37.39 28.76
-253 1 26.29 29.06 22.26
-254 1 36.52 26.18 15.62
-255 1 17.6 8.81 10.14
-256 1 21.95 25.19 17.69
-257 1 17.4 7.46 18.59
-258 1 6.15 29.7 35.99
-259 1 9.73 37.39 24.96
-260 1 28.58 28.21 36.19
-261 1 8.24 13.72 32.2
-262 1 13.25 34.6 22.71
-263 1 38.58 7.98 10.3
-264 1 18.29 29.75 23.51
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-268 1 33.88 26.44 1.96
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-271 1 23.63 8.41 10.95
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-280 1 15.58 37.85 34.06
-281 1 25.93 38.17 3.13
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-296 1 0.32 9.28 39.74
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-319 1 29.02 19.27 6.45
-320 1 19.09 36.35 19.84
-321 1 23.13 6.75 19.78
-322 1 8.02 34.1 26.95
-323 1 26.03 14.18 1.57
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-333 1 27.69 7.32 25.74
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-957 1 14.66 -0.14 5
-958 1 14.96 8.38 20.32
-959 1 1.89 23.03 10.1
-960 1 33.01 11.23 39.32
-961 1 32.68 6.79 32.04
-962 1 6.25 25.81 3.82
-963 1 18.37 31.97 14.57
-964 1 9.74 30.21 22.71
-965 1 3.09 1.52 19.38
-966 1 33.98 37.34 5.63
-967 1 32.19 28.35 15.8
-968 1 24.4 15.49 19.39
diff --git a/src/USER-BOCS/bocs/methanol.lmp b/src/USER-BOCS/bocs/methanol.lmp
deleted file mode 100644
index cb0a9420f0..0000000000
--- a/src/USER-BOCS/bocs/methanol.lmp
+++ /dev/null
@@ -1,69 +0,0 @@
-units real
-dimension 3
-boundary p p p
-atom_style atomic
-
-newton on
-timestep 1.0
-
-read_data methanol.data
-
-velocity all create 300.0 16802 dist gaussian
-
-pair_style table spline 15000
-
-pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0
-
-neigh_modify delay 0 every 1 check yes one 10000
-neighbor 12.0 bin
-
-thermo 500
-thermo_style custom step temp pe etotal press vol
-
-variable STEP equal step
-variable TEMP equal temp
-## volume from cubic angstroms to cubic nm
-variable VOL equal vol/1000.0
-## pressure from atm to bar
-variable PRESS equal press*1.01325
-variable PXX equal pxx*1.01325
-variable PYY equal pyy*1.01325
-variable PZZ equal pzz*1.01325
-variable PXY equal pxy*1.01325
-variable PXZ equal pxz*1.01325
-variable PYZ equal pyz*1.01325
-## energy from kcal/mol to kJ/mol
-variable KE equal ke*4.184
-variable PE equal pe*4.184
-variable UVDW equal evdwl*4.184
-
-
-##### SPECIAL COMMANDS FOR FIX_BOCS #####
-# ID group-ID style_name thermostat T_init T_end T_couple barostat P_start P_end P_couple pmatch_basis avg_vol N_sites N_coeffs coeff1 coeff2
-fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20
-
-# Report the modified pressure
-thermo_modify press 1_press
-
-
-
-## Save some data from simulation to files
-fix print_temp all print 500 "${STEP} ${TEMP}" file temp.dat screen no
-fix print_vol all print 500 "${STEP} ${VOL}" file vol.dat screen no
-fix print_press all print 500 "${STEP} ${PRESS}" file press.dat screen no
-fix print_ke all print 500 "${STEP} ${KE}" file kinetic_E.dat screen no
-fix print_pe all print 500 "${STEP} ${PE}" file potential_E.dat screen no
-fix print_ve all print 500 "${STEP} ${UVDW}" file vdw_E.dat screen no
-fix print_press_tens all print 500 "${STEP} ${PXX} ${PYY} ${PZZ} ${PXY} ${PXZ} ${PYZ}" file press_tens.dat screen no
-fix print_PV_eos all print 500 "${VOL} ${PRESS}" file pv_eos.dat screen no
-
-## Prints a configuration to dump.txt every 500 steps
-dump 1 all custom 500 dump.txt id type x y z fx fy fz
-
-# Write restart files to continue simulations
-restart 10000 state1.restart state2.restart
-
-## Run for this many steps
-run_style verlet
-run 10000
-
diff --git a/src/USER-BOCS/compute_pressure_bocs.cpp b/src/USER-BOCS/compute_pressure_bocs.cpp
index 8c0ae68817..29397f1fab 100644
--- a/src/USER-BOCS/compute_pressure_bocs.cpp
+++ b/src/USER-BOCS/compute_pressure_bocs.cpp
@@ -9,14 +9,14 @@
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
--------------------------------------------------------------------------
- USER-BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser
+-------------------------------------------------------------------------
+ USER-BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser
from The Pennsylvania State University
------------------------------------------------------------------------- */
#include <mpi.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cstring>
+#include <cstdlib>
#include "compute_pressure_bocs.h"
#include "atom.h"
#include "update.h"
@@ -41,8 +41,8 @@ ComputePressureBocs::ComputePressureBocs(LAMMPS *lmp, int narg, char **arg) :
Compute(lmp, narg, arg),
vptr(NULL), id_temp(NULL)
{
- if (narg < 4) error->all(FLERR,"Illegal compute pressure command");
- if (igroup) error->all(FLERR,"Compute pressure must use group all");
+ if (narg < 4) error->all(FLERR,"Illegal compute pressure/bocs command");
+ if (igroup) error->all(FLERR,"Compute pressure/bocs must use group all");
scalar_flag = vector_flag = 1;
size_vector = 6;
@@ -51,7 +51,7 @@ ComputePressureBocs::ComputePressureBocs(LAMMPS *lmp, int narg, char **arg) :
pressflag = 1;
timeflag = 1;
- p_match_flag = 0; // NJD MRD
+ p_match_flag = 0;
// store temperature ID used by pressure computation
// insure it is valid for temperature computation
@@ -64,9 +64,9 @@ ComputePressureBocs::ComputePressureBocs(LAMMPS *lmp, int narg, char **arg) :
int icompute = modify->find_compute(id_temp);
if (icompute < 0)
- error->all(FLERR,"Could not find compute pressure temperature ID");
+ error->all(FLERR,"Could not find compute pressure/bocs temperature ID");
if (modify->compute[icompute]->tempflag == 0)
- error->all(FLERR,"Compute pressure temperature ID does not "
+ error->all(FLERR,"Compute pressure/bocs temperature ID does not "
"compute temperature");
}
@@ -96,7 +96,7 @@ ComputePressureBocs::ComputePressureBocs(LAMMPS *lmp, int narg, char **arg) :
pairflag = 1;
bondflag = angleflag = dihedralflag = improperflag = 1;
kspaceflag = fixflag = 1;
- } else error->all(FLERR,"Illegal compute pressure command");
+ } else error->all(FLERR,"Illegal compute pressure/bocs command");
iarg++;
}
}
@@ -104,7 +104,7 @@ ComputePressureBocs::ComputePressureBocs(LAMMPS *lmp, int narg, char **arg) :
// error check
if (keflag && id_temp == NULL)
- error->all(FLERR,"Compute pressure requires temperature ID "
+ error->all(FLERR,"Compute pressure/bocs requires temperature ID "
"to include kinetic energy");
vector = new double[6];
@@ -135,7 +135,7 @@ void ComputePressureBocs::init()
if (keflag) {
int icompute = modify->find_compute(id_temp);
if (icompute < 0)
- error->all(FLERR,"Could not find compute pressure temperature ID");
+ error->all(FLERR,"Could not find compute pressure/bocs temperature ID");
temperature = modify->compute[icompute];
}
@@ -182,13 +182,13 @@ void ComputePressureBocs::init()
/* ----------------------------------------------------------------------
Compute the pressure correction for the analytical basis set
------------------------------------------------------------------------- */
-double ComputePressureBocs::get_cg_p_corr(int N_basis, double *phi_coeff,
+double ComputePressureBocs::get_cg_p_corr(int N_basis, double *phi_coeff,
int N_mol, double vavg, double vCG)
{
double correction = 0.0;
- for (int i = 1; i <= N_basis; ++i)
- {
- correction -= phi_coeff[i-1] * ( N_mol * i / vavg ) *
+ for (int i = 1; i <= N_basis; ++i)
+ {
+ correction -= phi_coeff[i-1] * ( N_mol * i / vavg ) *
pow( ( 1 / vavg ) * ( vCG - vavg ),i-1);
}
return correction;
@@ -201,7 +201,7 @@ double ComputePressureBocs::find_index(double * grid, double value)
{
int i;
double spacing = fabs(grid[1]-grid[0]);
- int gridsize = spline_length;
+ int gridsize = spline_length;
for (i = 0; i < (gridsize-1); ++i)
{
if (value >= grid[i] && value <= grid[i+1]) { return i; }
@@ -209,14 +209,14 @@ double ComputePressureBocs::find_index(double * grid, double value)
if (value >= grid[i] && value <= (grid[i] + spacing)) { return i; }
- for (int i = 0; i < gridsize; ++i)
- {
- fprintf(stderr, "grid %d: %f\n",i,grid[i]);
+ for (int i = 0; i < gridsize; ++i)
+ {
+ fprintf(stderr, "grid %d: %f\n",i,grid[i]);
}
char * errmsg = (char *) calloc(100,sizeof(char));
sprintf(errmsg,"Value %f does not fall within spline grid.\n",value);
error->all(FLERR,errmsg);
-
+
exit(1);
}
@@ -224,20 +224,20 @@ double ComputePressureBocs::find_index(double * grid, double value)
Compute the pressure correction for a spline basis set
------------------------------------------------------------------------- */
-double ComputePressureBocs::get_cg_p_corr(double ** grid, int basis_type,
+double ComputePressureBocs::get_cg_p_corr(double ** grid, int basis_type,
double vCG)
{
int i = find_index(grid[0],vCG);
double correction, deltax = vCG - grid[0][i];
-
+
if (basis_type == 1)
{
- correction = grid[1][i] + (deltax) *
+ correction = grid[1][i] + (deltax) *
( grid[1][i+1] - grid[1][i] ) / ( grid[0][i+1] - grid[0][i] );
}
else if (basis_type == 2)
{
- correction = grid[1][i] + (grid[2][i] * deltax) +
+ correction = grid[1][i] + (grid[2][i] * deltax) +
(grid[3][i] * pow(deltax,2)) + (grid[4][i] * pow(deltax,3));
}
else
@@ -248,21 +248,21 @@ double ComputePressureBocs::get_cg_p_corr(double ** grid, int basis_type,
}
/* ----------------------------------------------------------------------
- send cg info from fix_bocs to compute_pressure_bocs for the analytical
+ send cg info from fix_bocs to compute_pressure_bocs for the analytical
basis set
------------------------------------------------------------------------- */
-void ComputePressureBocs::send_cg_info(int basis_type, int sent_N_basis,
+void ComputePressureBocs::send_cg_info(int basis_type, int sent_N_basis,
double *sent_phi_coeff, int sent_N_mol, double sent_vavg)
{
- if (basis_type == 0) { p_basis_type = 0; }
- else
- {
- error->all(FLERR,"Incorrect basis type passed to ComputePressureBocs\n");
+ if (basis_type == 0) { p_basis_type = 0; }
+ else
+ {
+ error->all(FLERR,"Incorrect basis type passed to ComputePressureBocs\n");
}
p_match_flag = 1;
- N_basis = sent_N_basis;
+ N_basis = sent_N_basis;
phi_coeff = ((double *) calloc(N_basis, sizeof(double)) );
for (int i=0; i<N_basis; i++) { phi_coeff[i] = sent_phi_coeff[i]; }
@@ -271,16 +271,16 @@ void ComputePressureBocs::send_cg_info(int basis_type, int sent_N_basis,
}
/* ----------------------------------------------------------------------
- send cg info from fix_bocs to compute_pressure_bocs for a spline basis
+ send cg info from fix_bocs to compute_pressure_bocs for a spline basis
set
------------------------------------------------------------------------- */
-void ComputePressureBocs::send_cg_info(int basis_type,
+void ComputePressureBocs::send_cg_info(int basis_type,
double ** in_splines, int gridsize)
{
- if (basis_type == 1) { p_basis_type = 1; }
- else if (basis_type == 2) { p_basis_type = 2; }
- else
- {
+ if (basis_type == 1) { p_basis_type = 1; }
+ else if (basis_type == 2) { p_basis_type = 2; }
+ else
+ {
error->all(FLERR,"Incorrect basis type passed to ComputePressureBocs\n");
}
splines = in_splines;
@@ -302,7 +302,7 @@ double ComputePressureBocs::compute_scalar()
// invoke temperature if it hasn't been already
double t;
- double volume, correction = 0; // NJD MRD
+ double volume, correction = 0;
if (keflag) {
if (temperature->invoked_scalar != update->ntimestep)
t = temperature->compute_scalar();
@@ -311,28 +311,28 @@ double ComputePressureBocs::compute_scalar()
if (dimension == 3) {
inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd);
- volume = (domain->xprd * domain->yprd * domain->zprd); // NJD MRD
+ volume = (domain->xprd * domain->yprd * domain->zprd);
/* MRD NJD if block */
- if ( p_basis_type == 0 )
- {
- correction = get_cg_p_corr(N_basis,phi_coeff,N_mol,vavg,volume);
- }
- else if ( p_basis_type == 1 || p_basis_type == 2 )
- {
- correction = get_cg_p_corr(splines, p_basis_type, volume);
- }
+ if ( p_basis_type == 0 )
+ {
+ correction = get_cg_p_corr(N_basis,phi_coeff,N_mol,vavg,volume);
+ }
+ else if ( p_basis_type == 1 || p_basis_type == 2 )
+ {
+ correction = get_cg_p_corr(splines, p_basis_type, volume);
+ }
virial_compute(3,3);
if (keflag)
scalar = (temperature->dof * boltz * t +
- virial[0] + virial[1] + virial[2]) / 3.0 *
- inv_volume * nktv2p + (correction); // NJD MRD correction
+ virial[0] + virial[1] + virial[2]) / 3.0 *
+ inv_volume * nktv2p + (correction); correction
else
- scalar = (virial[0] + virial[1] + virial[2]) / 3.0 *
- inv_volume * nktv2p + (correction); // NJD MRD correction
+ scalar = (virial[0] + virial[1] + virial[2]) / 3.0 *
+ inv_volume * nktv2p + (correction); correction
} else {
- if (p_match_flag) // NJD MRD
+ if (p_match_flag)
{
error->all(FLERR,"Pressure matching not implemented in 2-d.\n");
exit(1);
diff --git a/src/USER-BOCS/compute_pressure_bocs.h b/src/USER-BOCS/compute_pressure_bocs.h
index d528009ad9..4fb932c508 100644
--- a/src/USER-BOCS/compute_pressure_bocs.h
+++ b/src/USER-BOCS/compute_pressure_bocs.h
@@ -9,36 +9,35 @@
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
--------------------------------------------------------------------------
- USER-BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser
+-------------------------------------------------------------------------
+ USER-BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser
from The Pennsylvania State University
------------------------------------------------------------------------- */
#ifdef COMPUTE_CLASS
-ComputeStyle(pressureBocs,ComputePressureBocs) // MRD NJD
+ComputeStyle(PRESSURE/BOCS,ComputePressureBocs)
#else
-// MRD NJD
-#ifndef LMP_COMPUTE_PRESSURE_BOCS_H
+
+#ifndef LMP_COMPUTE_PRESSURE_BOCS_H
#define LMP_COMPUTE_PRESSURE_BOCS_H
#include "compute.h"
namespace LAMMPS_NS {
// ComputePressure -> ComputePressureBocs MRD NJD
-class ComputePressureBocs : public Compute {
+class ComputePressureBocs : public Compute {
public:
- ComputePressureBocs(class LAMMPS *, int, char **); // MRD NJD
- virtual ~ComputePressureBocs(); // MRD NJD
+ ComputePressureBocs(class LAMMPS *, int, char **);
+ virtual ~ComputePressureBocs();
virtual void init();
virtual double compute_scalar();
virtual void compute_vector();
void reset_extra_compute_fix(const char *);
-// NJD MRD
- double compute_cg_scalar();
+ double compute_cg_scalar();
double get_cg_p_corr(int, double *, int, double, double);
double get_cg_fluct(double, double);
void send_cg_info(int, int, double*, int, double);
diff --git a/src/USER-BOCS/fix_bocs.cpp b/src/USER-BOCS/fix_bocs.cpp
index f7f974f372..ba74d6be1f 100644
--- a/src/USER-BOCS/fix_bocs.cpp
+++ b/src/USER-BOCS/fix_bocs.cpp
@@ -9,15 +9,15 @@
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
--------------------------------------------------------------------------
- USER-BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser
+-------------------------------------------------------------------------
+ USER-BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser
from The Pennsylvania State University
------------------------------------------------------------------------- */
-#include <string.h>
-#include <stdlib.h>
-#include <math.h>
-#include "fix_bocs.h"
+#include <cstring>
+#include <cstdlib>
+#include <cmath>
+#include "fix_bocs.h"
#include "math_extra.h"
#include "atom.h"
#include "force.h"
@@ -64,7 +64,7 @@ enum{ISO,ANISO,TRICLINIC};
NVT,NPH,NPT integrators for improved Nose-Hoover equations of motion
---------------------------------------------------------------------- */
-FixBocs::FixBocs(LAMMPS *lmp, int narg, char **arg) :
+FixBocs::FixBocs(LAMMPS *lmp, int narg, char **arg) :
Fix(lmp, narg, arg),
rfix(NULL), id_dilate(NULL), irregular(NULL), id_temp(NULL), id_press(NULL),
eta(NULL), eta_dot(NULL), eta_dotdot(NULL),
@@ -155,20 +155,18 @@ FixBocs::FixBocs(LAMMPS *lmp, int narg, char **arg) :
iarg += 4;
} else if (strcmp(arg[iarg],"iso") == 0) {
error->all(FLERR,"Illegal fix bocs command. Pressure fix must be "
- "cgiso . Use regular fix npt/nph for iso"); // MRD NJD
+ "cgiso . Use regular fix bocs for iso"); // MRD NJD
} else if (strcmp(arg[iarg],"cgiso") == 0) { // MRD NJD the whole else if
if (iarg+4 > narg)
- {
error->all(FLERR,"Illegal fix bocs command. cgiso must be "
"followed by: P_0 P_f P_coupl");
- }
p_match_flag = 1;
pcouple = XYZ;
- p_start[0] = p_start[1] = p_start[2] =
+ p_start[0] = p_start[1] = p_start[2] =
force->numeric(FLERR,arg[iarg+1]);
- p_stop[0] = p_stop[1] = p_stop[2] =
- force->numeric(FLERR,arg[iarg+2]);
- p_period[0] = p_period[1] = p_period[2] =
+ p_stop[0] = p_stop[1] = p_stop[2] =
+ force->numeric(FLERR,arg[iarg+2]);
+ p_period[0] = p_period[1] = p_period[2] =
force->numeric(FLERR,arg[iarg+3]);
p_flag[0] = p_flag[1] = p_flag[2] = 1;
@@ -179,38 +177,29 @@ FixBocs::FixBocs(LAMMPS *lmp, int narg, char **arg) :
}
iarg += 4;
- if ( strcmp(arg[iarg], "analytic") == 0 )
- {
- if (iarg + 4 > narg)
- {
+ if ( strcmp(arg[iarg], "analytic") == 0 ) {
+ if (iarg + 4 > narg) {
error->all(FLERR,"Illegal fix bocs command. basis type analytic"
" must be followed by: avg_vol n_mol n_pmatch_coeff");
}
p_basis_type = 0;
- vavg = atof(arg[iarg+1]);
- N_mol = atoi(arg[iarg+2]);
- N_p_match = atoi(arg[iarg+3]);
+ vavg = force->numeric(FLERR,arg[iarg+1]);
+ N_mol = force->inumeric(FLERR,arg[iarg+2]);
+ N_p_match = force->inumeric(FLERR,arg[iarg+3]);
p_match_coeffs = (double *) (calloc(N_p_match, sizeof(double)) );
iarg += 4;
if (iarg + N_p_match > narg)
- {
- error->all(FLERR,"Illegal fix bocs command. Missing coeffs.");
- }
+ error->all(FLERR,"Illegal fix bocs command. Missing coeffs.");
for (int pmatchi = 0; pmatchi < N_p_match; pmatchi++)
- {
- p_match_coeffs[pmatchi] = atof(arg[iarg+pmatchi]);
- }
+ p_match_coeffs[pmatchi] = force->numeric(FLERR,arg[iarg+pmatchi]);
iarg += (N_p_match);
- } else if (strcmp(arg[iarg], "linear_spline") == 0 )
- {
+ } else if (strcmp(arg[iarg], "linear_spline") == 0 ) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix bocs command. "
"Supply a file name after linear_spline.");
-
p_basis_type = 1;
spline_length = read_F_table( arg[iarg+1], p_basis_type );
iarg += 2;
- } else if (strcmp(arg[iarg], "cubic_spline") == 0 )
- {
+ } else if (strcmp(arg[iarg], "cubic_spline") == 0 ) {
if (iarg+2 > narg) error->all(FLERR,"Illegal fix bocs command. "
"Supply a file name after cubic_spline.");
p_basis_type = 2;
@@ -222,34 +211,34 @@ FixBocs::FixBocs(LAMMPS *lmp, int narg, char **arg) :
sprintf(errmsg,"CG basis type %s is not recognized\nSupported "
"basis types: analytic linear_spline cubic_spline",arg[iarg]);
error->all(FLERR,errmsg);
- } // END NJD MRD
+ } // END NJD MRD
} else if (strcmp(arg[iarg],"tchain") == 0) {
- if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix bocs command");
mtchain = force->inumeric(FLERR,arg[iarg+1]);
// used by FixNVTSllod to preserve non-default value
mtchain_default_flag = 0;
- if (mtchain < 1) error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ if (mtchain < 1) error->all(FLERR,"Illegal fix bocs command");
iarg += 2;
} else if (strcmp(arg[iarg],"pchain") == 0) {
- if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix bocs command");
mpchain = force->inumeric(FLERR,arg[iarg+1]);
- if (mpchain < 0) error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ if (mpchain < 0) error->all(FLERR,"Illegal fix bocs command");
iarg += 2;
} else if (strcmp(arg[iarg],"mtk") == 0) {
- if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix bocs command");
if (strcmp(arg[iarg+1],"yes") == 0) mtk_flag = 1;
else if (strcmp(arg[iarg+1],"no") == 0) mtk_flag = 0;
- else error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ else error->all(FLERR,"Illegal fix bocs command");
iarg += 2;
} else if (strcmp(arg[iarg],"tloop") == 0) {
- if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix bocs command");
nc_tchain = force->inumeric(FLERR,arg[iarg+1]);
- if (nc_tchain < 0) error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ if (nc_tchain < 0) error->all(FLERR,"Illegal fix bocs command");
iarg += 2;
} else if (strcmp(arg[iarg],"ploop") == 0) {
- if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix bocs command");
nc_pchain = force->inumeric(FLERR,arg[iarg+1]);
- if (nc_pchain < 0) error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ if (nc_pchain < 0) error->all(FLERR,"Illegal fix bocs command");
iarg += 2;
} else {
char * errmsg = (char *) calloc(80,sizeof(char));
@@ -422,7 +411,7 @@ FixBocs::FixBocs(LAMMPS *lmp, int narg, char **arg) :
// create a new compute pressure style
// id = fix-ID + press, compute group = all
// pass id_temp as 4th arg to pressure constructor
-
+
n = strlen(id) + 7;
id_press = new char[n];
strcpy(id_press,id);
@@ -431,7 +420,7 @@ FixBocs::FixBocs(LAMMPS *lmp, int narg, char **arg) :
newarg = new char*[4];
newarg[0] = id_press;
newarg[1] = (char *) "all";
- newarg[2] = (char *) "pressureBocs";
+ newarg[2] = (char *) "PRESSURE/BOCS";
newarg[3] = id_temp;
modify->add_compute(4,newarg);
delete [] newarg;
@@ -512,9 +501,9 @@ void FixBocs::init()
if ((p_flag[0] && dimflag[0]) || (p_flag[1] && dimflag[1]) ||
(p_flag[2] && dimflag[2]) || (p_flag[3] && dimflag[3]) ||
(p_flag[4] && dimflag[4]) || (p_flag[5] && dimflag[5]))
- error->all(FLERR,"Cannot use fix npt and fix deform on "
+ error->all(FLERR,"Cannot use fix bocs and fix deform on "
"same component of stress tensor");
- }
+ }
}
// set temperature and pressure ptrs
@@ -634,7 +623,7 @@ void FixBocs::init()
int FixBocs::read_F_table( char *filename, int p_basis_type )
{
char separator = ',';
- FILE *fpi;
+ FILE *fpi;
int N_columns = 2, n_entries = 0, i;
float f1, f2;
double n1, n2;
@@ -647,15 +636,15 @@ int FixBocs::read_F_table( char *filename, int p_basis_type )
{
while (fgets(line,199,fpi)) { ++n_entries; }
fclose(fpi);
- for (i = 0; i < N_columns; ++i)
- {
- data[i] = (double *) calloc(n_entries,sizeof(double));
+ for (i = 0; i < N_columns; ++i)
+ {
+ data[i] = (double *) calloc(n_entries,sizeof(double));
}
}
else
{
char * errmsg = (char *) calloc(50,sizeof(char));
- sprintf(errmsg,"Unable to open file: %s\n",filename);
+ sprintf(errmsg,"Unable to open file: %s\n",filename);
error->all(FLERR,errmsg);
}
@@ -679,10 +668,10 @@ int FixBocs::read_F_table( char *filename, int p_basis_type )
}
}
}
- else
- {
+ else
+ {
char * errmsg = (char *) calloc(50,sizeof(char));
- sprintf(errmsg,"Unable to open file: %s\n",filename);
+ sprintf(errmsg,"Unable to open file: %s\n",filename);
error->all(FLERR,errmsg);
}
fclose(fpi);
@@ -693,12 +682,12 @@ int FixBocs::read_F_table( char *filename, int p_basis_type )
splines[0] = (double *) calloc(n_entries,sizeof(double));
splines[1] = (double *) calloc(n_entries,sizeof(double));
int idxa, idxb;
- for (idxa = 0; idxa < 2; ++idxa)
- {
- for (idxb = 0; idxb < n_entries; ++idxb)
- {
- splines[idxa][idxb] = data[idxa][idxb];
- }
+ for (idxa = 0; idxa < 2; ++idxa)
+ {
+ for (idxb = 0; idxb < n_entries; ++idxb)
+ {
+ splines[idxa][idxb] = data[idxa][idxb];
+ }
}
}
else if (p_basis_type == 2)
@@ -720,7 +709,7 @@ int FixBocs::read_F_table( char *filename, int p_basis_type )
void FixBocs::build_cubic_splines( double **data )
{
double *a, *b, *d, *h, *alpha, *c, *l, *mu, *z;
- int n = spline_length;
+ int n = spline_length;
double alpha_i;
a = (double *) calloc(n,sizeof(double));
b = (double *) calloc(n+1,sizeof(double));
@@ -738,14 +727,14 @@ void FixBocs::build_cubic_splines( double **data )
b[i] = 0.0;
d[i] = 0.0;
- if (i<(n-1))
- {
+ if (i<(n-1))
+ {
h[i] = (data[0][i+1] - data[0][i]);
}
if (i>1 && i<(n-1))
{
- alpha_i = (3.0 / h[i]) * ( data[1][i+1] - data[1][i]) - (3.0 / h[i-1] )
+ alpha_i = (3.0 / h[i]) * ( data[1][i+1] - data[1][i]) - (3.0 / h[i-1] )
* ( data[1][i] - data[1][i-1] );
alpha[i-1] = alpha_i;
}
@@ -755,15 +744,15 @@ void FixBocs::build_cubic_splines( double **data )
z[0] = 0.0;
for (int i=1; i<n-1; i++)
- {
+ {
l[i] = 2*(data[0][i+1] - data[0][i-1]) - h[i-1] * mu[i-1];
mu[i] = h[i]/l[i];
z[i] = (alpha[i] - h[i-1] * z[i-1]) / l[i];
}
l[n-1] = 1.0;
mu[n-1] = 0.0;
- z[n-1] = 0.0;
-
+ z[n-1] = 0.0;
+
c[n] = 0.0;
b[n] = 0.0;
d[n] = 0.0;
@@ -777,7 +766,7 @@ void FixBocs::build_cubic_splines( double **data )
d[j] = (c[j+1]-c[j])/(3.0 * h[j]);
}
splines = (double **) calloc(5,sizeof(double *));
-
+
for ( idx = 0; idx < 5; ++idx)
{
splines[idx] = (double *) calloc(n-1,sizeof(double));
@@ -1488,15 +1477,15 @@ int FixBocs::modify_param(int narg, char **arg)
if (p_match_flag) // NJD MRD
{
- if ( p_basis_type == 0 )
- {
- ((ComputePressureBocs *)pressure)->send_cg_info(p_basis_type, N_p_match,
+ if ( p_basis_type == 0 )
+ {
+ ((ComputePressureBocs *)pressure)->send_cg_info(p_basis_type, N_p_match,
p_match_coeffs, N_mol, vavg);
}
- else if ( p_basis_type == 1 || p_basis_type == 2 )
- {
- ((ComputePressureBocs *)pressure)->send_cg_info(p_basis_type, splines,
- spline_length );
+ else if ( p_basis_type == 1 || p_basis_type == 2 )
+ {
+ ((ComputePressureBocs *)pressure)->send_cg_info(p_basis_type, splines,
+ spline_length );
}
}
diff --git a/src/USER-BOCS/fix_bocs.h b/src/USER-BOCS/fix_bocs.h
index 8e6eefdc69..34090e4f3a 100644
--- a/src/USER-BOCS/fix_bocs.h
+++ b/src/USER-BOCS/fix_bocs.h
@@ -9,20 +9,18 @@
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
--------------------------------------------------------------------------
- USER-BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser
+-------------------------------------------------------------------------
+ USER-BOCS written by: Nicholas J. H. Dunn and Michael R. DeLyser
from The Pennsylvania State University
------------------------------------------------------------------------- */
#ifdef FIX_CLASS
-// MRD NJD
+
FixStyle(bocs,FixBocs)
#else
-
-// MRD NJD
#ifndef LMP_FIX_BOCS_H
#define LMP_FIX_BOCS_H
@@ -30,7 +28,7 @@ FixStyle(bocs,FixBocs)
namespace LAMMPS_NS {
-// MRD NJD
+
class FixBocs : public Fix {
public:
FixBocs(class LAMMPS *, int, char **); // MRD NJD
@@ -54,10 +52,6 @@ class FixBocs : public Fix {
virtual void *extract(const char*,int &);
double memory_usage();
-// MRD NJD
- int read_F_table(char *, int);
- void build_cubic_splines(double **);
-
protected:
int dimension,which;
@@ -97,7 +91,7 @@ class FixBocs : public Fix {
int N_p_match;
double *p_match_coeffs;
double ** splines;
- int spline_length;
+ int spline_length;
int nlevels_respa;
@@ -156,6 +150,9 @@ class FixBocs : public Fix {
void nhc_temp_integrate();
void nhc_press_integrate();
+ int read_F_table(char *, int);
+ void build_cubic_splines(double **);
+
virtual void nve_x(); // may be overwritten by child classes
virtual void nve_v();
virtual void nh_v_press();
@@ -183,64 +180,64 @@ Self-explanatory. Check the input script syntax and compare to the
documentation for the command. You can use -echo screen as a
command-line option when running LAMMPS to see the offending line.
-E: Target temperature for fix nvt/npt/nph cannot be 0.0
+E: Target temperature for fix bocs cannot be 0.0
Self-explanatory.
-E: Invalid fix nvt/npt/nph command for a 2d simulation
+E: Invalid fix bocs command for a 2d simulation
Cannot control z dimension in a 2d model.
-E: Fix nvt/npt/nph dilate group ID does not exist
+E: Fix bocs dilate group ID does not exist
Self-explanatory.
-E: Invalid fix nvt/npt/nph command pressure settings
+E: Invalid fix bocs command pressure settings
If multiple dimensions are coupled, those dimensions must be
specified.
-E: Cannot use fix nvt/npt/nph on a non-periodic dimension
+E: Cannot use fix bocs on a non-periodic dimension
When specifying a diagonal pressure component, the dimension must be
periodic.
-E: Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension
+E: Cannot use fix bocs on a 2nd non-periodic dimension
When specifying an off-diagonal pressure component, the 2nd of the two
dimensions must be periodic. E.g. if the xy component is specified,
then the y dimension must be periodic.
-E: Cannot use fix nvt/npt/nph with yz scaling when z is non-periodic dimension
+E: Cannot use fix bocs with yz scaling when z is non-periodic dimension
The 2nd dimension in the barostatted tilt factor must be periodic.
-E: Cannot use fix nvt/npt/nph with xz scaling when z is non-periodic dimension
+E: Cannot use fix bocs with xz scaling when z is non-periodic dimension
The 2nd dimension in the barostatted tilt factor must be periodic.
-E: Cannot use fix nvt/npt/nph with xy scaling when y is non-periodic dimension
+E: Cannot use fix bocs with xy scaling when y is non-periodic dimension
The 2nd dimension in the barostatted tilt factor must be periodic.
-E: Cannot use fix nvt/npt/nph with both yz dynamics and yz scaling
+E: Cannot use fix bocs with both yz dynamics and yz scaling
Self-explanatory.
-E: Cannot use fix nvt/npt/nph with both xz dynamics and xz scaling
+E: Cannot use fix bocs with both xz dynamics and xz scaling
Self-explanatory.
-E: Cannot use fix nvt/npt/nph with both xy dynamics and xy scaling
+E: Cannot use fix bocs with both xy dynamics and xy scaling
Self-explanatory.
-E: Can not specify Pxy/Pxz/Pyz in fix nvt/npt/nph with non-triclinic box
+E: Can not specify Pxy/Pxz/Pyz in fix bocs with non-triclinic box
Only triclinic boxes can be used with off-diagonal pressure components.
See the region prism command for details.
-E: Invalid fix nvt/npt/nph pressure settings
+E: Invalid fix bocs pressure settings
Settings for coupled dimensions must be the same.
@@ -251,12 +248,12 @@ Self-explanatory.
E: Using update dipole flag requires atom attribute mu
Self-explanatory.
-
+
E: The dlm flag must be used with update dipole
-
+
Self-explanatory.
-E: Fix nvt/npt/nph damping parameters must be > 0.0
+E: Fix bocs damping parameters must be > 0.0
Self-explanatory.
@@ -264,15 +261,15 @@ E: Cannot use fix npt and fix deform on same component of stress tensor
This would be changing the same box dimension twice.
-E: Temperature ID for fix nvt/npt does not exist
+E: Temperature ID for fix bocs does not exist
Self-explanatory.
-E: Pressure ID for fix npt/nph does not exist
+E: Pressure ID for fix bocs does not exist
Self-explanatory.
-E: Fix npt/nph has tilted box too far in one step - periodic cell is too far from equilibrium state
+E: Fix bocs has tilted box too far in one step - periodic cell is too far from equilibrium state
Self-explanatory. The change in the box tilt is too extreme
on a short timescale.
--
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