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patch 11Apr17

This commit is contained in:
Steve Plimpton 2017-04-11 09:00:37 -06:00
parent 49dd9449b8
commit 4da8c1c4e2
12 changed files with 57 additions and 456 deletions
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4
doc/src/Manual.txt
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@ -1,7 +1,7 @@
<!-- HTML_ONLY -->
<HEAD>
<TITLE>LAMMPS Users Manual</TITLE>
<META NAME="docnumber" CONTENT="31 Mar 2017 version">
<META NAME="docnumber" CONTENT="11 Apr 2017 version">
<META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
<META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License.">
</HEAD>
@ -21,7 +21,7 @@
<H1></H1>
LAMMPS Documentation :c,h3
31 Mar 2017 version :c,h4
11 Apr 2017 version :c,h4
Version info: :h4

2
doc/src/Section_commands.txt
View File

@ -1155,7 +1155,7 @@ USER-OMP, t = OPT.
"zero"_dihedral_zero.html,
"hybrid"_dihedral_hybrid.html,
"charmm (ko)"_dihedral_charmm.html,
"charmmfsh"_dihedral_charmm.html,
"charmmfsw"_dihedral_charmm.html,
"class2 (ko)"_dihedral_class2.html,
"harmonic (io)"_dihedral_harmonic.html,
"helix (o)"_dihedral_helix.html,

2
doc/src/Section_howto.txt
View File

@ -215,7 +215,7 @@ documentation for the formula it computes.
"special_bonds"_special_bonds.html charmm
"special_bonds"_special_bonds.html amber :ul
NOTE: For CHARMM, the newer {charmmfsw} or {charmmfsh} styles were
NOTE: For CHARMM, newer {charmmfsw} or {charmmfsh} styles were
released in March 2017. We recommend they be used instead of the
older {charmm} styles. See discussion of the differences on the "pair
charmm"_pair_charmm.html and "dihedral charmm"_dihedral_charmm.html

33
doc/src/dihedral_charmm.txt
View File

@ -10,25 +10,25 @@ dihedral_style charmm command :h3
dihedral_style charmm/intel command :h3
dihedral_style charmm/kk command :h3
dihedral_style charmm/omp command :h3
dihedral_style charmmfsh command :h3
dihedral_style charmmfsw command :h3
[Syntax:]
dihedral_style style :pre
style = {charmm} or {charmmfsh} :ul
style = {charmm} or {charmmfsw} :ul
[Examples:]
dihedral_style charmm
dihedral_style charmmfsh
dihedral_style charmmfsw
dihedral_coeff 1 0.2 1 180 1.0
dihedral_coeff 2 1.8 1 0 1.0
dihedral_coeff 1 3.1 2 180 0.5 :pre
[Description:]
The {charmm} and {charmmfsh} dihedral styles use the potential
The {charmm} and {charmmfsw} dihedral styles use the potential
:c,image(Eqs/dihedral_charmm.jpg)
@ -38,10 +38,12 @@ field (see comment on weighting factors below). See
"(Cornell)"_#dihedral-Cornell for a description of the AMBER force
field.
NOTE: The newer {charmmfsh} style was released in March 2017. We
NOTE: The newer {charmmfsw} style was released in March 2017. We
recommend it be used instead of the older {charmm} style when running
a simulation with the CHARMM force field and Coulomb cutoffs, via the
"pair_style lj/charmmfsw/coul/charmmfsh"_pair_charmm.html command.
a simulation with the CHARMM force field, either with long-range
Coulombics or a Coulomb cutoff, via the "pair_style
lj/charmmfsw/coul/long"_pair_charmm.html and "pair_style
lj/charmmfsw/coul/charmmfsh"_pair_charmm.html commands respectively.
Otherwise the older {charmm} style is fine to use. See the discussion
below and more details on the "pair_style charmm"_pair_charmm.html doc
page.
@ -86,17 +88,18 @@ default). Otherwise 1-4 non-bonded interactions in dihedrals will be
computed twice.
For simulations using the CHARMM force field with a Coulomb cutoff,
the difference between the {charmm} and {charmmfsh} styles is in the
the difference between the {charmm} and {charmmfsw} styles is in the
computation of the 1-4 non-bond interactions, though only if the
distance between the two atoms is within the switching region of the
pairwise potential defined by the corresponding CHARMM pair style,
i.e. within the outer cutoff specified for the pair style. The
{charmmfsh} style should only be used when using the "pair_style
lj/charmmfsw/coul/charmmfsh"_pair_charmm.html to make the Coulombic
pairwise calculations consistent. Use the {charmm} style with
long-range Coulombics or the older "pair_style
lj/charmm/coul/charmm"_pair_charmm.html command. See the discussion
on the "CHARMM pair_style"_pair_charmm.html doc page for details.
{charmmfsw} style should only be used when using the corresponding
"pair_style lj/charmmfsw/coul/charmmfsw"_pair_charmm.html or
"pair_style lj/charmmfsw/coul/long"_pair_charmm.html commands. Use
the {charmm} style with the older "pair_style"_pair_charmm.html
commands that have just "charmm" in their style name. See the
discussion on the "CHARMM pair_style"_pair_charmm.html doc page for
details.
Note that for AMBER force fields, which use pair styles with "lj/cut",
the special_bonds 1-4 scaling factor should be set to the AMBER
@ -104,7 +107,7 @@ defaults (1/2 and 5/6) and all the dihedral weighting factors (4th
coeff above) must be set to 0.0. In this case, you can use any pair
style you wish, since the dihedral does not need any Lennard-Jones
parameter information and will not compute any 1-4 non-bonded
interactions. Likewise the {charmm} or {charmmfsh} styles are
interactions. Likewise the {charmm} or {charmmfsw} styles are
identical in this case since no 1-4 non-bonded interactions are
computed.

7
doc/src/pair_charmm.txt
View File

@ -99,9 +99,10 @@ artifacts.
NOTE: The newer {charmmfsw} or {charmmfsh} styles were released in
March 2017. We recommend they be used instead of the older {charmm}
styles. Eventually code from the new styles will propagate into the
related pair styles (e.g. implicit, accelerator, free energy
variants).
styles. This includes the newer "dihedral_style
charmmfsw"_dihedral_charmm.html command. Eventually code from the new
styles will propagate into the related pair styles (e.g. implicit,
accelerator, free energy variants).
The general CHARMM formulas are as follows

5
examples/cmap/in.cmap
View File

@ -9,11 +9,10 @@ boundary p p p
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
dihedral_style charmmfsw
improper_style harmonic
pair_style lj/charmm/coul/charmm 8 12
#pair_style lj/charmmfsw/coul/charmmfsh 8 12
pair_style lj/charmmfsw/coul/charmmfsh 8 12
pair_modify mix arithmetic
fix cmap all cmap charmm22.cmap

201
examples/cmap/log.5Oct16.cmap.g++.1
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@ -1,201 +0,0 @@
LAMMPS (5 Oct 2016)
# Created by charmm2lammps v1.8.2.6 beta on Thu Mar 3 20:56:57 EST 2016
units real
neigh_modify delay 2 every 1
#newton off
boundary p p p
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/charmm 8 12
#pair_style lj/charmmfsw/coul/charmmfsh 8 12
pair_modify mix arithmetic
fix cmap all cmap charmm22.cmap
Reading potential file charmm22.cmap with DATE: 2016-09-26
fix_modify cmap energy yes
read_data gagg.data fix cmap crossterm CMAP
orthogonal box = (-34.4147 -36.1348 -39.3491) to (45.5853 43.8652 40.6509)
1 by 1 by 1 MPI processor grid
reading atoms ...
34 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
12 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
33 bonds
reading angles ...
57 angles
reading dihedrals ...
75 dihedrals
reading impropers ...
7 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
13 = max # of 1-4 neighbors
16 = max # of special neighbors
special_bonds charmm
fix 1 all nve
#fix 1 all nvt temp 300 300 100.0
#fix 2 all shake 1e-9 500 0 m 1.0
velocity all create 0.0 12345678 dist uniform
thermo 1000
thermo_style custom step ecoul evdwl ebond eangle edihed f_cmap eimp
timestep 2.0
run 100000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 2 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7 -> bins = 12 12 12
Memory usage per processor = 14.6355 Mbytes
Step E_coul E_vdwl E_bond E_angle E_dihed f_cmap E_impro
0 26.542777 -0.93822087 1.2470497 4.8441789 4.5432816 -1.473352 0.10453023
1000 28.673005 -0.47724367 0.80029132 3.151679 4.4684446 -2.3928648 0.18604953
2000 27.67955 -1.170342 0.72018905 4.0400131 4.4713764 -2.5490207 0.21834436
3000 29.256656 -0.35856055 0.73303546 3.7411606 4.4710568 -2.8939692 0.37728884
4000 30.097549 -1.1353905 0.79007053 3.0688444 4.4091469 -2.3383587 0.20743631
5000 28.357525 -1.0723742 0.9180297 3.6579424 4.8792664 -2.3185572 0.088366962
6000 29.214175 -0.95299225 0.81926009 3.6805429 4.6742897 -2.9343577 0.26697813
7000 27.018614 -0.52423475 0.72502764 3.8840137 4.7780956 -2.3916009 0.24952584
8000 29.682167 -1.0939711 0.76111486 3.1090116 4.9359719 -2.5662984 0.1411154
9000 27.909695 -0.80905986 0.78952533 4.203187 4.1301204 -2.000402 0.088859259
10000 27.480298 -0.86273377 1.1293962 4.3857421 4.899282 -3.3895621 0.12126215
11000 28.303203 -1.0221152 0.62762348 4.055414 4.5863024 -2.5842816 0.17996907
12000 28.311127 -0.94227367 0.91859012 3.6673926 4.7018632 -3.902715 0.30065704
13000 30.818607 -1.5220116 0.95710386 3.3364371 4.543427 -3.0423067 0.16712905
14000 27.643736 -1.0144117 0.95806952 4.1046912 4.800236 -4.0534389 0.29293405
15000 27.660491 -1.0390086 0.78061056 4.1139174 4.7197202 -2.3670379 0.22126985
16000 27.845157 -0.63654502 0.78007478 3.9365994 4.949418 -3.1470214 0.22335355
17000 28.44772 -1.0255112 0.70402007 4.0573343 4.2887527 -2.2099596 0.048050962
18000 27.128323 -0.96218536 1.1327159 4.3222585 4.326607 -2.2881766 0.13491257
19000 27.337633 -0.78999574 0.80152298 4.2239689 4.7073478 -2.2924164 0.12710292
20000 27.780537 -0.46458072 0.79707671 3.7232618 4.943417 -2.5290628 0.26191223
21000 26.435484 -0.7803224 1.0753217 4.4196051 5.9945933 -2.3340925 0.16448475
22000 28.619429 -1.1623149 0.9401731 3.8508844 5.1636737 -2.5551846 0.25318434
23000 28.399338 -0.79700962 0.85575503 4.488526 4.5975422 -2.5663549 0.13601693
24000 29.645532 -1.158744 0.83180313 3.8193399 4.60319 -2.6847864 0.24260466
25000 28.695339 -1.4802204 0.76583757 3.6786272 4.8959496 -2.3627896 0.080867326
26000 28.149711 -1.029689 0.79383806 3.7885067 4.3345813 -2.1041553 0.14598209
27000 29.580373 -1.0525813 1.0262723 3.7767318 4.6119758 -2.2802386 0.088556038
28000 28.44308 -0.93411225 0.8794395 3.948079 4.780246 -2.1814583 0.14340149
29000 29.335621 -1.6087988 0.71803091 3.7819186 4.6688385 -2.4282242 0.16061111
30000 28.706138 -1.3938241 0.67713818 4.031275 4.4756505 -2.1807056 0.11461356
31000 27.451944 0.010297225 0.65064883 3.6402029 4.3607811 -2.5511516 0.12637237
32000 27.070878 -1.103158 1.1932199 5.1329709 4.5201653 -2.2224479 0.11215427
33000 29.889976 -1.6228316 0.69407996 3.5361991 4.3502767 -1.9847454 0.09089949
34000 28.223151 -0.927208 1.043253 3.4650939 5.1028142 -2.8127219 0.10648823
35000 27.985986 -0.48153861 0.63878449 3.3724641 4.9551679 -2.6565919 0.12123115
36000 28.580688 -1.4500694 1.055762 4.0490064 4.423782 -2.3103578 0.072747638
37000 29.192947 -0.49678176 1.1146731 2.9233947 4.5738603 -2.4376144 0.22874047
38000 26.954594 -0.53812359 0.79230685 4.3356989 5.0284656 -2.3791255 0.0486081
39000 27.567555 -0.57870028 0.73614374 4.191991 4.9209556 -2.6122044 0.08635571
40000 28.494172 -0.79057135 0.79072816 4.1893209 4.4826919 -2.4179635 0.14612898
41000 28.44904 -1.1002948 0.93405654 4.3586358 4.4338415 -2.2950944 0.15705834
42000 28.95725 -1.0297067 1.1632348 4.274711 4.9979487 -2.7611464 0.15944725
43000 28.640394 -0.70938882 0.68100893 3.1844315 5.1817454 -2.2837487 0.14189233
44000 27.997558 -1.0115099 0.59125208 4.0883422 4.6033907 -2.2775964 0.094273258
45000 27.67163 -0.67992747 1.1225552 3.9020703 4.8171056 -2.1952679 0.041418433
46000 28.822607 -0.6687953 0.74160059 3.3193715 4.5546965 -2.3024572 0.047569065
47000 29.20147 -1.4456785 0.79223353 3.8288813 4.5811826 -2.5154936 0.061230141
48000 27.843026 -1.0222301 0.87322137 4.3432743 4.4266307 -2.1414153 0.06802794
49000 28.199573 -1.1887794 1.2781088 4.0779644 4.5881353 -2.319775 0.094803547
50000 28.759212 -1.354416 0.68534569 3.8394841 4.2308134 -2.1281844 0.1395951
51000 27.876455 -1.5705462 0.76557156 4.5335223 4.523708 -2.203702 0.14679803
52000 27.930587 -1.2277489 0.96071516 3.960953 5.1152188 -2.4101451 0.060949521
53000 27.031236 -1.4746477 1.2341141 5.0540975 4.3656865 -2.1288513 0.092725656
54000 28.809394 -1.1162427 0.94350207 3.4013958 4.4755547 -2.3342811 0.18855912
55000 28.948415 -1.1560418 0.6260139 3.5386373 4.5244978 -2.340212 0.17474657
56000 28.048368 -0.95784532 0.76432571 4.1404665 4.4570033 -2.0899628 0.045693628
57000 28.707642 -1.366574 0.9907873 3.729903 4.3131997 -2.2777698 0.065420213
58000 26.361663 -1.0424403 1.0452563 5.0977108 4.7035231 -2.3101244 0.13671642
59000 29.218218 -1.2210564 0.62435875 3.4236327 4.5481681 -2.1575943 0.037984042
60000 27.655546 -1.1053224 0.86323501 3.7641375 4.8946898 -2.2422249 0.077725979
61000 27.252108 -1.3744824 1.1150806 5.0444848 4.4878135 -2.2743829 0.058331257
62000 27.163469 -1.1715781 0.72099321 4.5295501 4.9509918 -2.2993961 0.050401105
63000 29.581575 -1.2238537 0.86303245 3.1194038 5.2218965 -2.5002427 0.055032632
64000 27.897822 -1.1011516 0.74540883 4.2869228 4.3394269 -2.2552393 0.1403321
65000 27.083245 -1.0633392 0.92771724 5.0805224 4.2747962 -2.2388039 0.064196692
66000 29.072723 -1.5514209 0.89798805 4.2600224 4.4261812 -2.3524752 0.15067414
67000 27.308181 -0.72224802 0.97109517 4.5074578 4.4559352 -2.1381121 0.089297603
68000 27.505686 -0.43855431 0.80785812 4.1917251 5.0157721 -2.3382145 0.11105164
69000 29.041681 -0.64735378 0.89874684 3.3891579 4.3753361 -2.2320941 0.14716747
70000 29.735756 -1.7061457 0.9206878 3.5767878 4.3851664 -2.2516304 0.097196062
71000 28.224352 -0.92217702 0.86093586 3.9507157 4.5596589 -2.2173397 0.089116669
72000 29.282336 -1.056142 0.65185725 3.8735742 4.4839333 -2.4314756 0.071909704
73000 26.257283 -0.64273826 0.98300685 5.063943 5.045958 -2.5544375 0.2180275
74000 28.825119 -0.97736616 0.87201848 3.55875 4.3653309 -2.2303567 0.098963875
75000 29.239507 -0.96508809 0.74517323 3.4306236 4.7651921 -2.6077732 0.17883654
76000 27.349841 -0.50990238 1.1183613 4.4252451 4.4097775 -2.4125794 0.18483606
77000 28.130197 -1.4081219 0.94921357 4.2572132 4.5162849 -2.4013797 0.073744606
78000 28.235774 -0.9214321 0.6324981 3.8697686 4.8092154 -2.2272847 0.092108346
79000 26.732846 -0.55949486 1.0989617 5.0088609 4.4930687 -2.277945 0.03855146
80000 28.529208 -0.94244671 0.79407482 3.961106 4.3930011 -2.3127726 0.091124948
81000 29.603852 -1.6116062 1.060847 3.7824932 4.151001 -1.9139868 0.19875986
82000 28.232876 -1.1833011 1.0182713 3.4195758 5.1394333 -2.4632697 0.28501012
83000 29.565482 -1.3479552 0.99056973 3.7851802 4.4781011 -2.7872481 0.2031991
84000 28.780274 -1.3073882 1.0512637 4.004638 4.502282 -2.3789146 0.015656202
85000 27.262312 -1.1305346 1.203524 4.7938623 4.1747105 -2.0952844 0.054240361
86000 28.157348 -1.0662817 0.81163796 3.9912709 4.8320213 -2.255237 0.14698333
87000 28.445543 -1.3365026 0.78156195 4.4767689 4.4457575 -2.5008786 0.13879386
88000 27.656717 -1.1490599 0.87974869 4.4629952 4.7023033 -2.3258145 0.081904139
89000 28.838821 -1.020709 0.85587929 3.7110705 4.4938307 -2.4914483 0.11447952
90000 27.356497 -0.59107077 0.81879666 4.5209332 4.4703836 -2.3806717 0.071307775
91000 27.780445 -0.80564513 0.94752313 3.8468943 4.2924253 -2.1011134 0.1118672
92000 28.555276 -1.3514732 0.80826674 3.9590742 4.5775954 -2.4891232 0.054254978
93000 28.747267 -1.2133243 0.75507246 4.1319789 4.9048611 -2.4913887 0.13045693
94000 27.479343 -0.69973695 0.99696121 3.5966229 4.549025 -2.4155312 0.41745762
95000 27.726945 -1.1905026 1.1120842 4.7433275 4.5386861 -2.7947142 0.33671682
96000 28.021114 -1.0341645 0.6663033 4.2397505 4.6203984 -1.9904034 0.10972565
97000 28.382022 -1.3916008 1.180588 4.0729621 4.6741792 -2.554927 0.13462346
98000 27.895969 -0.7496449 1.3072185 4.2611888 4.3726077 -2.1320701 0.15376665
99000 28.517889 -1.2183957 1.279778 3.957647 4.2638434 -2.2888407 0.042705003
100000 28.109211 -1.2538948 0.83671785 4.3734766 4.544545 -2.3076497 0.042189096
Loop time of 2.84552 on 1 procs for 100000 steps with 34 atoms
Performance: 6072.706 ns/day, 0.004 hours/ns, 35142.973 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.94207 | 0.94207 | 0.94207 | 0.0 | 33.11
Bond | 1.6125 | 1.6125 | 1.6125 | 0.0 | 56.67
Neigh | 0.0073986 | 0.0073986 | 0.0073986 | 0.0 | 0.26
Comm | 0.012739 | 0.012739 | 0.012739 | 0.0 | 0.45
Output | 0.00075531 | 0.00075531 | 0.00075531 | 0.0 | 0.03
Modify | 0.21483 | 0.21483 | 0.21483 | 0.0 | 7.55
Other | | 0.05524 | | | 1.94
Nlocal: 34 ave 34 max 34 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 395 ave 395 max 395 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 395
Ave neighs/atom = 11.6176
Ave special neighs/atom = 9.52941
Neighbor list builds = 237
Dangerous builds = 0
Total wall time: 0:00:02

201
examples/cmap/log.5Oct16.cmap.g++.4
View File

@ -1,201 +0,0 @@
LAMMPS (5 Oct 2016)
# Created by charmm2lammps v1.8.2.6 beta on Thu Mar 3 20:56:57 EST 2016
units real
neigh_modify delay 2 every 1
#newton off
boundary p p p
atom_style full
bond_style harmonic
angle_style charmm
dihedral_style charmm
improper_style harmonic
pair_style lj/charmm/coul/charmm 8 12
#pair_style lj/charmmfsw/coul/charmmfsh 8 12
pair_modify mix arithmetic
fix cmap all cmap charmm22.cmap
Reading potential file charmm22.cmap with DATE: 2016-09-26
fix_modify cmap energy yes
read_data gagg.data fix cmap crossterm CMAP
orthogonal box = (-34.4147 -36.1348 -39.3491) to (45.5853 43.8652 40.6509)
1 by 2 by 2 MPI processor grid
reading atoms ...
34 atoms
scanning bonds ...
4 = max bonds/atom
scanning angles ...
6 = max angles/atom
scanning dihedrals ...
12 = max dihedrals/atom
scanning impropers ...
1 = max impropers/atom
reading bonds ...
33 bonds
reading angles ...
57 angles
reading dihedrals ...
75 dihedrals
reading impropers ...
7 impropers
4 = max # of 1-2 neighbors
7 = max # of 1-3 neighbors
13 = max # of 1-4 neighbors
16 = max # of special neighbors
special_bonds charmm
fix 1 all nve
#fix 1 all nvt temp 300 300 100.0
#fix 2 all shake 1e-9 500 0 m 1.0
velocity all create 0.0 12345678 dist uniform
thermo 1000
thermo_style custom step ecoul evdwl ebond eangle edihed f_cmap eimp
timestep 2.0
run 100000
Neighbor list info ...
1 neighbor list requests
update every 1 steps, delay 2 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7 -> bins = 12 12 12
Memory usage per processor = 15.9307 Mbytes
Step E_coul E_vdwl E_bond E_angle E_dihed f_cmap E_impro
0 26.542777 -0.93822087 1.2470497 4.8441789 4.5432816 -1.473352 0.10453023
1000 28.673005 -0.47724367 0.80029132 3.151679 4.4684446 -2.3928648 0.18604953
2000 27.67955 -1.170342 0.72018905 4.0400131 4.4713764 -2.5490207 0.21834436
3000 29.256656 -0.35856055 0.73303546 3.7411606 4.4710568 -2.8939692 0.37728884
4000 30.097549 -1.1353905 0.79007053 3.0688444 4.4091469 -2.3383587 0.20743631
5000 28.357525 -1.0723742 0.9180297 3.6579424 4.8792663 -2.3185572 0.088366962
6000 29.214175 -0.95299239 0.81926011 3.6805428 4.6742897 -2.9343578 0.26697816
7000 27.018614 -0.52423469 0.72502751 3.8840141 4.7780958 -2.3916014 0.24952572
8000 29.682494 -1.0940368 0.76113051 3.1089345 4.9357863 -2.5662256 0.14112613
9000 27.853918 -0.7913741 0.79503268 4.2177256 4.146792 -2.00475 0.090585666
10000 27.13754 -0.80551128 1.1325023 4.4718283 5.2460631 -3.4947725 0.11893125
11000 28.277434 -1.4897448 0.90075953 4.1895717 4.3594269 -1.9553119 0.090222212
12000 28.630973 -1.222206 0.67796385 3.3905661 4.9691334 -2.9052721 0.13897658
13000 28.593007 -0.95684026 0.75585196 3.7242568 4.7417932 -2.3893117 0.2074121
14000 26.147115 -0.6026921 0.93591488 5.1292829 4.9821952 -2.2571835 0.11872421
15000 26.29432 -0.82424162 1.048979 4.5569495 5.1189308 -2.9750422 0.16195676
16000 29.189992 -0.80998247 0.74093508 3.8299275 4.4536688 -2.5497538 0.19155639
17000 25.878012 -0.3519646 1.0988924 4.7359591 5.3923098 -2.7211029 0.13405223
18000 27.726135 -0.28229987 0.63072344 4.1777888 4.7237271 -2.2177157 0.15939372
19000 27.153504 -0.66477422 0.77910129 4.2036117 5.113851 -2.3494315 0.094793307
20000 28.044833 -1.2835827 0.88745367 3.9955526 4.5077788 -3.0116467 0.17197859
21000 27.205696 -0.74090037 1.0023251 4.3421733 4.912671 -2.3473271 0.26089356
22000 27.385785 -0.93740972 0.84554838 4.562743 4.883866 -2.2110955 0.11573301
23000 27.05534 -0.95605442 0.96719024 3.9277618 5.0359014 -2.6135949 0.21368061
24000 28.273378 -0.97543103 0.8983443 4.2067985 4.4782971 -2.4230505 0.30311692
25000 27.477789 -0.20383849 0.8380706 3.8037992 4.8312504 -2.5831791 0.093843746
26000 30.344199 -1.9773473 0.92882437 3.7821405 4.5176677 -2.3020968 0.2194307
27000 27.32767 -0.9803839 0.92988865 3.7611603 5.0328211 -2.4647656 0.18213622
28000 27.34208 -1.037938 0.74488346 4.1727342 4.7056812 -2.2718346 0.17741362
29000 27.682777 -0.51006495 0.57074224 4.7332237 4.7080462 -2.0491512 0.2130517
30000 24.925731 0.13670248 0.84976065 4.4143762 6.0677158 -3.5479173 0.28059419
31000 28.623419 -0.90725708 1.0710501 3.6930688 4.6639301 -2.2225373 0.20988139
32000 27.732286 -1.1948367 0.89230134 4.4398373 4.8923907 -3.5849327 0.49167488
33000 28.800772 -1.5319589 0.93455495 4.1634728 4.6107706 -2.3503486 0.22636535
34000 27.374398 -1.0957453 0.89450276 3.9829508 4.991786 -2.3548834 0.15869465
35000 28.38753 -0.89261166 0.90000776 3.536864 4.4293294 -2.4218118 0.10640557
36000 27.713974 0.088038031 0.85190574 3.8969601 4.6256355 -2.7935475 0.34671662
37000 29.13007 -1.378597 0.74412556 3.131538 4.6458653 -2.9373734 0.38035616
38000 28.556573 -1.4055344 1.139984 4.0035753 4.2938358 -2.489329 0.25338326
39000 26.447036 -1.1829705 0.87032438 5.0804461 4.5772023 -2.7346466 0.32165802
40000 27.991454 -0.64295679 0.61020872 4.165871 4.4623087 -2.2244194 0.13826991
41000 29.483296 -1.2400745 0.66926627 3.3473666 4.5766617 -2.3051145 0.12171554
42000 26.948627 -1.2162288 1.1440628 4.3993073 5.1176533 -2.4734485 0.15497709
43000 28.04459 -0.26543193 0.83647367 3.5160747 4.6964397 -2.2805068 0.12618821
44000 28.213608 -1.216128 0.9132792 4.0206483 4.9483599 -2.3387049 0.10132022
45000 28.283506 -1.0390766 0.86113772 4.504509 4.7209088 -2.3043085 0.14588362
46000 27.433853 -0.57912107 0.78448334 4.5998579 5.1181394 -2.6165094 0.18722528
47000 27.552939 -1.1128925 0.80087638 4.3448001 4.8062869 -2.4296883 0.2702479
48000 28.874034 -1.3242519 0.71770727 3.5648565 4.4671824 -2.2608958 0.16115978
49000 29.216186 -1.2210307 0.76937497 3.9260628 4.7550577 -2.7316081 0.085505664
50000 28.065856 -1.1545547 0.86953819 4.4137666 4.732157 -2.4450867 0.23320539
51000 26.308975 -0.99728352 0.90408444 4.2400186 5.6340425 -2.2090554 0.079882158
52000 28.517571 -1.5027398 0.83520278 3.8176552 4.3001251 -2.0731682 0.1665375
53000 28.77579 -1.3564268 0.97253881 3.6866407 4.8532347 -2.5330776 0.17668411
54000 29.135315 -1.0994106 0.67605671 3.6819254 4.3134408 -1.9796929 0.076951331
55000 26.168938 -0.76247492 0.88784685 4.6533473 6.0484793 -2.1334561 0.036876985
56000 27.471775 -0.68648837 1.0576168 4.0354311 4.4767052 -2.2368959 0.24950568
57000 29.787083 -1.4914384 1.0702944 3.5388133 4.5173097 -2.6694464 0.27937092
58000 28.705448 -1.3016617 0.63337853 3.9552713 4.4119825 -1.8774657 0.17540021
59000 29.130155 -0.91647363 0.84384883 3.1076903 4.5346348 -2.3457338 0.16674486
60000 26.874199 -0.81598034 1.3432151 5.1322624 4.9545484 -2.9566615 0.25950486
61000 27.401306 -0.82895856 1.1636949 4.020154 4.5745928 -2.601466 0.18061051
62000 28.930313 -1.5231967 0.85173243 4.3517328 4.4878662 -2.5859205 0.1755493
63000 26.56874 0.026147233 0.60836216 4.4231618 4.4390677 -2.1721849 0.08594237
64000 26.729023 -0.76953985 0.76734633 4.5104288 5.0886456 -2.2118551 0.11339216
65000 28.900471 -1.3901477 0.86194657 4.2774976 4.498325 -2.3672362 0.20668335
66000 26.884253 -0.21198879 0.98509625 4.0843117 4.4344172 -2.3289416 0.23631017
67000 27.210888 -0.84075559 1.0396559 4.7253607 4.4314589 -2.2985702 0.19326507
68000 28.042102 -1.1898715 1.053534 3.8748712 4.4358449 -2.3998723 0.2431659
69000 28.939141 -1.6968936 0.98155912 4.0460838 5.0075204 -2.5547087 0.28645131
70000 27.15577 -0.85202797 1.1469079 4.7645212 4.6133209 -2.3410451 0.086576572
71000 25.507417 -0.27780727 0.95157881 4.8759406 4.853401 -2.9598705 0.41011008
72000 29.804703 -1.4847015 0.96345767 3.6797304 4.3678377 -2.4594626 0.14480206
73000 28.602798 -1.4906143 0.72497266 4.2442974 4.5360598 -2.3621638 0.14385651
74000 28.4928 -0.91319873 1.0377472 3.8033127 4.3991601 -2.4051911 0.095567428
75000 26.38168 -0.70733237 1.1557817 5.697939 4.5935618 -2.4285007 0.058980519
76000 27.16626 -0.83631031 0.84844246 4.7460887 4.5801472 -2.1260014 0.12845946
77000 29.040661 -1.3089499 0.80285084 4.664804 4.5215895 -2.6861939 0.13215598
78000 27.477871 -1.0600977 0.88595045 4.6264017 5.4095605 -2.474411 0.10987174
79000 26.151797 -0.55779685 0.91382436 4.99964 4.9184022 -2.2547241 0.22854038
80000 28.14523 -0.54460026 0.8982411 3.5374555 4.3785673 -2.3196807 0.088567964
81000 29.029941 -1.6467789 0.79042284 3.7269899 4.7407998 -2.3795824 0.1408727
82000 27.920287 -0.72798032 1.0076975 3.4449461 4.5621371 -2.8239074 0.25103454
83000 29.131054 -1.114367 0.76887285 3.459639 4.5163922 -2.607825 0.19991648
84000 28.249768 -0.69944068 1.0510846 4.0436296 4.6430538 -2.4213355 0.077299966
85000 28.06888 -0.62132922 0.91829312 4.1294147 4.3099557 -2.354063 0.15866186
86000 28.664264 -1.1022906 0.87831695 4.5773522 4.6045802 -2.9206875 0.33950063
87000 27.960967 -1.2852756 0.77694253 3.9011301 4.9114139 -3.2374868 0.3068138
88000 27.190678 -1.2803268 1.1545301 4.5769709 5.2404761 -2.3825838 0.10356039
89000 26.792931 -0.44516641 1.0236244 4.2007253 4.7098685 -2.3608551 0.034447062
90000 27.173991 -0.87185611 1.065719 4.1953618 4.6856408 -2.6539232 0.16957757
91000 28.626528 -1.239257 0.89524651 4.7048012 4.6344201 -2.7367901 0.43534143
92000 27.661812 -1.109044 0.92817391 5.0294489 4.3890711 -2.4108669 0.12570139
93000 28.156793 -1.0820907 0.92812693 4.938385 4.4901426 -2.4023366 0.30135781
94000 28.842149 -1.3524969 1.1451109 4.3125908 4.6959035 -2.6747199 0.2254607
95000 27.862247 -1.2119045 1.0218976 4.2614082 4.4931316 -2.6902934 0.16345201
96000 27.084973 -0.93738328 1.3984324 4.5647189 4.4232205 -2.2834097 0.11217888
97000 27.587078 -0.89397255 0.78218462 3.8944421 4.3981479 -2.4205318 0.16570942
98000 27.981746 -1.2380545 0.84847869 4.311441 4.7340377 -2.4270441 0.023565612
99000 27.476625 -0.8569146 0.82550381 4.1656963 4.4064921 -2.4169708 0.160814
100000 26.121325 -0.63610855 1.0803389 4.9257118 4.7073263 -2.4010334 0.066303044
Loop time of 2.693 on 4 procs for 100000 steps with 34 atoms
Performance: 6416.646 ns/day, 0.004 hours/ns, 37133.367 timesteps/s
98.4% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.065478 | 0.2501 | 0.63682 | 45.6 | 9.29
Bond | 0.066944 | 0.44772 | 0.88814 | 53.7 | 16.63
Neigh | 0.0076509 | 0.0077319 | 0.0078275 | 0.1 | 0.29
Comm | 0.57917 | 1.4166 | 1.9823 | 46.9 | 52.60
Output | 0.0033755 | 0.0035856 | 0.0037644 | 0.2 | 0.13
Modify | 0.03866 | 0.1366 | 0.23978 | 24.6 | 5.07
Other | | 0.4306 | | | 15.99
Nlocal: 8.5 ave 15 max 2 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Nghost: 25.5 ave 32 max 19 min
Histogram: 1 1 0 0 0 0 0 0 1 1
Neighs: 98.75 ave 257 max 18 min
Histogram: 1 1 1 0 0 0 0 0 0 1
Total # of neighbors = 395
Ave neighs/atom = 11.6176
Ave special neighs/atom = 9.52941
Neighbor list builds = 294
Dangerous builds = 0
Total wall time: 0:00:02

26
src/MOLECULE/dihedral_charmmfsh.cpp → src/MOLECULE/dihedral_charmmfsw.cpp
View File

@ -21,7 +21,7 @@
#include <mpi.h>
#include <math.h>
#include <stdlib.h>
#include "dihedral_charmmfsh.h"
#include "dihedral_charmmfsw.h"
#include "atom.h"
#include "comm.h"
#include "neighbor.h"
@ -40,7 +40,7 @@ using namespace MathConst;
/* ---------------------------------------------------------------------- */
DihedralCharmmfsh::DihedralCharmmfsh(LAMMPS *lmp) : Dihedral(lmp)
DihedralCharmmfsw::DihedralCharmmfsw(LAMMPS *lmp) : Dihedral(lmp)
{
weightflag = 0;
writedata = 1;
@ -48,7 +48,7 @@ DihedralCharmmfsh::DihedralCharmmfsh(LAMMPS *lmp) : Dihedral(lmp)
/* ---------------------------------------------------------------------- */
DihedralCharmmfsh::~DihedralCharmmfsh()
DihedralCharmmfsw::~DihedralCharmmfsw()
{
if (allocated && !copymode) {
memory->destroy(setflag);
@ -63,7 +63,7 @@ DihedralCharmmfsh::~DihedralCharmmfsh()
/* ---------------------------------------------------------------------- */
void DihedralCharmmfsh::compute(int eflag, int vflag)
void DihedralCharmmfsw::compute(int eflag, int vflag)
{
int i1,i2,i3,i4,i,m,n,type;
double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
@ -322,7 +322,7 @@ void DihedralCharmmfsh::compute(int eflag, int vflag)
/* ---------------------------------------------------------------------- */
void DihedralCharmmfsh::allocate()
void DihedralCharmmfsw::allocate()
{
allocated = 1;
int n = atom->ndihedraltypes;
@ -342,7 +342,7 @@ void DihedralCharmmfsh::allocate()
set coeffs for one type
------------------------------------------------------------------------- */
void DihedralCharmmfsh::coeff(int narg, char **arg)
void DihedralCharmmfsw::coeff(int narg, char **arg)
{
if (narg != 5) error->all(FLERR,"Incorrect args for dihedral coefficients");
if (!allocated) allocate();
@ -384,7 +384,7 @@ void DihedralCharmmfsh::coeff(int narg, char **arg)
error check and initialize all values needed for force computation
------------------------------------------------------------------------- */
void DihedralCharmmfsh::init_style()
void DihedralCharmmfsw::init_style()
{
// insure use of CHARMM pair_style if any weight factors are non-zero
// set local ptrs to LJ 14 arrays setup by Pair
@ -392,14 +392,14 @@ void DihedralCharmmfsh::init_style()
if (weightflag) {
int itmp;
if (force->pair == NULL)
error->all(FLERR,"Dihedral charmmfsh is incompatible with Pair style");
error->all(FLERR,"Dihedral charmmfsw is incompatible with Pair style");
lj14_1 = (double **) force->pair->extract("lj14_1",itmp);
lj14_2 = (double **) force->pair->extract("lj14_2",itmp);
lj14_3 = (double **) force->pair->extract("lj14_3",itmp);
lj14_4 = (double **) force->pair->extract("lj14_4",itmp);
int *ptr = (int *) force->pair->extract("implicit",itmp);
if (!lj14_1 || !lj14_2 || !lj14_3 || !lj14_4 || !ptr)
error->all(FLERR,"Dihedral charmmfsh is incompatible with Pair style");
error->all(FLERR,"Dihedral charmmfsw is incompatible with Pair style");
implicit = *ptr;
}
@ -414,7 +414,7 @@ void DihedralCharmmfsh::init_style()
if (p_cutcoul == NULL || p_cutljinner == NULL ||
p_cutlj == NULL || p_dihedflag == NULL)
error->all(FLERR,"Dihedral charmmfsh is incompatible with Pair style");
error->all(FLERR,"Dihedral charmmfsw is incompatible with Pair style");
dihedflag = *p_dihedflag;
cut_coul14 = *p_cutcoul;
@ -433,7 +433,7 @@ void DihedralCharmmfsh::init_style()
proc 0 writes out coeffs to restart file
------------------------------------------------------------------------- */
void DihedralCharmmfsh::write_restart(FILE *fp)
void DihedralCharmmfsw::write_restart(FILE *fp)
{
fwrite(&k[1],sizeof(double),atom->ndihedraltypes,fp);
fwrite(&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp);
@ -446,7 +446,7 @@ void DihedralCharmmfsh::write_restart(FILE *fp)
proc 0 reads coeffs from restart file, bcasts them
------------------------------------------------------------------------- */
void DihedralCharmmfsh::read_restart(FILE *fp)
void DihedralCharmmfsw::read_restart(FILE *fp)
{
allocate();
@ -474,7 +474,7 @@ void DihedralCharmmfsh::read_restart(FILE *fp)
proc 0 writes to data file
------------------------------------------------------------------------- */
void DihedralCharmmfsh::write_data(FILE *fp)
void DihedralCharmmfsw::write_data(FILE *fp)
{
for (int i = 1; i <= atom->ndihedraltypes; i++)
fprintf(fp,"%d %g %d %d %g\n",i,k[i],multiplicity[i],shift[i],weight[i]);

16
src/MOLECULE/dihedral_charmmfsh.h → src/MOLECULE/dihedral_charmmfsw.h
View File

@ -13,22 +13,22 @@
#ifdef DIHEDRAL_CLASS
DihedralStyle(charmmfsh,DihedralCharmmfsh)
DihedralStyle(charmmfsw,DihedralCharmmfsw)
#else
#ifndef LMP_DIHEDRAL_CHARMMFSH_H
#define LMP_DIHEDRAL_CHARMMFSH_H
#ifndef LMP_DIHEDRAL_CHARMMFSW_H
#define LMP_DIHEDRAL_CHARMMFSW_H
#include <stdio.h>
#include "dihedral.h"
namespace LAMMPS_NS {
class DihedralCharmmfsh : public Dihedral {
class DihedralCharmmfsw : public Dihedral {
public:
DihedralCharmmfsh(class LAMMPS *);
virtual ~DihedralCharmmfsh();
DihedralCharmmfsw(class LAMMPS *);
virtual ~DihedralCharmmfsw();
virtual void compute(int, int);
virtual void coeff(int, char **);
virtual void init_style();
@ -73,9 +73,9 @@ E: Incorrect weight arg for dihedral coefficients
Self-explanatory. Check the input script or data file.
E: Dihedral charmmfsh is incompatible with Pair style
E: Dihedral charmmfsw is incompatible with Pair style
Dihedral style charmmfsh must be used with a pair style charmm
Dihedral style charmmfsw must be used with a pair style charmm
in order for the 1-4 epsilon/sigma parameters to be defined.
*/

14
src/fix_adapt.cpp
View File

@ -186,10 +186,10 @@ nadapt(0), id_fix_diam(NULL), id_fix_chg(NULL), adapt(NULL)
memory->create(adapt[m].array_orig,n+1,n+1,"adapt:array_orig");
// allocate bond style arrays:
n = atom->nbondtypes;
for (int m = 0; m < nadapt; ++m)
if (adapt[m].which == BOND)
// For now just use same storage and fake it to be one-dimensional:
memory->create(adapt[m].vector_orig,n+1,"adapt:vector_orig");
}
@ -389,7 +389,6 @@ void FixAdapt::init()
} else if (ad->which == BOND){
ad->bond = NULL;
anybond = 1;
// Use same routines from pair to strip any suffices:
int n = strlen(ad->bstyle) + 1;
char *bstyle = new char[n];
@ -404,7 +403,6 @@ void FixAdapt::init()
ad->bond = force->bond_match(bsuffix);
delete [] bsuffix;
}
// If not set grab regular one instead:
if (ad->bond == NULL) ad->bond = force->bond_match(bstyle);
if (ad->bond == NULL )
error->all(FLERR,"Fix adapt bond style does not exist");
@ -414,7 +412,7 @@ void FixAdapt::init()
if (ptr == NULL)
error->all(FLERR,"Fix adapt bond style param not supported");
// For bond styles you should use a vector
// for bond styles, use a vector
if (ad->bdim == 1) ad->vector = (double *) ptr;
@ -449,10 +447,10 @@ void FixAdapt::init()
for (i = ad->ilo; i <= ad->ihi; i++)
for (j = MAX(ad->jlo,i); j <= ad->jhi; j++)
ad->array_orig[i][j] = ad->array[i][j];
}else if (ad->which == PAIR && ad->pdim == 0){
} else if (ad->which == PAIR && ad->pdim == 0){
ad->scalar_orig = *ad->scalar;
}else if (ad->which == BOND && ad->bdim == 1){
} else if (ad->which == BOND && ad->bdim == 1){
for (i = ad->ilo; i <= ad->ihi; ++i )
ad->vector_orig[i] = ad->vector[i];
}
@ -612,8 +610,10 @@ void FixAdapt::change_settings()
modify->addstep_compute(update->ntimestep + nevery);
// re-initialize pair styles if any PAIR settings were changed
// ditto for bond styles if any BOND setitings were changes
// this resets other coeffs that may depend on changed values,
// and also offset and tail corrections
// and also offset and tail corrections
if (anypair) {
for (int m = 0; m < nadapt; m++) {
Adapt *ad = &adapt[m];

2
src/version.h
View File

@ -1 +1 @@
#define LAMMPS_VERSION "31 Mar 2017"
#define LAMMPS_VERSION "11 Apr 2017"