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<div class="section" id="fix-bocs-command">
<span id="index-0"></span><h1>fix bocs command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
fix ID group-ID bocs keyword values ...
keyword = <em>temp</em> or <em>cgiso</em> or <em>analytic</em> or <em>linear_spline</em> or <em>cubic_spline</em>
<em>temp</em> values = Tstart Tstop Tdamp
<em>cgiso</em> values = Pstart Pstop Pdamp
<em>basis set</em>
<em>analytic</em> values = V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N
<em>linear_spline</em> values = input_filename
<em>cubic_spline</em> values = input_filename
</pre>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">bocs</span> <span class="n">temp</span> <span class="mf">300.0</span> <span class="mf">300.0</span> <span class="mf">100.0</span> <span class="n">cgiso</span> <span class="mf">0.986</span> <span class="mf">0.986</span> <span class="mf">1000.0</span> <span class="n">analytic</span> <span class="mf">66476.015</span> <span class="mi">968</span> <span class="mi">2</span> <span class="mf">245030.10</span> <span class="mf">8962.20</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">bocs</span> <span class="n">temp</span> <span class="mf">300.0</span> <span class="mf">300.0</span> <span class="mf">100.0</span> <span class="n">cgiso</span> <span class="mf">0.986</span> <span class="mf">0.986</span> <span class="mf">1000.0</span> <span class="n">cubic_spline</span> <span class="n">input_Fv</span><span class="o">.</span><span class="n">dat</span>
<span class="n">compute</span> <span class="n">bocsPress</span> <span class="nb">all</span> <span class="n">pressureBocs</span> <span class="n">thermo_temp</span>
<span class="n">thermo_modify</span> <span class="n">press</span> <span class="n">bocsPress</span>
<span class="n">fix_modify</span> <span class="mi">1</span> <span class="n">press</span> <span class="n">bocsPress</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>These commands incorporate a pressure correction as described by
Dunn and Noid in <a class="reference internal" href="#bocs-dunn1"><span class="std std-ref">(Dunn1)</span></a> to the standard MTTK
barostat by Martyna et. al. in <a class="reference internal" href="#bocs-martyna"><span class="std std-ref">(Martyna)</span></a> .
The first half of the command mimics a standard fix npt command:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">bocs</span> <span class="n">temp</span> <span class="n">Tstart</span> <span class="n">Tstop</span> <span class="n">Tcoupl</span> <span class="n">cgiso</span> <span class="n">Pstart</span> <span class="n">Pstop</span> <span class="n">Pdamp</span>
</pre></div>
</div>
<p>The two differences are replacing <em>npt</em> with <em>bocs</em>, and replacing
<em>iso</em>/<em>aniso</em>/<em>etc</em> with <em>cgiso</em>.
The rest of the command details what form you would like to use for
the pressure correction equation. The choices are: <em>analytic</em>, <em>linear_spline</em>,
or <em>cubic_spline</em>.</p>
<p>With either spline method, the only argument that needs to follow it
is the name of a file that contains the desired pressure correction
as a function of volume. The file should be formatted so each line has:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Volume_i</span><span class="p">,</span> <span class="n">PressureCorrection_i</span>
</pre></div>
</div>
<p>Note both the COMMA and the SPACE separating the volume&#8217;s
value and its corresponding pressure correction. The volumes in the file
should be uniformly spaced. Both the volumes and the pressure corrections
should be provided in the proper units, e.g. if you are using <em>units real</em>,
the volumes should all be in cubic angstroms, and the pressure corrections
should all be in atomspheres. Furthermore, the table should start/end at a
volume considerably smaller/larger than you expect your system to sample
during the simulation. If the system ever reaches a volume outside of the
range provided, the simulation will stop.</p>
<p>With the <em>analytic</em> option, the arguments are as follows:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">...</span> <span class="n">analytic</span> <span class="n">V_avg</span> <span class="n">N_particles</span> <span class="n">N_coeff</span> <span class="n">Coeff_1</span> <span class="n">Coeff_2</span> <span class="o">...</span> <span class="n">Coeff_N</span>
</pre></div>
</div>
<p>Note that <em>V_avg</em> and <em>Coeff_i</em> should all be in the proper units, e.g. if you
are using <em>units real</em>, <em>V_avg</em> should be in cubic angstroms, and the
coefficients should all be in atmospheres * cubic angstroms.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>As this is computing a (modified) pressure, group-ID should be <em>all</em>.</p>
<p>The pressure correction has only been tested for use with an isotropic
pressure coupling in 3 dimensions.</p>
<p>There are three additional commands that must be supplied along with fix
bocs. They are given in the examples section. The name <em>bocsPress</em> can be
changed for any name of your choosing, provided it remains consistent across
all three commands. Additionally, the ID <em>1</em> in the <em>fix_modify</em> command must
match up with the <em>ID</em> specified in the original <em>fix bocs</em> command. Everything else
in those three commands must be unchanged. The first two commands can be
specified before the <em>fix bocs</em> command, but the <em>fix_modify</em> command must be
given after the original <em>fix bocs</em> command.</p>
<p>The <em>compute</em> command tells LAMMPS to compute the pressure using the modified
barostat.</p>
<p>The <em>thermo_modify</em> command tells LAMMPS to report the pressure from the modified
barostat instead of the default pressure, i.e. thermo_press.</p>
<p>The <em>fix_modify</em> command tells LAMMPS to use the pressure from the modified
barostat for the fix, instead of using the default presure, i.e. thermo_press.</p>
<p><strong>Related:</strong></p>
<p>For more details about the pressure correction and the entire BOCS software
package, visit the <a class="reference external" href="https://github.com/noid-group/BOCS">BOCS package on github</a> and read the release
paper by Dunn et. al. <a class="reference internal" href="#bocs-dunn2"><span class="std std-ref">(Dunn2)</span></a> .</p>
<hr class="docutils" />
<p id="bocs-dunn1"><strong>(Dunn1)</strong> Dunn and Noid, J Chem Phys, 143, 243148 (2015).</p>
<p id="bocs-martyna"><strong>(Martyna)</strong> Martyna, Tobias, and Klein, J Chem Phys, 101, 4177 (1994).</p>
<p id="bocs-dunn2"><strong>(Dunn2)</strong> Dunn, Lebold, DeLyser, Rudzinski, and Noid, J. Phys. Chem. B, 122, 3363 (2018).</p>
</div>
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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.

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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
175 1 16.9 35.09 22.94
176 1 15.18 6.74 2.33
177 1 40.54 12.58 31.65
178 1 21.21 37.62 14.35
179 1 33.52 38.19 14.89
180 1 22.06 12.49 29.81
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
265 1 3.74 13.22 31.05
266 1 30.78 0.7 24.57
267 1 24.5 12.94 10.81
268 1 33.88 26.44 1.96
269 1 29.92 22.6 9.59
270 1 15.87 21.94 33.44
271 1 23.63 8.41 10.95
272 1 26.53 0.01 7.58
273 1 33.88 8.73 2.52
274 1 39.74 31.46 36.87
275 1 13.28 39.54 37
276 1 24.74 35.41 32.14
277 1 17.3 34.32 6.85
278 1 24.43 13.36 5.63
279 1 31.23 17.12 7.11
280 1 15.58 37.85 34.06
281 1 25.93 38.17 3.13
282 1 31.84 34.34 39.67
283 1 14.41 17.74 14.43
284 1 9.4 1.78 29.53
285 1 8.29 29.61 6.81
286 1 7.13 17.36 -0.19
287 1 38.04 19.52 11.25
288 1 34.87 32.77 38.75
289 1 27.18 22.49 5.69
290 1 29.69 27.11 20.29
291 1 25.23 2.22 39.75
292 1 35.8 17.1 36.09
293 1 20.53 17.67 35.47
294 1 23.41 31.36 2.24
295 1 25.17 20.09 29.2
296 1 0.32 9.28 39.74
297 1 22.49 18.77 29.89
298 1 38.64 0.85 39.43
299 1 18.55 5.87 9.15
300 1 35.21 28.69 25.76
301 1 39.24 15.68 6.36
302 1 5.91 13.29 3.92
303 1 0.5 21.25 21.62
304 1 34.39 9.43 18.59
305 1 22.7 1.03 8.79
306 1 40.15 16.25 24.87
307 1 16.52 13.69 10.25
308 1 6.88 36.77 39.57
309 1 11.95 37.1 7.59
310 1 19.49 26.66 9.76
311 1 36.34 29.89 29.31
312 1 18.76 35.75 12.72
313 1 23.15 38.68 4.96
314 1 10.78 17.11 34.38
315 1 13.58 14.89 0.34
316 1 4.73 33.88 32.41
317 1 12.68 29.51 17.07
318 1 9.45 27 4.98
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
324 1 15.01 34.16 28.32
325 1 28.71 36.53 15.08
326 1 9.64 13.94 24.05
327 1 1.24 36.96 30.41
328 1 15.44 31.39 4.77
329 1 25.72 14.42 38.01
330 1 7.35 31.84 12.61
331 1 32.33 16.79 3.07
332 1 15.86 0.39 8.39
333 1 27.69 7.32 25.74
334 1 27.77 1.17 4.96
335 1 29.38 26.68 23.48
336 1 14.95 3.41 2.13
337 1 2.45 38.8 17.54
338 1 9.18 27.58 31.12
339 1 36.62 15.23 23.66
340 1 12.23 30.74 10.85
341 1 12.87 0.23 24.05
342 1 33.85 35.75 19.95
343 1 36.36 30.35 13.94
344 1 38.11 8.15 5.49
345 1 15.58 1.29 29.89
346 1 25.95 30.47 39.19
347 1 27.69 15.5 13.37
348 1 25.48 13.7 25.29
349 1 0.72 39.53 4.41
350 1 8.75 15.21 5.79
351 1 10.49 26.46 27.25
352 1 16.9 20.08 26.58
353 1 3.95 4.33 20.25
354 1 18.03 7.66 31.87
355 1 21.35 2.88 17.26
356 1 32.92 22.68 6.56
357 1 21.72 4.62 12.02
358 1 37.6 6.04 25.2
359 1 22.22 23.78 7.36
360 1 12.53 19.53 10.6
361 1 17.87 26.05 19.32
362 1 20.94 30.75 31.23
363 1 22.33 11.87 35.79
364 1 28.54 6.88 10.52
365 1 29.58 26.13 8.56
366 1 19.06 24.2 21.73
367 1 25.05 38.41 26.91
368 1 18.66 40.35 4.69
369 1 11.87 6.75 12.72
370 1 17.99 11.82 37.79
371 1 8.97 24.7 0.61
372 1 26.89 1.52 31.33
373 1 6.88 22.51 14.06
374 1 29.51 3.87 13.35
375 1 0.95 14.53 10
376 1 26.43 31.54 11.63
377 1 6.1 35.16 11.28
378 1 10.2 15.91 28.7
379 1 13.24 25.67 24.3
380 1 34.5 3.91 20.22
381 1 22.48 2.17 5.2
382 1 24.26 16.15 11.3
383 1 20.63 32.57 27.3
384 1 39.95 6.81 1.05
385 1 24.38 34.78 38.27
386 1 4.63 23.56 0.55
387 1 33.5 8.38 36.97
388 1 5.76 27.14 12.06
389 1 37.45 26.58 32.25
390 1 2.8 8.96 32.35
391 1 5.29 39.84 30.1
392 1 29.2 26.49 31.18
393 1 33.91 27.39 12.89
394 1 3.37 14.19 39.34
395 1 30.68 28.7 27
396 1 2.59 18.45 19.38
397 1 13.55 0.75 27.35
398 1 3.82 20.12 16.1
399 1 37.72 0.72 34.29
400 1 23.85 3.32 19.46
401 1 4.78 0.67 38.23
402 1 22.78 23.26 38.6
403 1 11.56 39.29 4.23
404 1 21.38 32.45 5.39
405 1 8.32 19.42 9.52
406 1 28.43 31.07 17.8
407 1 11.02 5.75 39.84
408 1 27.36 36.71 7.62
409 1 34.22 16.74 27.88
410 1 3.22 22.01 27.42
411 1 29.2 15.76 32.33
412 1 25.29 23.44 2.2
413 1 10.8 32.43 39.96
414 1 32.2 1.41 4.44
415 1 32.94 15.59 37.21
416 1 6.8 8.08 0.84
417 1 10.42 9.91 37.73
418 1 1.18 31.39 3.93
419 1 10.1 36.38 38.57
420 1 32.89 26.96 35.07
421 1 28.12 11.93 25.96
422 1 4.9 29.15 -0.25
423 1 2.21 27.99 3.72
424 1 11.33 3.94 25.55
425 1 3.3 30.26 10.78
426 1 11.57 27.26 19.31
427 1 21.79 32.67 13.3
428 1 4.96 26.53 33.78
429 1 33.41 32.87 18.46
430 1 13.92 30.37 20.3
431 1 16.91 3.5 11.57
432 1 -0.06 4.42 34.05
433 1 7.04 24.33 16.85
434 1 28.66 11.93 19.73
435 1 30.21 1.75 36.36
436 1 3.91 6.2 6.26
437 1 7.01 25.6 27.34
438 1 34 1.06 18.12
439 1 29.14 8.5 3.09
440 1 40.13 23.52 16.94
441 1 21.69 22.38 26.78
442 1 18.44 32.85 39.84
443 1 38.87 1.99 27.63
444 1 10.47 12.02 33.68
445 1 9.65 19.94 21.88
446 1 25.04 8.12 27.89
447 1 12.18 16.78 31.09
448 1 38.31 8.2 30.6
449 1 0.11 5.21 18.12
450 1 23.48 7.88 38.7
451 1 7.9 11.99 7.04
452 1 2.09 34.5 8.64
453 1 19 18.3 0.42
454 1 37.94 18.06 15.21
455 1 25.05 33.33 29.55
456 1 33.74 37.88 34.54
457 1 36.07 29.5 17.47
458 1 27.7 13.54 10.46
459 1 27.18 23.18 21.06
460 1 17.49 2.04 23.22
461 1 23.84 26.31 36.76
462 1 31.08 32.24 24.92
463 1 17.7 28.73 16.66
464 1 1.59 15.5 18.04
465 1 33.49 18.99 8.75
466 1 1.19 8.43 28.01
467 1 5.43 20.26 22.25
468 1 23.3 5.31 15.05
469 1 27.09 4.47 21.96
470 1 26.61 27.48 28.83
471 1 13 3.18 13.4
472 1 36.09 34.56 10.58
473 1 19.09 15.33 7.48
474 1 12.94 18.16 22.07
475 1 38.8 16.16 36.73
476 1 16.73 39.94 -0.46
477 1 3.64 12.56 9.42
478 1 27.64 3.31 18.29
479 1 15.58 12.36 4.52
480 1 15.37 11.18 18.19
481 1 37.52 11.23 14.94
482 1 37.16 2.3 10.01
483 1 36.19 9.86 21.99
484 1 36.38 21.09 4.76
485 1 38.15 12.94 25.35
486 1 15.1 29.65 24.64
487 1 16.54 29.12 38.85
488 1 33.86 11.39 14.4
489 1 27.99 18.55 9.87
490 1 0.66 1.26 8.28
491 1 29.89 33.84 29.75
492 1 6.64 33.3 6.74
493 1 31.47 0.39 11.25
494 1 8.76 15.96 10.74
495 1 39.6 15.8 21.04
496 1 22.38 28.55 19.85
497 1 25.87 6.23 5.4
498 1 36.24 26.67 38.61
499 1 23.05 8.79 7.01
500 1 32.05 4.16 8.87
501 1 35.3 13.36 38.03
502 1 39.91 25.91 36.45
503 1 32.17 17.27 31.82
504 1 29.99 21.54 20.57
505 1 9.39 0.57 34.17
506 1 22.12 17.22 13.03
507 1 15.23 16.27 24.39
508 1 26.32 25.89 13.26
509 1 39.25 3.46 1.34
510 1 32.56 10.28 7.96
511 1 25.76 14.8 34.79
512 1 32.12 5.38 36.94
513 1 17.74 15.37 14.87
514 1 21.93 3.26 25.26
515 1 24.05 0.48 36.27
516 1 8.2 19.02 33.92
517 1 33.07 25.88 24.79
518 1 12.54 0.52 32.8
519 1 18.5 6.34 23.21
520 1 35.93 10.26 34.79
521 1 19.33 11.86 6.94
522 1 1.63 5.31 25.43
523 1 30.62 36.78 30.77
524 1 12.25 26.79 13.74
525 1 21 1.47 13.99
526 1 22.24 29.36 34.11
527 1 29.05 1.74 0.24
528 1 19.34 25.14 39.77
529 1 12.9 25.42 35.42
530 1 4.1 20.69 33.31
531 1 35.38 5.64 9.17
532 1 5.01 34.03 23.36
533 1 15.7 10.01 7.1
534 1 25.95 19.48 24.73
535 1 11.15 4.16 21.43
536 1 1.47 3.23 13.72
537 1 26.54 36.76 17.48
538 1 7.65 30.6 27.73
539 1 18.59 3.05 3.32
540 1 6.92 36.14 15.67
541 1 12.72 36.21 32.72
542 1 16.33 26.24 14.35
543 1 21.66 12.61 26.18
544 1 15.72 32.37 10.71
545 1 27.57 15.75 4.97
546 1 20.18 39.13 18.44
547 1 18.77 17.09 4.74
548 1 12.75 14.08 17.89
549 1 10.71 37.26 35.13
550 1 20.88 32.12 9.94
551 1 8.69 0.06 9.54
552 1 1.58 12.61 26.42
553 1 10.29 22.73 13.14
554 1 23.31 25.7 4.97
555 1 36.7 30.78 5.26
556 1 5.6 28.71 23.76
557 1 13.04 7.91 15.46
558 1 40.24 33.53 34.5
559 1 39.7 18.36 34.25
560 1 23.52 22.84 21.14
561 1 32.82 27.9 5.02
562 1 1.52 33.77 27.04
563 1 31.48 18.68 13.1
564 1 34 24.07 34.55
565 1 34.72 25.03 30.45
566 1 18.92 5.7 16.54
567 1 15.26 40.2 16.97
568 1 24.55 16.8 26.26
569 1 17.59 18.03 31.75
570 1 12.08 27.38 38.42
571 1 31.42 21.91 35.27
572 1 9.68 6.93 36.96
573 1 22.93 15.19 2.53
574 1 11.83 24.38 2.24
575 1 16.02 12.44 31.42
576 1 20.24 10.7 20.15
577 1 37.38 17.37 40.63
578 1 3.74 17.41 22.49
579 1 23.21 9.86 23.99
580 1 2.49 36.56 38
581 1 20.51 1.54 22.62
582 1 8.23 33.44 33.15
583 1 30.93 8.12 14.85
584 1 36.35 3.92 37.65
585 1 5.57 10.63 28.64
586 1 30.24 22.84 4.6
587 1 3.24 15.97 7.43
588 1 22.64 0.7 27.09
589 1 1.64 40.37 27.74
590 1 30.53 35.28 3.5
591 1 25.55 4.7 2.53
592 1 22.04 29.56 12.29
593 1 3.42 8.76 2.28
594 1 16.37 37.65 7.87
595 1 20.65 12.75 2.9
596 1 8.07 20.49 2.6
597 1 20.04 24.72 28.2
598 1 29.75 0.33 16.1
599 1 31.36 33.09 8.02
600 1 8.6 10.56 2.65
601 1 20.55 33.93 33.71
602 1 23.11 -0.42 31.7
603 1 27.07 6.69 18.5
604 1 15.65 23.71 11.8
605 1 23.88 24.17 30.1
606 1 0.79 32.46 16.99
607 1 25.96 20.19 2.43
608 1 35.16 12.33 4.73
609 1 16.53 17.12 10.45
610 1 19.74 35.94 8.62
611 1 -0.24 28.29 28.3
612 1 33.15 4.39 12.64
613 1 24.27 18.59 33.59
614 1 0.3 9.61 23.54
615 1 5.52 10.89 34.71
616 1 9.85 26.26 34.42
617 1 25.54 37.74 39.13
618 1 4.11 29.65 5.81
619 1 30.86 22.72 31.07
620 1 39.54 34.54 23.24
621 1 15.03 9.34 12.11
622 1 21.93 38.49 9.53
623 1 18.21 19.2 16.65
624 1 38.71 32.83 14.49
625 1 37.74 36.38 31.43
626 1 7.57 2.2 1.07
627 1 12.27 10.05 1.53
628 1 18.32 19.55 12.51
629 1 12.49 24.81 16.57
630 1 35.07 31.62 22.85
631 1 4.91 19.68 30.45
632 1 11.36 2.92 36.19
633 1 26.76 35.53 1.29
634 1 1.13 14.55 14.77
635 1 8.2 25.14 37.83
636 1 -0.5 0.85 23.08
637 1 17.95 18.01 37.61
638 1 2.44 37.75 0.71
639 1 3.77 23.41 17.91
640 1 3.34 14.41 35.96
641 1 14.89 31.42 31.76
642 1 15.72 22.91 30.66
643 1 37.42 3.13 5.51
644 1 1.51 38.14 20.78
645 1 12.55 18.16 25.81
646 1 18.98 15.88 29.21
647 1 17.33 32.04 27.87
648 1 31.21 37.38 22.84
649 1 11.88 32.4 31
650 1 25.1 2.19 12.69
651 1 38.85 39.1 27.87
652 1 5.9 16.14 33.34
653 1 6.3 17.5 36.46
654 1 2.28 25.02 12.53
655 1 19.33 25.49 6.78
656 1 8.57 37.22 8.4
657 1 22 38.61 24.14
658 1 35.63 3.23 2.15
659 1 37.35 22.64 9.99
660 1 25.46 28.22 33.18
661 1 13.99 4.21 9.07
662 1 9.04 40.64 37.59
663 1 17.46 6.49 27.93
664 1 1.42 6.14 30.2
665 1 25.82 28.28 10.33
666 1 30.71 30.2 -0.02
667 1 8.05 29.32 0.62
668 1 6.49 3.17 6.65
669 1 7.77 39.88 26.03
670 1 28.53 12.14 30.96
671 1 6.25 12.64 39.55
672 1 3.78 7.96 25.83
673 1 28.69 29.58 6.61
674 1 5.32 18.55 8.6
675 1 5.3 11.44 14.19
676 1 39 12.03 36.99
677 1 11.08 32.51 19.12
678 1 38.48 1.03 20.34
679 1 38.47 11.31 10.12
680 1 3.65 20.3 11.99
681 1 27.18 11.39 3.4
682 1 29.61 20.72 38.86
683 1 31.88 4.82 24.75
684 1 14.52 36.61 25.66
685 1 21.68 19.96 24.58
686 1 1.2 13.59 23.16
687 1 37.71 5.97 35.28
688 1 19.81 22.04 37.54
689 1 40.67 27.07 10.14
690 1 38.57 13.96 13.75
691 1 18.15 17.19 21.63
692 1 3.76 27.51 30.32
693 1 11.39 25.09 7.96
694 1 28.95 22.02 13.33
695 1 31.72 35.46 35.33
696 1 15.17 6.03 23.94
697 1 9.63 9.42 22.18
698 1 27.76 4.1 38.61
699 1 27.37 37.46 11.07
700 1 35.69 15.24 6.39
701 1 21.92 33.09 36.84
702 1 4.79 15.51 13.28
703 1 9.31 26.44 22.8
704 1 30.14 38.31 6.98
705 1 4.33 6.66 13.77
706 1 3.66 27.15 37.83
707 1 0.44 24.06 29.62
708 1 35.4 9.59 9.8
709 1 33.77 39.44 21.41
710 1 29.2 18.74 24.38
711 1 34.14 30 7.36
712 1 16.02 4.37 6.43
713 1 35.75 39.41 40.58
714 1 15.32 11.84 23.24
715 1 32.52 24.39 20.97
716 1 11.45 2.9 7.16
717 1 7.07 34.28 36.04
718 1 11.41 8.83 7.57
719 1 29.29 27.79 16.55
720 1 2.41 9.16 16.14
721 1 13.14 38.07 12.01
722 1 37.45 14.26 18.3
723 1 34.64 18.37 16.65
724 1 29.26 34.28 33.46
725 1 13.67 19.83 3.04
726 1 19.64 2.6 32.95
727 1 23.61 23.55 11.34
728 1 6.87 22.5 36.5
729 1 36.78 28.34 22.96
730 1 11.3 13.98 9.84
731 1 20.82 19.73 9.16
732 1 12.65 12.61 6.16
733 1 9.25 7.81 25.28
734 1 25.4 29.36 5.84
735 1 17.86 9.06 4.45
736 1 35.84 40.51 26.06
737 1 26.97 21.28 31.59
738 1 39.94 38.14 24.86
739 1 3.16 17.07 2.49
740 1 14.08 15.4 36.99
741 1 26.1 13.88 29.68
742 1 26.36 20 20.56
743 1 12.02 6.35 27.65
744 1 11.21 19.14 15.27
745 1 35.86 22.93 26.81
746 1 32.26 12.62 2.68
747 1 29.36 4.91 6.86
748 1 20.14 7.97 29.32
749 1 25.53 11.2 36.18
750 1 30.36 14.25 24.79
751 1 29.84 38.37 39.29
752 1 15.79 36.4 4.26
753 1 32.59 14.17 10.29
754 1 13.89 34.54 15.42
755 1 12.13 33.62 7.27
756 1 25.86 23.81 33.97
757 1 18.4 31.27 34.96
758 1 6.58 40.49 17.57
759 1 5.64 39.86 23.05
760 1 25.32 33 16.24
761 1 0.98 10.99 12.21
762 1 32.86 23.75 12.41
763 1 32.91 1.3 26.94
764 1 9.46 8.66 31.47
765 1 17.49 15.53 1.82
766 1 8.17 18.16 15.3
767 1 4.84 30.63 26.32
768 1 6.75 37.1 30.8
769 1 7.16 5.72 15.74
770 1 20.09 17.82 19.18
771 1 1.02 27.99 32.54
772 1 21.44 1.28 38.4
773 1 21.06 14.62 37.08
774 1 27.82 18.99 15.96
775 1 33.51 21.46 22.82
776 1 8.29 2.79 17.09
777 1 18.14 11.41 28.62
778 1 17.94 28.54 32.73
779 1 36.1 9.54 40.1
780 1 36.55 2.62 22.97
781 1 27.29 10.41 39.35
782 1 22.04 37.76 2.02
783 1 23.01 30.08 16.58
784 1 6.34 15.31 21.61
785 1 7.3 22.39 7.74
786 1 38 5.77 21.04
787 1 32.93 12.85 26.58
788 1 22.43 15.36 16.72
789 1 18.54 2.38 8.35
790 1 0.62 31.88 23.84
791 1 39.56 30.3 21.7
792 1 7.56 11.78 25.2
793 1 16.05 3.98 26.72
794 1 24.33 36.16 13.16
795 1 26.38 31.24 35.77
796 1 14.94 26.46 -0.44
797 1 3.53 28 19.79
798 1 11.94 32.27 25.88
799 1 34.59 15.06 19.23
800 1 3.51 10.62 24.22
801 1 13.18 21.59 35.52
802 1 19.95 13.15 16.23
803 1 24.48 9.63 19.58
804 1 37.7 34.42 19.19
805 1 22.84 19.59 5.52
806 1 34.62 36.75 12.26
807 1 10.33 21.85 25.15
808 1 21.51 29.7 7.23
809 1 34.05 3 30.58
810 1 12.43 29.67 5.59
811 1 18.94 21.82 29.31
812 1 39.21 17.7 4
813 1 7.04 2.97 37.09
814 1 30.87 10.8 22.09
815 1 33.54 7.16 23.15
816 1 32.82 32.27 11.47
817 1 21.8 14.54 21.61
818 1 38.83 6.69 13.68
819 1 30.37 39.05 18.66
820 1 31.21 15.08 13.79
821 1 1.07 11.97 35.04
822 1 26.02 35.8 35.47
823 1 27.64 33.32 8.04
824 1 39.57 36.88 4.39
825 1 14.48 30.97 36.87
826 1 36.86 27.04 8.96
827 1 34.73 26.27 19.55
828 1 29.24 29.12 10.86
829 1 8.35 39.9 13.92
830 1 5.43 5.1 31.85
831 1 18.36 22.31 5.89
832 1 2.46 27.35 16.36
833 1 21.76 37.05 27.45
834 1 29.32 17.11 2.28
835 1 3.58 21.98 3.09
836 1 10.61 9.17 10.69
837 1 25.15 17.54 6.05
838 1 3.4 22.81 7.03
839 1 16.12 23.66 38.29
840 1 8.67 4.79 31.8
841 1 27.82 0.02 20.45
842 1 4.46 2.44 29.46
843 1 39.11 22.69 36.33
844 1 4.26 2.45 34.43
845 1 13.47 3.5 30.9
846 1 26.92 22.55 26.54
847 1 5.66 30.07 30.65
848 1 31.58 35.68 25.46
849 1 31.23 5.65 27.78
850 1 8.76 19.49 28.61
851 1 24.13 8.02 2.3
852 1 8.27 6.8 4.93
853 1 15.31 34.36 37.63
854 1 3.96 35.82 26.97
855 1 24.95 4.01 29.96
856 1 26.54 25.95 19.15
857 1 17.76 29.23 5.35
858 1 16.95 21.79 0.78
859 1 17.52 39.02 13.01
860 1 20.5 22.86 10.41
861 1 27.67 27.07 2.78
862 1 37.1 31.02 2.03
863 1 37.17 2.24 16.34
864 1 24.51 34.69 10.28
865 1 17.38 13.41 21.4
866 1 38 9.37 17.94
867 1 35.67 25.27 5.3
868 1 22.66 4.47 0.97
869 1 20.06 28.17 27.42
870 1 27.33 2.38 9.79
871 1 36.4 10.73 31.42
872 1 0.53 9.45 6.96
873 1 12.89 9.03 25.13
874 1 37.5 23.54 21.33
875 1 7.19 28.87 19.11
876 1 21.45 32.81 22.71
877 1 8.76 8.3 13.51
878 1 10.24 31.46 3.73
879 1 15.93 9.7 35.82
880 1 14.92 19.46 39.91
881 1 13.02 22.03 27.3
882 1 34.57 1.59 34.73
883 1 0.5 21.04 30.77
884 1 24.84 32.67 4.97
885 1 30.96 4.24 17.34
886 1 23.63 8.84 32.7
887 1 6.84 3.83 26.13
888 1 31.57 9.23 27.06
889 1 14.99 35.15 0.07
890 1 36.29 40.01 8.22
891 1 18 36.86 35.66
892 1 11.5 29.22 0.37
893 1 35.18 36.03 24.88
894 1 14.49 9.41 27.73
895 1 10.12 12.91 0.99
896 1 11.91 29.4 27.3
897 1 25.51 28.68 14.56
898 1 29.32 12.95 35.59
899 1 2.96 0.59 0.53
900 1 5.47 5.35 9.88
901 1 8.93 39.33 1.78
902 1 39.68 38.49 12.33
903 1 3.78 1.24 11.85
904 1 29.54 33.76 11.99
905 1 7.48 6.16 28.8
906 1 10.83 33.63 36.96
907 1 22.03 19.06 21.39
908 1 31.68 31 3.71
909 1 35.32 0.3 30.88
910 1 9.93 35.42 14.85
911 1 21.01 10.66 12.97
912 1 22.54 21.62 33.81
913 1 12.48 12.46 25.15
914 1 0.64 27.93 39.01
915 1 13.88 27.29 3.8
916 1 13.03 20.93 19.25
917 1 5.7 37.48 34.09
918 1 2.27 35.08 14.29
919 1 21.75 26.44 13.48
920 1 10.66 11.35 17.49
921 1 36.67 34.72 27.69
922 1 8.23 22.8 33.36
923 1 4.79 4.05 3.48
924 1 35.61 35 35.21
925 1 31.38 37.67 10.06
926 1 26.44 35.58 27.52
927 1 25.53 4.47 8.03
928 1 38.81 33.08 31.55
929 1 29.62 39.68 34.32
930 1 0.76 3.88 10.61
931 1 24.06 30.13 24.84
932 1 18.77 8.38 37.02
933 1 2.81 24.14 24.45
934 1 11.33 1.25 19.69
935 1 1.61 26.53 6.48
936 1 9.52 29.81 35.98
937 1 7.83 31.75 20.77
938 1 9.67 23.93 20.57
939 1 33.96 16.95 24.79
940 1 37.55 37.31 37.17
941 1 6.2 24.19 31.13
942 1 17.79 4.35 30.56
943 1 13.51 20.25 30.45
944 1 14.76 12.48 13.13
945 1 32.56 27.52 30.41
946 1 35.81 40.1 4.85
947 1 39.01 25.43 27.07
948 1 22.8 5.53 32.22
949 1 2.35 39.55 32.5
950 1 3.31 31.51 34.19
951 1 40.63 37.01 15.9
952 1 18.43 35.86 30.77
953 1 37.01 39.18 15.57
954 1 6.74 6.26 21.64
955 1 5.22 24.94 22.53
956 1 25.2 11.08 13.98
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

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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
# Compute the modified pressure
compute bocsPress all pressureBocs thermo_temp
# Report the modified pressure
thermo_modify press bocsPress
# Use the modified pressure for fix bocs instead of thermo_press
fix_modify 1 press bocsPress
## 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

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/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
the GNU General Public License.
See the README file in the top-level LAMMPS directory.
------------------------------------------------------------------------- */
#ifndef LMP_COMPUTE_H
#define LMP_COMPUTE_H
#include "pointers.h"
namespace LAMMPS_NS {
class Compute : protected Pointers {
public:
static int instance_total; // # of Compute classes ever instantiated
char *id,*style;
int igroup,groupbit;
double scalar; // computed global scalar
double *vector; // computed global vector
double **array; // computed global array
double *vector_atom; // computed per-atom vector
double **array_atom; // computed per-atom array
double *vector_local; // computed local vector
double **array_local; // computed local array
int scalar_flag; // 0/1 if compute_scalar() function exists
int vector_flag; // 0/1 if compute_vector() function exists
int array_flag; // 0/1 if compute_array() function exists
int size_vector; // length of global vector
int size_array_rows; // rows in global array
int size_array_cols; // columns in global array
int size_vector_variable; // 1 if vec length is unknown in advance
int size_array_rows_variable; // 1 if array rows is unknown in advance
int peratom_flag; // 0/1 if compute_peratom() function exists
int size_peratom_cols; // 0 = vector, N = columns in peratom array
int local_flag; // 0/1 if compute_local() function exists
int size_local_rows; // rows in local vector or array
int size_local_cols; // 0 = vector, N = columns in local array
int extscalar; // 0/1 if global scalar is intensive/extensive
int extvector; // 0/1/-1 if global vector is all int/ext/extlist
int *extlist; // list of 0/1 int/ext for each vec component
int extarray; // 0/1 if global array is all intensive/extensive
int tempflag; // 1 if Compute can be used as temperature
// must have both compute_scalar, compute_vector
int pressflag; // 1 if Compute can be used as pressure (uses virial)
// must have both compute_scalar, compute_vector
int pressatomflag; // 1 if Compute calculates per-atom virial
int peflag; // 1 if Compute calculates PE (uses Force energies)
int peatomflag; // 1 if Compute calculates per-atom PE
int create_attribute; // 1 if compute stores attributes that need
// setting when a new atom is created
int tempbias; // 0/1 if Compute temp includes self/extra bias
int timeflag; // 1 if Compute stores list of timesteps it's called on
int ntime; // # of entries in time list
int maxtime; // max # of entries time list can hold
bigint *tlist; // list of timesteps the Compute is called on
int invoked_flag; // non-zero if invoked or accessed this step, 0 if not
bigint invoked_scalar; // last timestep on which compute_scalar() was invoked
bigint invoked_vector; // ditto for compute_vector()
bigint invoked_array; // ditto for compute_array()
bigint invoked_peratom; // ditto for compute_peratom()
bigint invoked_local; // ditto for compute_local()
double dof; // degrees-of-freedom for temperature
int comm_forward; // size of forward communication (0 if none)
int comm_reverse; // size of reverse communication (0 if none)
int dynamic_group_allow; // 1 if can be used with dynamic group, else 0
// KOKKOS host/device flag and data masks
ExecutionSpace execution_space;
unsigned int datamask_read,datamask_modify;
int copymode;
Compute(class LAMMPS *, int, char **);
virtual ~Compute();
void modify_params(int, char **);
void reset_extra_dof();
virtual void init() = 0;
virtual void init_list(int, class NeighList *) {}
virtual void setup() {}
virtual double compute_scalar() {return 0.0;}
virtual void compute_vector() {}
virtual void compute_array() {}
virtual void compute_peratom() {}
virtual void compute_local() {}
virtual void set_arrays(int) {}
// NJD MRD Adding these lines is the only modification needed for USER-BOCS
virtual void send_cg_info(int, int, double*, int, double) {}
virtual void send_cg_info(int, double **, int) {}
virtual int pack_forward_comm(int, int *, double *, int, int *) {return 0;}
virtual void unpack_forward_comm(int, int, double *) {}
virtual int pack_reverse_comm(int, int, double *) {return 0;}
virtual void unpack_reverse_comm(int, int *, double *) {}
virtual void dof_remove_pre() {}
virtual int dof_remove(int) {return 0;}
virtual void remove_bias(int, double *) {}
virtual void remove_bias_thr(int, double *, double *) {}
virtual void remove_bias_all() {}
virtual void reapply_bias_all() {}
virtual void restore_bias(int, double *) {}
virtual void restore_bias_thr(int, double *, double *) {}
virtual void restore_bias_all() {}
virtual void reset_extra_compute_fix(const char *);
virtual void lock_enable() {}
virtual void lock_disable() {}
virtual int lock_length() {return 0;}
virtual void lock(class Fix *, bigint, bigint) {}
virtual void unlock(class Fix *) {}
virtual void refresh() {}
void addstep(bigint);
int matchstep(bigint);
void clearstep();
virtual double memory_usage() {return 0.0;}
virtual void pair_setup_callback(int, int) {}
virtual void pair_tally_callback(int, int, int, int,
double, double, double,
double, double, double) {}
protected:
int instance_me; // which Compute class instantiation I am
double natoms_temp; // # of atoms used for temperature calculation
double extra_dof; // extra DOF for temperature computes
int fix_dof; // DOF due to fixes
int dynamic; // recount atoms for temperature computes
int dynamic_user; // user request for temp compute to be dynamic
double vbias[3]; // stored velocity bias for one atom
double **vbiasall; // stored velocity bias for all atoms
int maxbias; // size of vbiasall array
inline int sbmask(int j) const {
return j >> SBBITS & 3;
}
// union data struct for packing 32-bit and 64-bit ints into double bufs
// see atom_vec.h for documentation
union ubuf {
double d;
int64_t i;
ubuf(double arg) : d(arg) {}
ubuf(int64_t arg) : i(arg) {}
ubuf(int arg) : i(arg) {}
};
// private methods
void adjust_dof_fix();
};
}
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
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: Compute ID must be alphanumeric or underscore characters
Self-explanatory.
E: Could not find compute group ID
Self-explanatory.
E: Compute does not allow an extra compute or fix to be reset
This is an internal LAMMPS error. Please report it to the
developers.
*/

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This user package implements 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).
doi: 10.1063/1.4937383
The USER-BOCS user package for LAMMPS is part of the BOCS software package:
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).
The MOD_COMPUTE_H file is identical to the original compute.h except for
the two lines (three with comments) needed for USER-BOCS to work.
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.

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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.

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File diff suppressed because it is too large Load Diff

991
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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
175 1 16.9 35.09 22.94
176 1 15.18 6.74 2.33
177 1 40.54 12.58 31.65
178 1 21.21 37.62 14.35
179 1 33.52 38.19 14.89
180 1 22.06 12.49 29.81
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
265 1 3.74 13.22 31.05
266 1 30.78 0.7 24.57
267 1 24.5 12.94 10.81
268 1 33.88 26.44 1.96
269 1 29.92 22.6 9.59
270 1 15.87 21.94 33.44
271 1 23.63 8.41 10.95
272 1 26.53 0.01 7.58
273 1 33.88 8.73 2.52
274 1 39.74 31.46 36.87
275 1 13.28 39.54 37
276 1 24.74 35.41 32.14
277 1 17.3 34.32 6.85
278 1 24.43 13.36 5.63
279 1 31.23 17.12 7.11
280 1 15.58 37.85 34.06
281 1 25.93 38.17 3.13
282 1 31.84 34.34 39.67
283 1 14.41 17.74 14.43
284 1 9.4 1.78 29.53
285 1 8.29 29.61 6.81
286 1 7.13 17.36 -0.19
287 1 38.04 19.52 11.25
288 1 34.87 32.77 38.75
289 1 27.18 22.49 5.69
290 1 29.69 27.11 20.29
291 1 25.23 2.22 39.75
292 1 35.8 17.1 36.09
293 1 20.53 17.67 35.47
294 1 23.41 31.36 2.24
295 1 25.17 20.09 29.2
296 1 0.32 9.28 39.74
297 1 22.49 18.77 29.89
298 1 38.64 0.85 39.43
299 1 18.55 5.87 9.15
300 1 35.21 28.69 25.76
301 1 39.24 15.68 6.36
302 1 5.91 13.29 3.92
303 1 0.5 21.25 21.62
304 1 34.39 9.43 18.59
305 1 22.7 1.03 8.79
306 1 40.15 16.25 24.87
307 1 16.52 13.69 10.25
308 1 6.88 36.77 39.57
309 1 11.95 37.1 7.59
310 1 19.49 26.66 9.76
311 1 36.34 29.89 29.31
312 1 18.76 35.75 12.72
313 1 23.15 38.68 4.96
314 1 10.78 17.11 34.38
315 1 13.58 14.89 0.34
316 1 4.73 33.88 32.41
317 1 12.68 29.51 17.07
318 1 9.45 27 4.98
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
324 1 15.01 34.16 28.32
325 1 28.71 36.53 15.08
326 1 9.64 13.94 24.05
327 1 1.24 36.96 30.41
328 1 15.44 31.39 4.77
329 1 25.72 14.42 38.01
330 1 7.35 31.84 12.61
331 1 32.33 16.79 3.07
332 1 15.86 0.39 8.39
333 1 27.69 7.32 25.74
334 1 27.77 1.17 4.96
335 1 29.38 26.68 23.48
336 1 14.95 3.41 2.13
337 1 2.45 38.8 17.54
338 1 9.18 27.58 31.12
339 1 36.62 15.23 23.66
340 1 12.23 30.74 10.85
341 1 12.87 0.23 24.05
342 1 33.85 35.75 19.95
343 1 36.36 30.35 13.94
344 1 38.11 8.15 5.49
345 1 15.58 1.29 29.89
346 1 25.95 30.47 39.19
347 1 27.69 15.5 13.37
348 1 25.48 13.7 25.29
349 1 0.72 39.53 4.41
350 1 8.75 15.21 5.79
351 1 10.49 26.46 27.25
352 1 16.9 20.08 26.58
353 1 3.95 4.33 20.25
354 1 18.03 7.66 31.87
355 1 21.35 2.88 17.26
356 1 32.92 22.68 6.56
357 1 21.72 4.62 12.02
358 1 37.6 6.04 25.2
359 1 22.22 23.78 7.36
360 1 12.53 19.53 10.6
361 1 17.87 26.05 19.32
362 1 20.94 30.75 31.23
363 1 22.33 11.87 35.79
364 1 28.54 6.88 10.52
365 1 29.58 26.13 8.56
366 1 19.06 24.2 21.73
367 1 25.05 38.41 26.91
368 1 18.66 40.35 4.69
369 1 11.87 6.75 12.72
370 1 17.99 11.82 37.79
371 1 8.97 24.7 0.61
372 1 26.89 1.52 31.33
373 1 6.88 22.51 14.06
374 1 29.51 3.87 13.35
375 1 0.95 14.53 10
376 1 26.43 31.54 11.63
377 1 6.1 35.16 11.28
378 1 10.2 15.91 28.7
379 1 13.24 25.67 24.3
380 1 34.5 3.91 20.22
381 1 22.48 2.17 5.2
382 1 24.26 16.15 11.3
383 1 20.63 32.57 27.3
384 1 39.95 6.81 1.05
385 1 24.38 34.78 38.27
386 1 4.63 23.56 0.55
387 1 33.5 8.38 36.97
388 1 5.76 27.14 12.06
389 1 37.45 26.58 32.25
390 1 2.8 8.96 32.35
391 1 5.29 39.84 30.1
392 1 29.2 26.49 31.18
393 1 33.91 27.39 12.89
394 1 3.37 14.19 39.34
395 1 30.68 28.7 27
396 1 2.59 18.45 19.38
397 1 13.55 0.75 27.35
398 1 3.82 20.12 16.1
399 1 37.72 0.72 34.29
400 1 23.85 3.32 19.46
401 1 4.78 0.67 38.23
402 1 22.78 23.26 38.6
403 1 11.56 39.29 4.23
404 1 21.38 32.45 5.39
405 1 8.32 19.42 9.52
406 1 28.43 31.07 17.8
407 1 11.02 5.75 39.84
408 1 27.36 36.71 7.62
409 1 34.22 16.74 27.88
410 1 3.22 22.01 27.42
411 1 29.2 15.76 32.33
412 1 25.29 23.44 2.2
413 1 10.8 32.43 39.96
414 1 32.2 1.41 4.44
415 1 32.94 15.59 37.21
416 1 6.8 8.08 0.84
417 1 10.42 9.91 37.73
418 1 1.18 31.39 3.93
419 1 10.1 36.38 38.57
420 1 32.89 26.96 35.07
421 1 28.12 11.93 25.96
422 1 4.9 29.15 -0.25
423 1 2.21 27.99 3.72
424 1 11.33 3.94 25.55
425 1 3.3 30.26 10.78
426 1 11.57 27.26 19.31
427 1 21.79 32.67 13.3
428 1 4.96 26.53 33.78
429 1 33.41 32.87 18.46
430 1 13.92 30.37 20.3
431 1 16.91 3.5 11.57
432 1 -0.06 4.42 34.05
433 1 7.04 24.33 16.85
434 1 28.66 11.93 19.73
435 1 30.21 1.75 36.36
436 1 3.91 6.2 6.26
437 1 7.01 25.6 27.34
438 1 34 1.06 18.12
439 1 29.14 8.5 3.09
440 1 40.13 23.52 16.94
441 1 21.69 22.38 26.78
442 1 18.44 32.85 39.84
443 1 38.87 1.99 27.63
444 1 10.47 12.02 33.68
445 1 9.65 19.94 21.88
446 1 25.04 8.12 27.89
447 1 12.18 16.78 31.09
448 1 38.31 8.2 30.6
449 1 0.11 5.21 18.12
450 1 23.48 7.88 38.7
451 1 7.9 11.99 7.04
452 1 2.09 34.5 8.64
453 1 19 18.3 0.42
454 1 37.94 18.06 15.21
455 1 25.05 33.33 29.55
456 1 33.74 37.88 34.54
457 1 36.07 29.5 17.47
458 1 27.7 13.54 10.46
459 1 27.18 23.18 21.06
460 1 17.49 2.04 23.22
461 1 23.84 26.31 36.76
462 1 31.08 32.24 24.92
463 1 17.7 28.73 16.66
464 1 1.59 15.5 18.04
465 1 33.49 18.99 8.75
466 1 1.19 8.43 28.01
467 1 5.43 20.26 22.25
468 1 23.3 5.31 15.05
469 1 27.09 4.47 21.96
470 1 26.61 27.48 28.83
471 1 13 3.18 13.4
472 1 36.09 34.56 10.58
473 1 19.09 15.33 7.48
474 1 12.94 18.16 22.07
475 1 38.8 16.16 36.73
476 1 16.73 39.94 -0.46
477 1 3.64 12.56 9.42
478 1 27.64 3.31 18.29
479 1 15.58 12.36 4.52
480 1 15.37 11.18 18.19
481 1 37.52 11.23 14.94
482 1 37.16 2.3 10.01
483 1 36.19 9.86 21.99
484 1 36.38 21.09 4.76
485 1 38.15 12.94 25.35
486 1 15.1 29.65 24.64
487 1 16.54 29.12 38.85
488 1 33.86 11.39 14.4
489 1 27.99 18.55 9.87
490 1 0.66 1.26 8.28
491 1 29.89 33.84 29.75
492 1 6.64 33.3 6.74
493 1 31.47 0.39 11.25
494 1 8.76 15.96 10.74
495 1 39.6 15.8 21.04
496 1 22.38 28.55 19.85
497 1 25.87 6.23 5.4
498 1 36.24 26.67 38.61
499 1 23.05 8.79 7.01
500 1 32.05 4.16 8.87
501 1 35.3 13.36 38.03
502 1 39.91 25.91 36.45
503 1 32.17 17.27 31.82
504 1 29.99 21.54 20.57
505 1 9.39 0.57 34.17
506 1 22.12 17.22 13.03
507 1 15.23 16.27 24.39
508 1 26.32 25.89 13.26
509 1 39.25 3.46 1.34
510 1 32.56 10.28 7.96
511 1 25.76 14.8 34.79
512 1 32.12 5.38 36.94
513 1 17.74 15.37 14.87
514 1 21.93 3.26 25.26
515 1 24.05 0.48 36.27
516 1 8.2 19.02 33.92
517 1 33.07 25.88 24.79
518 1 12.54 0.52 32.8
519 1 18.5 6.34 23.21
520 1 35.93 10.26 34.79
521 1 19.33 11.86 6.94
522 1 1.63 5.31 25.43
523 1 30.62 36.78 30.77
524 1 12.25 26.79 13.74
525 1 21 1.47 13.99
526 1 22.24 29.36 34.11
527 1 29.05 1.74 0.24
528 1 19.34 25.14 39.77
529 1 12.9 25.42 35.42
530 1 4.1 20.69 33.31
531 1 35.38 5.64 9.17
532 1 5.01 34.03 23.36
533 1 15.7 10.01 7.1
534 1 25.95 19.48 24.73
535 1 11.15 4.16 21.43
536 1 1.47 3.23 13.72
537 1 26.54 36.76 17.48
538 1 7.65 30.6 27.73
539 1 18.59 3.05 3.32
540 1 6.92 36.14 15.67
541 1 12.72 36.21 32.72
542 1 16.33 26.24 14.35
543 1 21.66 12.61 26.18
544 1 15.72 32.37 10.71
545 1 27.57 15.75 4.97
546 1 20.18 39.13 18.44
547 1 18.77 17.09 4.74
548 1 12.75 14.08 17.89
549 1 10.71 37.26 35.13
550 1 20.88 32.12 9.94
551 1 8.69 0.06 9.54
552 1 1.58 12.61 26.42
553 1 10.29 22.73 13.14
554 1 23.31 25.7 4.97
555 1 36.7 30.78 5.26
556 1 5.6 28.71 23.76
557 1 13.04 7.91 15.46
558 1 40.24 33.53 34.5
559 1 39.7 18.36 34.25
560 1 23.52 22.84 21.14
561 1 32.82 27.9 5.02
562 1 1.52 33.77 27.04
563 1 31.48 18.68 13.1
564 1 34 24.07 34.55
565 1 34.72 25.03 30.45
566 1 18.92 5.7 16.54
567 1 15.26 40.2 16.97
568 1 24.55 16.8 26.26
569 1 17.59 18.03 31.75
570 1 12.08 27.38 38.42
571 1 31.42 21.91 35.27
572 1 9.68 6.93 36.96
573 1 22.93 15.19 2.53
574 1 11.83 24.38 2.24
575 1 16.02 12.44 31.42
576 1 20.24 10.7 20.15
577 1 37.38 17.37 40.63
578 1 3.74 17.41 22.49
579 1 23.21 9.86 23.99
580 1 2.49 36.56 38
581 1 20.51 1.54 22.62
582 1 8.23 33.44 33.15
583 1 30.93 8.12 14.85
584 1 36.35 3.92 37.65
585 1 5.57 10.63 28.64
586 1 30.24 22.84 4.6
587 1 3.24 15.97 7.43
588 1 22.64 0.7 27.09
589 1 1.64 40.37 27.74
590 1 30.53 35.28 3.5
591 1 25.55 4.7 2.53
592 1 22.04 29.56 12.29
593 1 3.42 8.76 2.28
594 1 16.37 37.65 7.87
595 1 20.65 12.75 2.9
596 1 8.07 20.49 2.6
597 1 20.04 24.72 28.2
598 1 29.75 0.33 16.1
599 1 31.36 33.09 8.02
600 1 8.6 10.56 2.65
601 1 20.55 33.93 33.71
602 1 23.11 -0.42 31.7
603 1 27.07 6.69 18.5
604 1 15.65 23.71 11.8
605 1 23.88 24.17 30.1
606 1 0.79 32.46 16.99
607 1 25.96 20.19 2.43
608 1 35.16 12.33 4.73
609 1 16.53 17.12 10.45
610 1 19.74 35.94 8.62
611 1 -0.24 28.29 28.3
612 1 33.15 4.39 12.64
613 1 24.27 18.59 33.59
614 1 0.3 9.61 23.54
615 1 5.52 10.89 34.71
616 1 9.85 26.26 34.42
617 1 25.54 37.74 39.13
618 1 4.11 29.65 5.81
619 1 30.86 22.72 31.07
620 1 39.54 34.54 23.24
621 1 15.03 9.34 12.11
622 1 21.93 38.49 9.53
623 1 18.21 19.2 16.65
624 1 38.71 32.83 14.49
625 1 37.74 36.38 31.43
626 1 7.57 2.2 1.07
627 1 12.27 10.05 1.53
628 1 18.32 19.55 12.51
629 1 12.49 24.81 16.57
630 1 35.07 31.62 22.85
631 1 4.91 19.68 30.45
632 1 11.36 2.92 36.19
633 1 26.76 35.53 1.29
634 1 1.13 14.55 14.77
635 1 8.2 25.14 37.83
636 1 -0.5 0.85 23.08
637 1 17.95 18.01 37.61
638 1 2.44 37.75 0.71
639 1 3.77 23.41 17.91
640 1 3.34 14.41 35.96
641 1 14.89 31.42 31.76
642 1 15.72 22.91 30.66
643 1 37.42 3.13 5.51
644 1 1.51 38.14 20.78
645 1 12.55 18.16 25.81
646 1 18.98 15.88 29.21
647 1 17.33 32.04 27.87
648 1 31.21 37.38 22.84
649 1 11.88 32.4 31
650 1 25.1 2.19 12.69
651 1 38.85 39.1 27.87
652 1 5.9 16.14 33.34
653 1 6.3 17.5 36.46
654 1 2.28 25.02 12.53
655 1 19.33 25.49 6.78
656 1 8.57 37.22 8.4
657 1 22 38.61 24.14
658 1 35.63 3.23 2.15
659 1 37.35 22.64 9.99
660 1 25.46 28.22 33.18
661 1 13.99 4.21 9.07
662 1 9.04 40.64 37.59
663 1 17.46 6.49 27.93
664 1 1.42 6.14 30.2
665 1 25.82 28.28 10.33
666 1 30.71 30.2 -0.02
667 1 8.05 29.32 0.62
668 1 6.49 3.17 6.65
669 1 7.77 39.88 26.03
670 1 28.53 12.14 30.96
671 1 6.25 12.64 39.55
672 1 3.78 7.96 25.83
673 1 28.69 29.58 6.61
674 1 5.32 18.55 8.6
675 1 5.3 11.44 14.19
676 1 39 12.03 36.99
677 1 11.08 32.51 19.12
678 1 38.48 1.03 20.34
679 1 38.47 11.31 10.12
680 1 3.65 20.3 11.99
681 1 27.18 11.39 3.4
682 1 29.61 20.72 38.86
683 1 31.88 4.82 24.75
684 1 14.52 36.61 25.66
685 1 21.68 19.96 24.58
686 1 1.2 13.59 23.16
687 1 37.71 5.97 35.28
688 1 19.81 22.04 37.54
689 1 40.67 27.07 10.14
690 1 38.57 13.96 13.75
691 1 18.15 17.19 21.63
692 1 3.76 27.51 30.32
693 1 11.39 25.09 7.96
694 1 28.95 22.02 13.33
695 1 31.72 35.46 35.33
696 1 15.17 6.03 23.94
697 1 9.63 9.42 22.18
698 1 27.76 4.1 38.61
699 1 27.37 37.46 11.07
700 1 35.69 15.24 6.39
701 1 21.92 33.09 36.84
702 1 4.79 15.51 13.28
703 1 9.31 26.44 22.8
704 1 30.14 38.31 6.98
705 1 4.33 6.66 13.77
706 1 3.66 27.15 37.83
707 1 0.44 24.06 29.62
708 1 35.4 9.59 9.8
709 1 33.77 39.44 21.41
710 1 29.2 18.74 24.38
711 1 34.14 30 7.36
712 1 16.02 4.37 6.43
713 1 35.75 39.41 40.58
714 1 15.32 11.84 23.24
715 1 32.52 24.39 20.97
716 1 11.45 2.9 7.16
717 1 7.07 34.28 36.04
718 1 11.41 8.83 7.57
719 1 29.29 27.79 16.55
720 1 2.41 9.16 16.14
721 1 13.14 38.07 12.01
722 1 37.45 14.26 18.3
723 1 34.64 18.37 16.65
724 1 29.26 34.28 33.46
725 1 13.67 19.83 3.04
726 1 19.64 2.6 32.95
727 1 23.61 23.55 11.34
728 1 6.87 22.5 36.5
729 1 36.78 28.34 22.96
730 1 11.3 13.98 9.84
731 1 20.82 19.73 9.16
732 1 12.65 12.61 6.16
733 1 9.25 7.81 25.28
734 1 25.4 29.36 5.84
735 1 17.86 9.06 4.45
736 1 35.84 40.51 26.06
737 1 26.97 21.28 31.59
738 1 39.94 38.14 24.86
739 1 3.16 17.07 2.49
740 1 14.08 15.4 36.99
741 1 26.1 13.88 29.68
742 1 26.36 20 20.56
743 1 12.02 6.35 27.65
744 1 11.21 19.14 15.27
745 1 35.86 22.93 26.81
746 1 32.26 12.62 2.68
747 1 29.36 4.91 6.86
748 1 20.14 7.97 29.32
749 1 25.53 11.2 36.18
750 1 30.36 14.25 24.79
751 1 29.84 38.37 39.29
752 1 15.79 36.4 4.26
753 1 32.59 14.17 10.29
754 1 13.89 34.54 15.42
755 1 12.13 33.62 7.27
756 1 25.86 23.81 33.97
757 1 18.4 31.27 34.96
758 1 6.58 40.49 17.57
759 1 5.64 39.86 23.05
760 1 25.32 33 16.24
761 1 0.98 10.99 12.21
762 1 32.86 23.75 12.41
763 1 32.91 1.3 26.94
764 1 9.46 8.66 31.47
765 1 17.49 15.53 1.82
766 1 8.17 18.16 15.3
767 1 4.84 30.63 26.32
768 1 6.75 37.1 30.8
769 1 7.16 5.72 15.74
770 1 20.09 17.82 19.18
771 1 1.02 27.99 32.54
772 1 21.44 1.28 38.4
773 1 21.06 14.62 37.08
774 1 27.82 18.99 15.96
775 1 33.51 21.46 22.82
776 1 8.29 2.79 17.09
777 1 18.14 11.41 28.62
778 1 17.94 28.54 32.73
779 1 36.1 9.54 40.1
780 1 36.55 2.62 22.97
781 1 27.29 10.41 39.35
782 1 22.04 37.76 2.02
783 1 23.01 30.08 16.58
784 1 6.34 15.31 21.61
785 1 7.3 22.39 7.74
786 1 38 5.77 21.04
787 1 32.93 12.85 26.58
788 1 22.43 15.36 16.72
789 1 18.54 2.38 8.35
790 1 0.62 31.88 23.84
791 1 39.56 30.3 21.7
792 1 7.56 11.78 25.2
793 1 16.05 3.98 26.72
794 1 24.33 36.16 13.16
795 1 26.38 31.24 35.77
796 1 14.94 26.46 -0.44
797 1 3.53 28 19.79
798 1 11.94 32.27 25.88
799 1 34.59 15.06 19.23
800 1 3.51 10.62 24.22
801 1 13.18 21.59 35.52
802 1 19.95 13.15 16.23
803 1 24.48 9.63 19.58
804 1 37.7 34.42 19.19
805 1 22.84 19.59 5.52
806 1 34.62 36.75 12.26
807 1 10.33 21.85 25.15
808 1 21.51 29.7 7.23
809 1 34.05 3 30.58
810 1 12.43 29.67 5.59
811 1 18.94 21.82 29.31
812 1 39.21 17.7 4
813 1 7.04 2.97 37.09
814 1 30.87 10.8 22.09
815 1 33.54 7.16 23.15
816 1 32.82 32.27 11.47
817 1 21.8 14.54 21.61
818 1 38.83 6.69 13.68
819 1 30.37 39.05 18.66
820 1 31.21 15.08 13.79
821 1 1.07 11.97 35.04
822 1 26.02 35.8 35.47
823 1 27.64 33.32 8.04
824 1 39.57 36.88 4.39
825 1 14.48 30.97 36.87
826 1 36.86 27.04 8.96
827 1 34.73 26.27 19.55
828 1 29.24 29.12 10.86
829 1 8.35 39.9 13.92
830 1 5.43 5.1 31.85
831 1 18.36 22.31 5.89
832 1 2.46 27.35 16.36
833 1 21.76 37.05 27.45
834 1 29.32 17.11 2.28
835 1 3.58 21.98 3.09
836 1 10.61 9.17 10.69
837 1 25.15 17.54 6.05
838 1 3.4 22.81 7.03
839 1 16.12 23.66 38.29
840 1 8.67 4.79 31.8
841 1 27.82 0.02 20.45
842 1 4.46 2.44 29.46
843 1 39.11 22.69 36.33
844 1 4.26 2.45 34.43
845 1 13.47 3.5 30.9
846 1 26.92 22.55 26.54
847 1 5.66 30.07 30.65
848 1 31.58 35.68 25.46
849 1 31.23 5.65 27.78
850 1 8.76 19.49 28.61
851 1 24.13 8.02 2.3
852 1 8.27 6.8 4.93
853 1 15.31 34.36 37.63
854 1 3.96 35.82 26.97
855 1 24.95 4.01 29.96
856 1 26.54 25.95 19.15
857 1 17.76 29.23 5.35
858 1 16.95 21.79 0.78
859 1 17.52 39.02 13.01
860 1 20.5 22.86 10.41
861 1 27.67 27.07 2.78
862 1 37.1 31.02 2.03
863 1 37.17 2.24 16.34
864 1 24.51 34.69 10.28
865 1 17.38 13.41 21.4
866 1 38 9.37 17.94
867 1 35.67 25.27 5.3
868 1 22.66 4.47 0.97
869 1 20.06 28.17 27.42
870 1 27.33 2.38 9.79
871 1 36.4 10.73 31.42
872 1 0.53 9.45 6.96
873 1 12.89 9.03 25.13
874 1 37.5 23.54 21.33
875 1 7.19 28.87 19.11
876 1 21.45 32.81 22.71
877 1 8.76 8.3 13.51
878 1 10.24 31.46 3.73
879 1 15.93 9.7 35.82
880 1 14.92 19.46 39.91
881 1 13.02 22.03 27.3
882 1 34.57 1.59 34.73
883 1 0.5 21.04 30.77
884 1 24.84 32.67 4.97
885 1 30.96 4.24 17.34
886 1 23.63 8.84 32.7
887 1 6.84 3.83 26.13
888 1 31.57 9.23 27.06
889 1 14.99 35.15 0.07
890 1 36.29 40.01 8.22
891 1 18 36.86 35.66
892 1 11.5 29.22 0.37
893 1 35.18 36.03 24.88
894 1 14.49 9.41 27.73
895 1 10.12 12.91 0.99
896 1 11.91 29.4 27.3
897 1 25.51 28.68 14.56
898 1 29.32 12.95 35.59
899 1 2.96 0.59 0.53
900 1 5.47 5.35 9.88
901 1 8.93 39.33 1.78
902 1 39.68 38.49 12.33
903 1 3.78 1.24 11.85
904 1 29.54 33.76 11.99
905 1 7.48 6.16 28.8
906 1 10.83 33.63 36.96
907 1 22.03 19.06 21.39
908 1 31.68 31 3.71
909 1 35.32 0.3 30.88
910 1 9.93 35.42 14.85
911 1 21.01 10.66 12.97
912 1 22.54 21.62 33.81
913 1 12.48 12.46 25.15
914 1 0.64 27.93 39.01
915 1 13.88 27.29 3.8
916 1 13.03 20.93 19.25
917 1 5.7 37.48 34.09
918 1 2.27 35.08 14.29
919 1 21.75 26.44 13.48
920 1 10.66 11.35 17.49
921 1 36.67 34.72 27.69
922 1 8.23 22.8 33.36
923 1 4.79 4.05 3.48
924 1 35.61 35 35.21
925 1 31.38 37.67 10.06
926 1 26.44 35.58 27.52
927 1 25.53 4.47 8.03
928 1 38.81 33.08 31.55
929 1 29.62 39.68 34.32
930 1 0.76 3.88 10.61
931 1 24.06 30.13 24.84
932 1 18.77 8.38 37.02
933 1 2.81 24.14 24.45
934 1 11.33 1.25 19.69
935 1 1.61 26.53 6.48
936 1 9.52 29.81 35.98
937 1 7.83 31.75 20.77
938 1 9.67 23.93 20.57
939 1 33.96 16.95 24.79
940 1 37.55 37.31 37.17
941 1 6.2 24.19 31.13
942 1 17.79 4.35 30.56
943 1 13.51 20.25 30.45
944 1 14.76 12.48 13.13
945 1 32.56 27.52 30.41
946 1 35.81 40.1 4.85
947 1 39.01 25.43 27.07
948 1 22.8 5.53 32.22
949 1 2.35 39.55 32.5
950 1 3.31 31.51 34.19
951 1 40.63 37.01 15.9
952 1 18.43 35.86 30.77
953 1 37.01 39.18 15.57
954 1 6.74 6.26 21.64
955 1 5.22 24.94 22.53
956 1 25.2 11.08 13.98
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

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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
# Compute the modified pressure
compute bocsPress all pressureBocs thermo_temp
# Report the modified pressure
thermo_modify press bocsPress
# Use the modified pressure for fix bocs instead of thermo_press
fix_modify 1 press bocsPress
## 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

441
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/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
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
from The Pennsylvania State University
------------------------------------------------------------------------- */
#include <mpi.h>
#include <string.h>
#include <stdlib.h>
#include "compute_pressure_bocs.h"
#include "atom.h"
#include "update.h"
#include "domain.h"
#include "modify.h"
#include "fix.h"
#include "force.h"
#include "pair.h"
#include "bond.h"
#include "angle.h"
#include "dihedral.h"
#include "improper.h"
#include "kspace.h"
#include "error.h"
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
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");
scalar_flag = vector_flag = 1;
size_vector = 6;
extscalar = 0;
extvector = 0;
pressflag = 1;
timeflag = 1;
p_match_flag = 0; // NJD MRD
// store temperature ID used by pressure computation
// insure it is valid for temperature computation
if (strcmp(arg[3],"NULL") == 0) id_temp = NULL;
else {
int n = strlen(arg[3]) + 1;
id_temp = new char[n];
strcpy(id_temp,arg[3]);
int icompute = modify->find_compute(id_temp);
if (icompute < 0)
error->all(FLERR,"Could not find compute pressure temperature ID");
if (modify->compute[icompute]->tempflag == 0)
error->all(FLERR,"Compute pressure temperature ID does not "
"compute temperature");
}
// process optional args
if (narg == 4) {
keflag = 1;
pairflag = 1;
bondflag = angleflag = dihedralflag = improperflag = 1;
kspaceflag = fixflag = 1;
} else {
keflag = 0;
pairflag = 0;
bondflag = angleflag = dihedralflag = improperflag = 0;
kspaceflag = fixflag = 0;
int iarg = 4;
while (iarg < narg) {
if (strcmp(arg[iarg],"ke") == 0) keflag = 1;
else if (strcmp(arg[iarg],"pair") == 0) pairflag = 1;
else if (strcmp(arg[iarg],"bond") == 0) bondflag = 1;
else if (strcmp(arg[iarg],"angle") == 0) angleflag = 1;
else if (strcmp(arg[iarg],"dihedral") == 0) dihedralflag = 1;
else if (strcmp(arg[iarg],"improper") == 0) improperflag = 1;
else if (strcmp(arg[iarg],"kspace") == 0) kspaceflag = 1;
else if (strcmp(arg[iarg],"fix") == 0) fixflag = 1;
else if (strcmp(arg[iarg],"virial") == 0) {
pairflag = 1;
bondflag = angleflag = dihedralflag = improperflag = 1;
kspaceflag = fixflag = 1;
} else error->all(FLERR,"Illegal compute pressure command");
iarg++;
}
}
// error check
if (keflag && id_temp == NULL)
error->all(FLERR,"Compute pressure requires temperature ID "
"to include kinetic energy");
vector = new double[6];
nvirial = 0;
vptr = NULL;
}
/* ---------------------------------------------------------------------- */
ComputePressureBocs::~ComputePressureBocs()
{
delete [] id_temp;
delete [] vector;
delete [] vptr;
}
/* ---------------------------------------------------------------------- */
void ComputePressureBocs::init()
{
boltz = force->boltz;
nktv2p = force->nktv2p;
dimension = domain->dimension;
// set temperature compute, must be done in init()
// fixes could have changed or compute_modify could have changed it
if (keflag) {
int icompute = modify->find_compute(id_temp);
if (icompute < 0)
error->all(FLERR,"Could not find compute pressure temperature ID");
temperature = modify->compute[icompute];
}
// detect contributions to virial
// vptr points to all virial[6] contributions
delete [] vptr;
nvirial = 0;
vptr = NULL;
if (pairflag && force->pair) nvirial++;
if (bondflag && atom->molecular && force->bond) nvirial++;
if (angleflag && atom->molecular && force->angle) nvirial++;
if (dihedralflag && atom->molecular && force->dihedral) nvirial++;
if (improperflag && atom->molecular && force->improper) nvirial++;
if (fixflag)
for (int i = 0; i < modify->nfix; i++)
if (modify->fix[i]->virial_flag) nvirial++;
if (nvirial) {
vptr = new double*[nvirial];
nvirial = 0;
if (pairflag && force->pair) vptr[nvirial++] = force->pair->virial;
if (bondflag && force->bond) vptr[nvirial++] = force->bond->virial;
if (angleflag && force->angle) vptr[nvirial++] = force->angle->virial;
if (dihedralflag && force->dihedral)
vptr[nvirial++] = force->dihedral->virial;
if (improperflag && force->improper)
vptr[nvirial++] = force->improper->virial;
if (fixflag)
for (int i = 0; i < modify->nfix; i++)
if (modify->fix[i]->virial_flag)
vptr[nvirial++] = modify->fix[i]->virial;
}
// flag Kspace contribution separately, since not summed across procs
if (kspaceflag && force->kspace) kspace_virial = force->kspace->virial;
else kspace_virial = NULL;
}
/* Extra functions added for BOCS */
/* ----------------------------------------------------------------------
Compute the pressure correction for the analytical basis set
------------------------------------------------------------------------- */
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 ) *
pow( ( 1 / vavg ) * ( vCG - vavg ),i-1);
}
return correction;
}
/* ----------------------------------------------------------------------
Find the relevant index position if using a spline basis set
------------------------------------------------------------------------- */
double ComputePressureBocs::find_index(double * grid, double value)
{
int i;
double spacing = fabs(grid[1]-grid[0]);
int gridsize = spline_length;
for (i = 0; i < (gridsize-1); ++i)
{
if (value >= grid[i] && value <= grid[i+1]) { return i; }
}
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]);
}
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);
}
/* ----------------------------------------------------------------------
Compute the pressure correction for a spline basis set
------------------------------------------------------------------------- */
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) *
( 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) +
(grid[3][i] * pow(deltax,2)) + (grid[4][i] * pow(deltax,3));
}
else
{
error->all(FLERR,"bad spline type passed to get_cg_p_corr()\n");
}
return correction;
}
/* ----------------------------------------------------------------------
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,
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");
}
p_match_flag = 1;
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]; }
N_mol = sent_N_mol;
vavg = sent_vavg;
}
/* ----------------------------------------------------------------------
send cg info from fix_bocs to compute_pressure_bocs for a spline basis
set
------------------------------------------------------------------------- */
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
{
error->all(FLERR,"Incorrect basis type passed to ComputePressureBocs\n");
}
splines = in_splines;
spline_length = gridsize;
p_match_flag = 1;
}
/* End of new functions for BOCS */
/* ----------------------------------------------------------------------
compute total pressure, averaged over Pxx, Pyy, Pzz
------------------------------------------------------------------------- */
double ComputePressureBocs::compute_scalar()
{
invoked_scalar = update->ntimestep;
if (update->vflag_global != invoked_scalar)
error->all(FLERR,"Virial was not tallied on needed timestep");
// invoke temperature if it hasn't been already
double t;
double volume, correction = 0; // NJD MRD
if (keflag) {
if (temperature->invoked_scalar != update->ntimestep)
t = temperature->compute_scalar();
else t = temperature->scalar;
}
if (dimension == 3) {
inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd);
volume = (domain->xprd * domain->yprd * domain->zprd); // NJD MRD
/* 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);
}
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
else
scalar = (virial[0] + virial[1] + virial[2]) / 3.0 *
inv_volume * nktv2p + (correction); // NJD MRD correction
} else {
if (p_match_flag) // NJD MRD
{
error->all(FLERR,"Pressure matching not implemented in 2-d.\n");
exit(1);
} // The rest of this can probably be deleted.
inv_volume = 1.0 / (domain->xprd * domain->yprd);
virial_compute(2,2);
if (keflag)
scalar = (temperature->dof * boltz * t +
virial[0] + virial[1]) / 2.0 * inv_volume * nktv2p;
else
scalar = (virial[0] + virial[1]) / 2.0 * inv_volume * nktv2p;
}
return scalar;
}
/* ----------------------------------------------------------------------
compute pressure tensor
assume KE tensor has already been computed
------------------------------------------------------------------------- */
void ComputePressureBocs::compute_vector()
{
invoked_vector = update->ntimestep;
if (update->vflag_global != invoked_vector)
error->all(FLERR,"Virial was not tallied on needed timestep");
if (force->kspace && kspace_virial && force->kspace->scalar_pressure_flag)
error->all(FLERR,"Must use 'kspace_modify pressure/scalar no' for "
"tensor components with kspace_style msm");
// invoke temperature if it hasn't been already
double *ke_tensor;
if (keflag) {
if (temperature->invoked_vector != update->ntimestep)
temperature->compute_vector();
ke_tensor = temperature->vector;
}
if (dimension == 3) {
inv_volume = 1.0 / (domain->xprd * domain->yprd * domain->zprd);
virial_compute(6,3);
if (keflag) {
for (int i = 0; i < 6; i++)
vector[i] = (ke_tensor[i] + virial[i]) * inv_volume * nktv2p;
} else
for (int i = 0; i < 6; i++)
vector[i] = virial[i] * inv_volume * nktv2p;
} else {
inv_volume = 1.0 / (domain->xprd * domain->yprd);
virial_compute(4,2);
if (keflag) {
vector[0] = (ke_tensor[0] + virial[0]) * inv_volume * nktv2p;
vector[1] = (ke_tensor[1] + virial[1]) * inv_volume * nktv2p;
vector[3] = (ke_tensor[3] + virial[3]) * inv_volume * nktv2p;
vector[2] = vector[4] = vector[5] = 0.0;
} else {
vector[0] = virial[0] * inv_volume * nktv2p;
vector[1] = virial[1] * inv_volume * nktv2p;
vector[3] = virial[3] * inv_volume * nktv2p;
vector[2] = vector[4] = vector[5] = 0.0;
}
}
}
/* ---------------------------------------------------------------------- */
void ComputePressureBocs::virial_compute(int n, int ndiag)
{
int i,j;
double v[6],*vcomponent;
for (i = 0; i < n; i++) v[i] = 0.0;
// sum contributions to virial from forces and fixes
for (j = 0; j < nvirial; j++) {
vcomponent = vptr[j];
for (i = 0; i < n; i++) v[i] += vcomponent[i];
}
// sum virial across procs
MPI_Allreduce(v,virial,n,MPI_DOUBLE,MPI_SUM,world);
// KSpace virial contribution is already summed across procs
if (kspace_virial)
for (i = 0; i < n; i++) virial[i] += kspace_virial[i];
// LJ long-range tail correction, only if pair contributions are included
if (force->pair && pairflag && force->pair->tail_flag)
for (i = 0; i < ndiag; i++) virial[i] += force->pair->ptail * inv_volume;
}
/* ---------------------------------------------------------------------- */
void ComputePressureBocs::reset_extra_compute_fix(const char *id_new)
{
delete [] id_temp;
int n = strlen(id_new) + 1;
id_temp = new char[n];
strcpy(id_temp,id_new);
}

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/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
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
from The Pennsylvania State University
------------------------------------------------------------------------- */
#ifdef COMPUTE_CLASS
ComputeStyle(pressureBocs,ComputePressureBocs) // MRD NJD
#else
// MRD NJD
#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 {
public:
ComputePressureBocs(class LAMMPS *, int, char **); // MRD NJD
virtual ~ComputePressureBocs(); // MRD NJD
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 get_cg_p_corr(int, double *, int, double, double);
double get_cg_fluct(double, double);
void send_cg_info(int, int, double*, int, double);
void send_cg_info(int, double **, int);
double get_cg_p_corr(double **, int, double);
double find_index(double* , double);
protected:
double boltz,nktv2p,inv_volume;
int nvirial,dimension;
double **vptr;
double *kspace_virial;
Compute *temperature;
char *id_temp;
double virial[6];
int keflag,pairflag,bondflag,angleflag,dihedralflag,improperflag;
int fixflag,kspaceflag;
// NJD MRD
int p_basis_type;
int p_match_flag;
double vavg;
int N_mol;
int N_basis;
double *phi_coeff;
double ** splines;
int spline_length;
void virial_compute(int, int);
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
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: Compute pressure must use group all
Virial contributions computed by potentials (pair, bond, etc) are
computed on all atoms.
E: Could not find compute pressure temperature ID
The compute ID for calculating temperature does not exist.
E: Compute pressure temperature ID does not compute temperature
The compute ID assigned to a pressure computation must compute
temperature.
E: Compute pressure requires temperature ID to include kinetic energy
The keflag cannot be used unless a temperature compute is provided.
E: Virial was not tallied on needed timestep
You are using a thermo keyword that requires potentials to
have tallied the virial, but they didn't on this timestep. See the
variable doc page for ideas on how to make this work.
E: Must use 'kspace_modify pressure/scalar no' for tensor components with kspace_style msm
Otherwise MSM will compute only a scalar pressure. See the kspace_modify
command for details on this setting.
*/

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<div class="section" id="fix-bocs-command">
<span id="index-0"></span><h1>fix bocs command</h1>
<div class="section" id="syntax">
<h2>Syntax</h2>
<pre class="literal-block">
fix ID group-ID bocs keyword values ...
keyword = <em>temp</em> or <em>cgiso</em> or <em>analytic</em> or <em>linear_spline</em> or <em>cubic_spline</em>
<em>temp</em> values = Tstart Tstop Tdamp
<em>cgiso</em> values = Pstart Pstop Pdamp
<em>basis set</em>
<em>analytic</em> values = V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N
<em>linear_spline</em> values = input_filename
<em>cubic_spline</em> values = input_filename
</pre>
</div>
<div class="section" id="examples">
<h2>Examples</h2>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">bocs</span> <span class="n">temp</span> <span class="mf">300.0</span> <span class="mf">300.0</span> <span class="mf">100.0</span> <span class="n">cgiso</span> <span class="mf">0.986</span> <span class="mf">0.986</span> <span class="mf">1000.0</span> <span class="n">analytic</span> <span class="mf">66476.015</span> <span class="mi">968</span> <span class="mi">2</span> <span class="mf">245030.10</span> <span class="mf">8962.20</span>
<span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">bocs</span> <span class="n">temp</span> <span class="mf">300.0</span> <span class="mf">300.0</span> <span class="mf">100.0</span> <span class="n">cgiso</span> <span class="mf">0.986</span> <span class="mf">0.986</span> <span class="mf">1000.0</span> <span class="n">cubic_spline</span> <span class="n">input_Fv</span><span class="o">.</span><span class="n">dat</span>
<span class="n">compute</span> <span class="n">bocsPress</span> <span class="nb">all</span> <span class="n">pressureBocs</span> <span class="n">thermo_temp</span>
<span class="n">thermo_modify</span> <span class="n">press</span> <span class="n">bocsPress</span>
<span class="n">fix_modify</span> <span class="mi">1</span> <span class="n">press</span> <span class="n">bocsPress</span>
</pre></div>
</div>
</div>
<div class="section" id="description">
<h2>Description</h2>
<p>These commands incorporate a pressure correction as described by
Dunn and Noid in <a class="reference internal" href="#bocs-dunn1"><span class="std std-ref">(Dunn1)</span></a> to the standard MTTK
barostat by Martyna et. al. in <a class="reference internal" href="#bocs-martyna"><span class="std std-ref">(Martyna)</span></a> .
The first half of the command mimics a standard fix npt command:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">fix</span> <span class="mi">1</span> <span class="nb">all</span> <span class="n">bocs</span> <span class="n">temp</span> <span class="n">Tstart</span> <span class="n">Tstop</span> <span class="n">Tcoupl</span> <span class="n">cgiso</span> <span class="n">Pstart</span> <span class="n">Pstop</span> <span class="n">Pdamp</span>
</pre></div>
</div>
<p>The two differences are replacing <em>npt</em> with <em>bocs</em>, and replacing
<em>iso</em>/<em>aniso</em>/<em>etc</em> with <em>cgiso</em>.
The rest of the command details what form you would like to use for
the pressure correction equation. The choices are: <em>analytic</em>, <em>linear_spline</em>,
or <em>cubic_spline</em>.</p>
<p>With either spline method, the only argument that needs to follow it
is the name of a file that contains the desired pressure correction
as a function of volume. The file should be formatted so each line has:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Volume_i</span><span class="p">,</span> <span class="n">PressureCorrection_i</span>
</pre></div>
</div>
<p>Note both the COMMA and the SPACE separating the volume&#8217;s
value and its corresponding pressure correction. The volumes in the file
should be uniformly spaced. Both the volumes and the pressure corrections
should be provided in the proper units, e.g. if you are using <em>units real</em>,
the volumes should all be in cubic angstroms, and the pressure corrections
should all be in atomspheres. Furthermore, the table should start/end at a
volume considerably smaller/larger than you expect your system to sample
during the simulation. If the system ever reaches a volume outside of the
range provided, the simulation will stop.</p>
<p>With the <em>analytic</em> option, the arguments are as follows:</p>
<div class="highlight-default"><div class="highlight"><pre><span></span><span class="o">...</span> <span class="n">analytic</span> <span class="n">V_avg</span> <span class="n">N_particles</span> <span class="n">N_coeff</span> <span class="n">Coeff_1</span> <span class="n">Coeff_2</span> <span class="o">...</span> <span class="n">Coeff_N</span>
</pre></div>
</div>
<p>Note that <em>V_avg</em> and <em>Coeff_i</em> should all be in the proper units, e.g. if you
are using <em>units real</em>, <em>V_avg</em> should be in cubic angstroms, and the
coefficients should all be in atmospheres * cubic angstroms.</p>
</div>
<div class="section" id="restrictions">
<h2>Restrictions</h2>
<p>As this is computing a (modified) pressure, group-ID should be <em>all</em>.</p>
<p>The pressure correction has only been tested for use with an isotropic
pressure coupling in 3 dimensions.</p>
<p>There are three additional commands that must be supplied along with fix
bocs. They are given in the examples section. The name <em>bocsPress</em> can be
changed for any name of your choosing, provided it remains consistent across
all three commands. Additionally, the ID <em>1</em> in the <em>fix_modify</em> command must
match up with the <em>ID</em> specified in the original <em>fix bocs</em> command. Everything else
in those three commands must be unchanged. The first two commands can be
specified before the <em>fix bocs</em> command, but the <em>fix_modify</em> command must be
given after the original <em>fix bocs</em> command.</p>
<p>The <em>compute</em> command tells LAMMPS to compute the pressure using the modified
barostat.</p>
<p>The <em>thermo_modify</em> command tells LAMMPS to report the pressure from the modified
barostat instead of the default pressure, i.e. thermo_press.</p>
<p>The <em>fix_modify</em> command tells LAMMPS to use the pressure from the modified
barostat for the fix, instead of using the default presure, i.e. thermo_press.</p>
<p><strong>Related:</strong></p>
<p>For more details about the pressure correction and the entire BOCS software
package, visit the <a class="reference external" href="https://github.com/noid-group/BOCS">BOCS package on github</a> and read the release
paper by Dunn et. al. <a class="reference internal" href="#bocs-dunn2"><span class="std std-ref">(Dunn2)</span></a> .</p>
<hr class="docutils" />
<p id="bocs-dunn1"><strong>(Dunn1)</strong> Dunn and Noid, J Chem Phys, 143, 243148 (2015).</p>
<p id="bocs-martyna"><strong>(Martyna)</strong> Martyna, Tobias, and Klein, J Chem Phys, 101, 4177 (1994).</p>
<p id="bocs-dunn2"><strong>(Dunn2)</strong> Dunn, Lebold, DeLyser, Rudzinski, and Noid, J. Phys. Chem. B, 122, 3363 (2018).</p>
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<"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)
:line
fix bocs command :h3
[Syntax:]
fix ID group-ID bocs keyword values ... :pre
keyword = {temp} or {cgiso} or {analytic} or {linear_spline} or {cubic_spline}
{temp} values = Tstart Tstop Tdamp
{cgiso} values = Pstart Pstop Pdamp
{basis set}
{analytic} values = V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N
{linear_spline} values = input_filename
{cubic_spline} values = input_filename :pre
:ule
[Examples:]
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 :pre
fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 cubic_spline input_Fv.dat :pre
compute bocsPress all pressureBocs thermo_temp
thermo_modify press bocsPress
fix_modify 1 press bocsPress :pre
[Description:]
These commands incorporate a pressure correction as described by
Dunn and Noid in "(Dunn1)"_#bocs-Dunn1 to the standard MTTK
barostat by Martyna et. al. in "(Martyna)"_#bocs-Martyna .
The first half of the command mimics a standard fix npt command:
fix 1 all bocs temp Tstart Tstop Tcoupl cgiso Pstart Pstop Pdamp :pre
The two differences are replacing {npt} with {bocs}, and replacing
{iso}/{aniso}/{etc} with {cgiso}.
The rest of the command details what form you would like to use for
the pressure correction equation. The choices are: {analytic}, {linear_spline},
or {cubic_spline}.
With either spline method, the only argument that needs to follow it
is the name of a file that contains the desired pressure correction
as a function of volume. The file should be formatted so each line has:
Volume_i, PressureCorrection_i :pre
Note both the COMMA and the SPACE separating the volume's
value and its corresponding pressure correction. The volumes in the file
should be uniformly spaced. Both the volumes and the pressure corrections
should be provided in the proper units, e.g. if you are using {units real},
the volumes should all be in cubic angstroms, and the pressure corrections
should all be in atomspheres. Furthermore, the table should start/end at a
volume considerably smaller/larger than you expect your system to sample
during the simulation. If the system ever reaches a volume outside of the
range provided, the simulation will stop.
With the {analytic} option, the arguments are as follows:
... analytic V_avg N_particles N_coeff Coeff_1 Coeff_2 ... Coeff_N :pre
Note that {V_avg} and {Coeff_i} should all be in the proper units, e.g. if you
are using {units real}, {V_avg} should be in cubic angstroms, and the
coefficients should all be in atmospheres * cubic angstroms.
[Restrictions:]
As this is computing a (modified) pressure, group-ID should be {all}.
The pressure correction has only been tested for use with an isotropic
pressure coupling in 3 dimensions.
There are three additional commands that must be supplied along with fix
bocs. They are given in the examples section. The name {bocsPress} can be
changed for any name of your choosing, provided it remains consistent across
all three commands. Additionally, the ID {1} in the {fix_modify} command must
match up with the {ID} specified in the original {fix bocs} command. Everything else
in those three commands must be unchanged. The first two commands can be
specified before the {fix bocs} command, but the {fix_modify} command must be
given after the original {fix bocs} command.
The {compute} command tells LAMMPS to compute the pressure using the modified
barostat.
The {thermo_modify} command tells LAMMPS to report the pressure from the modified
barostat instead of the default pressure, i.e. thermo_press.
The {fix_modify} command tells LAMMPS to use the pressure from the modified
barostat for the fix, instead of using the default presure, i.e. thermo_press.
[Related:]
For more details about the pressure correction and the entire BOCS software
package, visit the "BOCS package on github"_bocsgithub and read the release
paper by Dunn et. al. "(Dunn2)"_#bocs-Dunn2 .
:link(bocsgithub,https://github.com/noid-group/BOCS)
:line
:link(bocs-Dunn1)
[(Dunn1)] Dunn and Noid, J Chem Phys, 143, 243148 (2015).
:link(bocs-Martyna)
[(Martyna)] Martyna, Tobias, and Klein, J Chem Phys, 101, 4177 (1994).
:link(bocs-Dunn2)
[(Dunn2)] Dunn, Lebold, DeLyser, Rudzinski, and Noid, J. Phys. Chem. B, 122, 3363 (2018).

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/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
http://lammps.sandia.gov, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
Copyright (2003) Sandia Corporation. Under the terms of Contract
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
certain rights in this software. This software is distributed under
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
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
#include "fix.h"
namespace LAMMPS_NS {
// MRD NJD
class FixBocs : public Fix {
public:
FixBocs(class LAMMPS *, int, char **); // MRD NJD
virtual ~FixBocs(); // MRD NJD
int setmask();
virtual void init();
virtual void setup(int);
virtual void initial_integrate(int);
virtual void final_integrate();
void initial_integrate_respa(int, int, int);
void final_integrate_respa(int, int);
virtual void pre_exchange();
double compute_scalar();
virtual double compute_vector(int);
void write_restart(FILE *);
virtual int pack_restart_data(double *); // pack restart data
virtual void restart(char *);
int modify_param(int, char **);
void reset_target(double);
void reset_dt();
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;
double dtv,dtf,dthalf,dt4,dt8,dto;
double boltz,nktv2p,tdof;
double vol0; // reference volume
double t0; // reference temperature
// used for barostat mass
double t_start,t_stop;
double t_current,t_target,ke_target;
double t_freq;
int tstat_flag; // 1 if control T
int pstat_flag; // 1 if control P
int pstyle,pcouple,allremap;
int p_flag[6]; // 1 if control P on this dim, 0 if not
double p_start[6],p_stop[6];
double p_freq[6],p_target[6];
double omega[6],omega_dot[6];
double omega_mass[6];
double p_current[6];
double drag,tdrag_factor; // drag factor on particle thermostat
double pdrag_factor; // drag factor on barostat
int kspace_flag; // 1 if KSpace invoked, 0 if not
int nrigid; // number of rigid fixes
int dilate_group_bit; // mask for dilation group
int *rfix; // indices of rigid fixes
char *id_dilate; // group name to dilate
class Irregular *irregular; // for migrating atoms after box flips
// MRD NJD
int p_basis_type;
int p_match_flag;
double vavg;
int N_mol;
int N_p_match;
double *p_match_coeffs;
double ** splines;
int spline_length;
int nlevels_respa;
double *step_respa;
char *id_temp,*id_press;
class Compute *temperature,*pressure;
int tcomputeflag,pcomputeflag; // 1 = compute was created by fix
// 0 = created externally
double *eta,*eta_dot; // chain thermostat for particles
double *eta_dotdot;
double *eta_mass;
int mtchain; // length of chain
int mtchain_default_flag; // 1 = mtchain is default
double *etap; // chain thermostat for barostat
double *etap_dot;
double *etap_dotdot;
double *etap_mass;
int mpchain; // length of chain
int mtk_flag; // 0 if using Hoover barostat
int pdim; // number of barostatted dims
double p_freq_max; // maximum barostat frequency
double p_hydro; // hydrostatic target pressure
int nc_tchain,nc_pchain;
double factor_eta;
double sigma[6]; // scaled target stress
double fdev[6]; // deviatoric force on barostat
int deviatoric_flag; // 0 if target stress tensor is hydrostatic
double h0_inv[6]; // h_inv of reference (zero strain) box
int nreset_h0; // interval for resetting h0
double mtk_term1,mtk_term2; // Martyna-Tobias-Klein corrections
int eta_mass_flag; // 1 if eta_mass updated, 0 if not.
int omega_mass_flag; // 1 if omega_mass updated, 0 if not.
int etap_mass_flag; // 1 if etap_mass updated, 0 if not.
int dipole_flag; // 1 if dipole is updated, 0 if not.
int dlm_flag; // 1 if using the DLM rotational integrator, 0 if not
int scaleyz; // 1 if yz scaled with lz
int scalexz; // 1 if xz scaled with lz
int scalexy; // 1 if xy scaled with ly
int flipflag; // 1 if box flips are invoked as needed
int pre_exchange_flag; // set if pre_exchange needed for box flips
double fixedpoint[3]; // location of dilation fixed-point
void couple();
virtual void remap();
void nhc_temp_integrate();
void nhc_press_integrate();
virtual void nve_x(); // may be overwritten by child classes
virtual void nve_v();
virtual void nh_v_press();
virtual void nh_v_temp();
virtual void compute_temp_target();
virtual int size_restart_global();
void compute_sigma();
void compute_deviatoric();
double compute_strain_energy();
void compute_press_target();
void nh_omega_dot();
};
}
#endif
#endif
/* ERROR/WARNING messages:
E: Illegal ... command
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
Self-explanatory.
E: Invalid fix nvt/npt/nph command for a 2d simulation
Cannot control z dimension in a 2d model.
E: Fix nvt/npt/nph dilate group ID does not exist
Self-explanatory.
E: Invalid fix nvt/npt/nph 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
When specifying a diagonal pressure component, the dimension must be
periodic.
E: Cannot use fix nvt/npt/nph 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
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
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
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
Self-explanatory.
E: Cannot use fix nvt/npt/nph with both xz dynamics and xz scaling
Self-explanatory.
E: Cannot use fix nvt/npt/nph 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
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
Settings for coupled dimensions must be the same.
E: Using update dipole flag requires atom style sphere
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
Self-explanatory.
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
Self-explanatory.
E: Pressure ID for fix npt/nph 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
Self-explanatory. The change in the box tilt is too extreme
on a short timescale.
E: Could not find fix_modify temperature ID
The compute ID for computing temperature does not exist.
E: Fix_modify temperature ID does not compute temperature
The compute ID assigned to the fix must compute temperature.
W: Temperature for fix modify is not for group all
The temperature compute is being used with a pressure calculation
which does operate on group all, so this may be inconsistent.
E: Pressure ID for fix modify does not exist
Self-explanatory.
E: Could not find fix_modify pressure ID
The compute ID for computing pressure does not exist.
E: Fix_modify pressure ID does not compute pressure
The compute ID assigned to the fix must compute pressure.
*/