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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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examples/USER/bocs/README

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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.

examples/USER/bocs/lammps_nb_MET-MET.table

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examples/USER/bocs/methanol.data

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examples/USER/bocs/methanol.lmp

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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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