From c5e884fb41a4baa0788e3ef0ff1b378df9eaab34 Mon Sep 17 00:00:00 2001
From: MICHAEL ROBERT DELYSER
<mrd5285@aci-lgn-005.acib.production.int.aci.ics.psu.edu>
Date: Thu, 26 Apr 2018 09:34:47 -0400
Subject: [PATCH] USER-BOCS
---
doc/src/USER/atc/man_fix_bocs.html | 301 +++
examples/USER/bocs/README | 6 +
examples/USER/bocs/lammps_nb_MET-MET.table | 2505 ++++++++++++++++++
examples/USER/bocs/methanol.data | 991 +++++++
examples/USER/bocs/methanol.lmp | 73 +
src/USER-BOCS/MOD_COMPUTE_H | 207 ++
src/USER-BOCS/README | 34 +
src/USER-BOCS/bocs/README | 6 +
src/USER-BOCS/bocs/lammps_nb_MET-MET.table | 2505 ++++++++++++++++++
src/USER-BOCS/bocs/methanol.data | 991 +++++++
src/USER-BOCS/bocs/methanol.lmp | 73 +
src/USER-BOCS/compute_pressure_bocs.cpp | 441 ++++
src/USER-BOCS/compute_pressure_bocs.h | 115 +
src/USER-BOCS/doc/fix_bocs.html | 301 +++
src/USER-BOCS/doc/fix_bocs.txt | 120 +
src/USER-BOCS/fix_bocs.cpp | 2703 ++++++++++++++++++++
src/USER-BOCS/fix_bocs.h | 305 +++
17 files changed, 11677 insertions(+)
create mode 100644 doc/src/USER/atc/man_fix_bocs.html
create mode 100644 examples/USER/bocs/README
create mode 100644 examples/USER/bocs/lammps_nb_MET-MET.table
create mode 100644 examples/USER/bocs/methanol.data
create mode 100644 examples/USER/bocs/methanol.lmp
create mode 100644 src/USER-BOCS/MOD_COMPUTE_H
create mode 100644 src/USER-BOCS/README
create mode 100644 src/USER-BOCS/bocs/README
create mode 100644 src/USER-BOCS/bocs/lammps_nb_MET-MET.table
create mode 100644 src/USER-BOCS/bocs/methanol.data
create mode 100644 src/USER-BOCS/bocs/methanol.lmp
create mode 100644 src/USER-BOCS/compute_pressure_bocs.cpp
create mode 100644 src/USER-BOCS/compute_pressure_bocs.h
create mode 100644 src/USER-BOCS/doc/fix_bocs.html
create mode 100644 src/USER-BOCS/doc/fix_bocs.txt
create mode 100644 src/USER-BOCS/fix_bocs.cpp
create mode 100644 src/USER-BOCS/fix_bocs.h
diff --git a/doc/src/USER/atc/man_fix_bocs.html b/doc/src/USER/atc/man_fix_bocs.html
new file mode 100644
index 0000000000..9d21d2c0bc
--- /dev/null
+++ b/doc/src/USER/atc/man_fix_bocs.html
@@ -0,0 +1,301 @@
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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’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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diff --git a/examples/USER/bocs/README b/examples/USER/bocs/README
new file mode 100644
index 0000000000..ae1739f8c0
--- /dev/null
+++ b/examples/USER/bocs/README
@@ -0,0 +1,6 @@
+This folder contains the files to run a NPT simulation of 1 site CG methanol
+while employing a correction to the barostat.
+The pair force was computed via the Multi-Scale Coarse-Graining method.
+The resulting model was then iteratively pressure matched.
+The model accurately reproduces both structural (RDF) and thermodynamic
+(Pressure-Volume EoS) properties of the underlying OPLS-AA model of methanol.
diff --git a/examples/USER/bocs/lammps_nb_MET-MET.table b/examples/USER/bocs/lammps_nb_MET-MET.table
new file mode 100644
index 0000000000..c6d9fc6ca2
--- /dev/null
+++ b/examples/USER/bocs/lammps_nb_MET-MET.table
@@ -0,0 +1,2505 @@
+#Converted from table.xvg
+
+nb_METMET
+N 2500
+
+1 0.010000 573.151769 380.122371
+2 0.020000 569.356836 378.855163
+3 0.030000 565.574570 377.588193
+4 0.040000 561.805210 376.320985
+5 0.050000 558.048279 375.053776
+6 0.060000 554.304015 373.786807
+7 0.070000 550.572419 372.519598
+8 0.080000 546.853728 371.252390
+9 0.090000 543.147467 369.985421
+10 0.100000 539.453872 368.718212
+11 0.110000 535.773184 367.451004
+12 0.120000 532.104924 366.184034
+13 0.130000 528.449331 364.916826
+14 0.140000 524.806644 363.649618
+15 0.150000 521.176386 362.382648
+16 0.160000 517.559034 361.115440
+17 0.170000 513.954111 359.848231
+18 0.180000 510.361855 358.581262
+19 0.190000 506.782505 357.314054
+20 0.200000 503.215583 356.046845
+21 0.210000 499.661568 354.779876
+22 0.220000 496.119981 353.512667
+23 0.230000 492.591300 352.245459
+24 0.240000 489.075287 350.978489
+25 0.250000 485.571702 349.711281
+26 0.260000 482.081023 348.444073
+27 0.270000 478.602772 347.177103
+28 0.280000 475.137428 345.909895
+29 0.290000 471.684751 344.642686
+30 0.300000 468.244503 343.375717
+31 0.310000 464.817161 342.108509
+32 0.320000 461.402486 340.841300
+33 0.330000 458.000239 339.574331
+34 0.340000 454.610899 338.307122
+35 0.350000 451.234226 337.039914
+36 0.360000 447.870220 335.772945
+37 0.370000 444.518642 334.505736
+38 0.380000 441.179971 333.238528
+39 0.390000 437.853967 331.971558
+40 0.400000 434.540631 330.704350
+41 0.410000 431.239962 329.437141
+42 0.420000 427.951721 328.170172
+43 0.430000 424.676386 326.902964
+44 0.440000 421.413719 325.635755
+45 0.450000 418.163719 324.368786
+46 0.460000 414.926386 323.101577
+47 0.470000 411.701721 321.834369
+48 0.480000 408.489723 320.567400
+49 0.490000 405.290392 319.300191
+50 0.500000 402.103728 318.032983
+51 0.510000 398.929732 316.766013
+52 0.520000 395.768403 315.498805
+53 0.530000 392.619742 314.231597
+54 0.540000 389.483748 312.964627
+55 0.550000 386.360421 311.697419
+56 0.560000 383.249761 310.430210
+57 0.570000 380.151769 309.163241
+58 0.580000 377.066444 307.896033
+59 0.590000 373.993786 306.628824
+60 0.600000 370.934034 305.361855
+61 0.610000 367.886711 304.094646
+62 0.620000 364.852055 302.827438
+63 0.630000 361.830067 301.560468
+64 0.640000 358.820746 300.293260
+65 0.650000 355.824331 299.026052
+66 0.660000 352.840344 297.759082
+67 0.670000 349.869025 296.491874
+68 0.680000 346.910373 295.224904
+69 0.690000 343.964627 293.957696
+70 0.700000 341.031310 292.690488
+71 0.710000 338.110660 291.423518
+72 0.720000 335.202916 290.156310
+73 0.730000 332.307600 288.889101
+74 0.740000 329.425191 287.622132
+75 0.750000 326.555210 286.354924
+76 0.760000 323.697897 285.087715
+77 0.770000 320.853489 283.820746
+78 0.780000 318.021511 282.553537
+79 0.790000 315.202438 281.286329
+80 0.800000 312.395793 280.019359
+81 0.810000 309.602055 278.752151
+82 0.820000 306.820746 277.484943
+83 0.830000 304.052342 276.217973
+84 0.840000 301.296367 274.950765
+85 0.850000 298.553298 273.683556
+86 0.860000 295.822658 272.416587
+87 0.870000 293.104924 271.149379
+88 0.880000 290.399857 269.882170
+89 0.890000 287.707218 268.615201
+90 0.900000 285.027486 267.347992
+91 0.910000 282.360421 266.080784
+92 0.920000 279.705784 264.813815
+93 0.930000 277.064054 263.546606
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diff --git a/examples/USER/bocs/methanol.data b/examples/USER/bocs/methanol.data
new file mode 100644
index 0000000000..01f66de6f6
--- /dev/null
+++ b/examples/USER/bocs/methanol.data
@@ -0,0 +1,991 @@
+LAMMPS Description
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diff --git a/examples/USER/bocs/methanol.lmp b/examples/USER/bocs/methanol.lmp
new file mode 100644
index 0000000000..13a71aa67e
--- /dev/null
+++ b/examples/USER/bocs/methanol.lmp
@@ -0,0 +1,73 @@
+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
+
diff --git a/src/USER-BOCS/MOD_COMPUTE_H b/src/USER-BOCS/MOD_COMPUTE_H
new file mode 100644
index 0000000000..91bd09e288
--- /dev/null
+++ b/src/USER-BOCS/MOD_COMPUTE_H
@@ -0,0 +1,207 @@
+/* -*- 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.
+
+*/
diff --git a/src/USER-BOCS/README b/src/USER-BOCS/README
new file mode 100644
index 0000000000..996375ccf7
--- /dev/null
+++ b/src/USER-BOCS/README
@@ -0,0 +1,34 @@
+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.
+
+
diff --git a/src/USER-BOCS/bocs/README b/src/USER-BOCS/bocs/README
new file mode 100644
index 0000000000..ae1739f8c0
--- /dev/null
+++ b/src/USER-BOCS/bocs/README
@@ -0,0 +1,6 @@
+This folder contains the files to run a NPT simulation of 1 site CG methanol
+while employing a correction to the barostat.
+The pair force was computed via the Multi-Scale Coarse-Graining method.
+The resulting model was then iteratively pressure matched.
+The model accurately reproduces both structural (RDF) and thermodynamic
+(Pressure-Volume EoS) properties of the underlying OPLS-AA model of methanol.
diff --git a/src/USER-BOCS/bocs/lammps_nb_MET-MET.table b/src/USER-BOCS/bocs/lammps_nb_MET-MET.table
new file mode 100644
index 0000000000..c6d9fc6ca2
--- /dev/null
+++ b/src/USER-BOCS/bocs/lammps_nb_MET-MET.table
@@ -0,0 +1,2505 @@
+#Converted from table.xvg
+
+nb_METMET
+N 2500
+
+1 0.010000 573.151769 380.122371
+2 0.020000 569.356836 378.855163
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diff --git a/src/USER-BOCS/bocs/methanol.data b/src/USER-BOCS/bocs/methanol.data
new file mode 100644
index 0000000000..01f66de6f6
--- /dev/null
+++ b/src/USER-BOCS/bocs/methanol.data
@@ -0,0 +1,991 @@
+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
+
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+2 1 18.38 15.72 26.03
+3 1 3.52 1.77 23.57
+4 1 31.09 11.38 12.17
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diff --git a/src/USER-BOCS/bocs/methanol.lmp b/src/USER-BOCS/bocs/methanol.lmp
new file mode 100644
index 0000000000..13a71aa67e
--- /dev/null
+++ b/src/USER-BOCS/bocs/methanol.lmp
@@ -0,0 +1,73 @@
+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
+
diff --git a/src/USER-BOCS/compute_pressure_bocs.cpp b/src/USER-BOCS/compute_pressure_bocs.cpp
new file mode 100644
index 0000000000..8c0ae68817
--- /dev/null
+++ b/src/USER-BOCS/compute_pressure_bocs.cpp
@@ -0,0 +1,441 @@
+/* ----------------------------------------------------------------------
+ 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);
+}
diff --git a/src/USER-BOCS/compute_pressure_bocs.h b/src/USER-BOCS/compute_pressure_bocs.h
new file mode 100644
index 0000000000..d528009ad9
--- /dev/null
+++ b/src/USER-BOCS/compute_pressure_bocs.h
@@ -0,0 +1,115 @@
+/* -*- 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.
+
+*/
diff --git a/src/USER-BOCS/doc/fix_bocs.html b/src/USER-BOCS/doc/fix_bocs.html
new file mode 100644
index 0000000000..9d21d2c0bc
--- /dev/null
+++ b/src/USER-BOCS/doc/fix_bocs.html
@@ -0,0 +1,301 @@
+
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+<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
+<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
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+<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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+</ul>
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+<li class="toctree-l1"><a class="reference internal" href="commands.html">Commands</a></li>
+<li class="toctree-l1"><a class="reference internal" href="fixes.html">Fixes</a></li>
+<li class="toctree-l1"><a class="reference internal" href="computes.html">Computes</a></li>
+<li class="toctree-l1"><a class="reference internal" href="pairs.html">Pair Styles</a></li>
+<li class="toctree-l1"><a class="reference internal" href="bonds.html">Bond Styles</a></li>
+<li class="toctree-l1"><a class="reference internal" href="angles.html">Angle Styles</a></li>
+<li class="toctree-l1"><a class="reference internal" href="dihedrals.html">Dihedral Styles</a></li>
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+ <li><a href="Manual.html">Docs</a> »</li>
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+ <li>fix bocs command</li>
+ <li class="wy-breadcrumbs-aside">
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+ <a href="http://lammps.sandia.gov">Website</a>
+ <a href="Section_commands.html#comm">Commands</a>
+
+ </li>
+ </ul>
+ <hr/>
+
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+ <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
+ <div itemprop="articleBody">
+
+ <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’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>
+</div>
+
+
+ </div>
+ </div>
+ <footer>
+
+
+ <hr/>
+
+ <div role="contentinfo">
+ <p>
+ © Copyright 2013 Sandia Corporation.
+ </p>
+ </div>
+ Built with <a href="http://sphinx-doc.org/">Sphinx</a> using a <a href="https://github.com/snide/sphinx_rtd_theme">theme</a> provided by <a href="https://readthedocs.org">Read the Docs</a>.
+
+</footer>
+
+ </div>
+ </div>
+
+ </section>
+
+ </div>
+
+
+
+
+
+ <script type="text/javascript">
+ var DOCUMENTATION_OPTIONS = {
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diff --git a/src/USER-BOCS/doc/fix_bocs.txt b/src/USER-BOCS/doc/fix_bocs.txt
new file mode 100644
index 0000000000..e6b9013921
--- /dev/null
+++ b/src/USER-BOCS/doc/fix_bocs.txt
@@ -0,0 +1,120 @@
+<"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).
+
+
+
diff --git a/src/USER-BOCS/fix_bocs.cpp b/src/USER-BOCS/fix_bocs.cpp
new file mode 100644
index 0000000000..8f729393b6
--- /dev/null
+++ b/src/USER-BOCS/fix_bocs.cpp
@@ -0,0 +1,2703 @@
+/* ----------------------------------------------------------------------
+ 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 <string.h>
+#include <stdlib.h>
+#include <math.h>
+#include "fix_bocs.h"
+#include "math_extra.h"
+#include "atom.h"
+#include "force.h"
+#include "group.h"
+#include "comm.h"
+#include "neighbor.h"
+#include "irregular.h"
+#include "modify.h"
+#include "fix_deform.h"
+#include "compute.h"
+#include "kspace.h"
+#include "update.h"
+#include "respa.h"
+#include "domain.h"
+#include "memory.h"
+#include "error.h"
+
+
+using namespace LAMMPS_NS;
+using namespace FixConst;
+
+static const char cite_user_bocs_package[] =
+ "USER-BOCS package:\n\n"
+ "@Article{Dunn2018,\n"
+ " author = {NJH Dunn, KM Lebold, MR DeLyser, JF Rudzinski, WG Noid},\n"
+ " title = {BOCS: Bottom-Up Open-Source Coarse-Graining Software},\n"
+ " journal = {J. Phys. Chem. B},\n"
+ " year = 2018,\n"
+ " volume = 122,\n"
+ " pages = {3363--3377}\n"
+ "}\n\n";
+
+
+#define DELTAFLIP 0.1
+#define TILTMAX 1.5
+
+enum{NOBIAS,BIAS};
+enum{NONE,XYZ,XY,YZ,XZ};
+enum{ISO,ANISO,TRICLINIC};
+
+/* ----------------------------------------------------------------------
+ NVT,NPH,NPT integrators for improved Nose-Hoover equations of motion
+ ---------------------------------------------------------------------- */
+
+FixBocs::FixBocs(LAMMPS *lmp, int narg, char **arg) :
+ Fix(lmp, narg, arg),
+ rfix(NULL), id_dilate(NULL), irregular(NULL), id_temp(NULL), id_press(NULL),
+ eta(NULL), eta_dot(NULL), eta_dotdot(NULL),
+ eta_mass(NULL), etap(NULL), etap_dot(NULL), etap_dotdot(NULL),
+ etap_mass(NULL)
+{
+ if (lmp->citeme) lmp->citeme->add(cite_user_bocs_package);
+
+ if (narg < 4) error->all(FLERR,"Illegal fix bocs command");
+
+ restart_global = 1;
+ dynamic_group_allow = 1;
+ time_integrate = 1;
+ scalar_flag = 1;
+ vector_flag = 1;
+ global_freq = 1;
+ extscalar = 1;
+ extvector = 0;
+
+ // default values
+
+ pcouple = NONE;
+ drag = 0.0;
+ allremap = 1;
+ id_dilate = NULL;
+ mtchain = mpchain = 3;
+ nc_tchain = nc_pchain = 1;
+ mtk_flag = 1;
+ deviatoric_flag = 0;
+ nreset_h0 = 0;
+ eta_mass_flag = 1;
+ omega_mass_flag = 0;
+ etap_mass_flag = 0;
+ flipflag = 1;
+ dipole_flag = 0;
+ dlm_flag = 0;
+
+ tcomputeflag = 0;
+ pcomputeflag = 0;
+ id_temp = NULL;
+ id_press = NULL;
+
+ // turn on tilt factor scaling, whenever applicable
+
+ dimension = domain->dimension;
+
+ scaleyz = scalexz = scalexy = 0;
+ if (domain->yperiodic && domain->xy != 0.0) scalexy = 1;
+ if (domain->zperiodic && dimension == 3) {
+ if (domain->yz != 0.0) scaleyz = 1;
+ if (domain->xz != 0.0) scalexz = 1;
+ }
+
+ // set fixed-point to default = center of cell
+
+ fixedpoint[0] = 0.5*(domain->boxlo[0]+domain->boxhi[0]);
+ fixedpoint[1] = 0.5*(domain->boxlo[1]+domain->boxhi[1]);
+ fixedpoint[2] = 0.5*(domain->boxlo[2]+domain->boxhi[2]);
+
+ // used by FixNVTSllod to preserve non-default value
+
+ mtchain_default_flag = 1;
+
+ tstat_flag = 0;
+ double t_period = 0.0;
+
+ double p_period[6];
+ for (int i = 0; i < 6; i++) {
+ p_start[i] = p_stop[i] = p_period[i] = p_target[i] = 0.0;
+ p_flag[i] = 0;
+ }
+
+ // process keywords
+
+ int iarg = 3;
+
+ while (iarg < narg) {
+ if (strcmp(arg[iarg],"temp") == 0) {
+ if (iarg+4 > narg) error->all(FLERR,"Illegal fix bocs command");
+ tstat_flag = 1;
+ t_start = force->numeric(FLERR,arg[iarg+1]);
+ t_target = t_start;
+ t_stop = force->numeric(FLERR,arg[iarg+2]);
+ t_period = force->numeric(FLERR,arg[iarg+3]);
+ if (t_start <= 0.0 || t_stop <= 0.0)
+ error->all(FLERR,
+ "Target temperature for fix bocs cannot be 0.0");
+ iarg += 4;
+ } else if (strcmp(arg[iarg],"iso") == 0) {
+/* if (iarg+4 > narg) error->all(FLERR,"Illegal fix bocs command");
+ pcouple = XYZ;
+ p_start[0] = p_start[1] = p_start[2] = force->numeric(FLERR,arg[iarg+1]);
+ p_stop[0] = p_stop[1] = p_stop[2] = force->numeric(FLERR,arg[iarg+2]);
+ p_period[0] = p_period[1] = p_period[2] =
+ force->numeric(FLERR,arg[iarg+3]);
+ p_flag[0] = p_flag[1] = p_flag[2] = 1;
+ if (dimension == 2) {
+ p_start[2] = p_stop[2] = p_period[2] = 0.0;
+ p_flag[2] = 0;
+ }
+ iarg += 4;*/
+ error->all(FLERR,"Illegal fix bocs command. Pressure fix must be "
+ "cgiso . Use regular fix npt/nph for iso"); // MRD NJD
+ } else if (strcmp(arg[iarg],"cgiso") == 0) { // MRD NJD the whole else if
+ if (iarg+4 > narg)
+ {
+ error->all(FLERR,"Illegal fix bocs command. cgiso must be "
+ "followed by: P_0 P_f P_coupl");
+ }
+ p_match_flag = 1;
+ pcouple = XYZ;
+ p_start[0] = p_start[1] = p_start[2] =
+ force->numeric(FLERR,arg[iarg+1]);
+ p_stop[0] = p_stop[1] = p_stop[2] =
+ force->numeric(FLERR,arg[iarg+2]);
+ p_period[0] = p_period[1] = p_period[2] =
+ force->numeric(FLERR,arg[iarg+3]);
+
+ p_flag[0] = p_flag[1] = p_flag[2] = 1;
+ p_flag[3] = p_flag[4] = p_flag[5] = 0; // MRD
+ if (dimension == 2) { // Later I force 3D... MRD
+ p_start[2] = p_stop[2] = p_period[2] = 0.0;
+ p_flag[2] = 0;
+ }
+ iarg += 4;
+
+ if ( strcmp(arg[iarg], "analytic") == 0 )
+ {
+ if (iarg + 4 > narg)
+ {
+ error->all(FLERR,"Illegal fix bocs command. basis type analytic"
+ " must be followed by: avg_vol n_mol n_pmatch_coeff");
+ }
+ p_basis_type = 0;
+ vavg = atof(arg[iarg+1]);
+ N_mol = atoi(arg[iarg+2]);
+ N_p_match = atoi(arg[iarg+3]);
+ p_match_coeffs = (double *) (calloc(N_p_match, sizeof(double)) );
+ iarg += 4;
+ if (iarg + N_p_match > narg)
+ {
+ error->all(FLERR,"Illegal fix bocs command. Missing coeffs.");
+ }
+ for (int pmatchi = 0; pmatchi < N_p_match; pmatchi++)
+ {
+ p_match_coeffs[pmatchi] = atof(arg[iarg+pmatchi]);
+ }
+ iarg += (N_p_match);
+ } else if (strcmp(arg[iarg], "linear_spline") == 0 )
+ {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix bocs command. "
+ "Supply a file name after linear_spline.");
+
+ p_basis_type = 1;
+ spline_length = read_F_table( arg[iarg+1], p_basis_type );
+ iarg += 2;
+ } else if (strcmp(arg[iarg], "cubic_spline") == 0 )
+ {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix bocs command. "
+ "Supply a file name after cubic_spline.");
+ p_basis_type = 2;
+ spline_length = read_F_table( arg[iarg+1], p_basis_type );
+// build_cubic_splines(); MRD I moved this into read_F_table
+// and that's why I pass p_basis_type in there too. I was having
+// a fight getting "double ** data" stuff to work
+ iarg += 2;
+ } else
+ {
+ char * errmsg = (char *) calloc(150,sizeof(char));
+ sprintf(errmsg,"CG basis type %s is not recognized\nSupported "
+ "basis types: analytic linear_spline cubic_spline",arg[iarg]);
+ error->all(FLERR,errmsg);
+ } // END NJD MRD
+ } /*else if (strcmp(arg[iarg],"aniso") == 0) {
+ if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ pcouple = NONE;
+ p_start[0] = p_start[1] = p_start[2] = force->numeric(FLERR,arg[iarg+1]);
+ p_stop[0] = p_stop[1] = p_stop[2] = force->numeric(FLERR,arg[iarg+2]);
+ p_period[0] = p_period[1] = p_period[2] =
+ force->numeric(FLERR,arg[iarg+3]);
+ p_flag[0] = p_flag[1] = p_flag[2] = 1;
+ if (dimension == 2) {
+ p_start[2] = p_stop[2] = p_period[2] = 0.0;
+ p_flag[2] = 0;
+ }
+ iarg += 4;
+ } else if (strcmp(arg[iarg],"tri") == 0) {
+ if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ pcouple = NONE;
+ scalexy = scalexz = scaleyz = 0;
+ p_start[0] = p_start[1] = p_start[2] = force->numeric(FLERR,arg[iarg+1]);
+ p_stop[0] = p_stop[1] = p_stop[2] = force->numeric(FLERR,arg[iarg+2]);
+ p_period[0] = p_period[1] = p_period[2] =
+ force->numeric(FLERR,arg[iarg+3]);
+ p_flag[0] = p_flag[1] = p_flag[2] = 1;
+ p_start[3] = p_start[4] = p_start[5] = 0.0;
+ p_stop[3] = p_stop[4] = p_stop[5] = 0.0;
+ p_period[3] = p_period[4] = p_period[5] =
+ force->numeric(FLERR,arg[iarg+3]);
+ p_flag[3] = p_flag[4] = p_flag[5] = 1;
+ if (dimension == 2) {
+ p_start[2] = p_stop[2] = p_period[2] = 0.0;
+ p_flag[2] = 0;
+ p_start[3] = p_stop[3] = p_period[3] = 0.0;
+ p_flag[3] = 0;
+ p_start[4] = p_stop[4] = p_period[4] = 0.0;
+ p_flag[4] = 0;
+ }
+ iarg += 4;
+ } else if (strcmp(arg[iarg],"x") == 0) {
+ if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ p_start[0] = force->numeric(FLERR,arg[iarg+1]);
+ p_stop[0] = force->numeric(FLERR,arg[iarg+2]);
+ p_period[0] = force->numeric(FLERR,arg[iarg+3]);
+ p_flag[0] = 1;
+ deviatoric_flag = 1;
+ iarg += 4;
+ } else if (strcmp(arg[iarg],"y") == 0) {
+ if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ p_start[1] = force->numeric(FLERR,arg[iarg+1]);
+ p_stop[1] = force->numeric(FLERR,arg[iarg+2]);
+ p_period[1] = force->numeric(FLERR,arg[iarg+3]);
+ p_flag[1] = 1;
+ deviatoric_flag = 1;
+ iarg += 4;
+ } else if (strcmp(arg[iarg],"z") == 0) {
+ if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ p_start[2] = force->numeric(FLERR,arg[iarg+1]);
+ p_stop[2] = force->numeric(FLERR,arg[iarg+2]);
+ p_period[2] = force->numeric(FLERR,arg[iarg+3]);
+ p_flag[2] = 1;
+ deviatoric_flag = 1;
+ iarg += 4;
+ if (dimension == 2)
+ error->all(FLERR,"Invalid fix nvt/npt/nph command for a 2d simulation");
+
+ } else if (strcmp(arg[iarg],"yz") == 0) {
+ if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ p_start[3] = force->numeric(FLERR,arg[iarg+1]);
+ p_stop[3] = force->numeric(FLERR,arg[iarg+2]);
+ p_period[3] = force->numeric(FLERR,arg[iarg+3]);
+ p_flag[3] = 1;
+ deviatoric_flag = 1;
+ scaleyz = 0;
+ iarg += 4;
+ if (dimension == 2)
+ error->all(FLERR,"Invalid fix nvt/npt/nph command for a 2d simulation");
+ } else if (strcmp(arg[iarg],"xz") == 0) {
+ if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ p_start[4] = force->numeric(FLERR,arg[iarg+1]);
+ p_stop[4] = force->numeric(FLERR,arg[iarg+2]);
+ p_period[4] = force->numeric(FLERR,arg[iarg+3]);
+ p_flag[4] = 1;
+ deviatoric_flag = 1;
+ scalexz = 0;
+ iarg += 4;
+ if (dimension == 2)
+ error->all(FLERR,"Invalid fix nvt/npt/nph command for a 2d simulation");
+ } else if (strcmp(arg[iarg],"xy") == 0) {
+ if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ p_start[5] = force->numeric(FLERR,arg[iarg+1]);
+ p_stop[5] = force->numeric(FLERR,arg[iarg+2]);
+ p_period[5] = force->numeric(FLERR,arg[iarg+3]);
+ p_flag[5] = 1;
+ deviatoric_flag = 1;
+ scalexy = 0;
+ iarg += 4;
+
+ } else if (strcmp(arg[iarg],"couple") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ if (strcmp(arg[iarg+1],"xyz") == 0) pcouple = XYZ;
+ else if (strcmp(arg[iarg+1],"xy") == 0) pcouple = XY;
+ else if (strcmp(arg[iarg+1],"yz") == 0) pcouple = YZ;
+ else if (strcmp(arg[iarg+1],"xz") == 0) pcouple = XZ;
+ else if (strcmp(arg[iarg+1],"none") == 0) pcouple = NONE;
+ else error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ iarg += 2;
+
+ } else if (strcmp(arg[iarg],"drag") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ drag = force->numeric(FLERR,arg[iarg+1]);
+ if (drag < 0.0) error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ iarg += 2;
+ } else if (strcmp(arg[iarg],"dilate") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ if (strcmp(arg[iarg+1],"all") == 0) allremap = 1;
+ else {
+ allremap = 0;
+ delete [] id_dilate;
+ int n = strlen(arg[iarg+1]) + 1;
+ id_dilate = new char[n];
+ strcpy(id_dilate,arg[iarg+1]);
+ int idilate = group->find(id_dilate);
+ if (idilate == -1)
+ error->all(FLERR,"Fix nvt/npt/nph dilate group ID does not exist");
+ }
+ iarg += 2;
+
+ }*/ else if (strcmp(arg[iarg],"tchain") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ mtchain = force->inumeric(FLERR,arg[iarg+1]);
+ // used by FixNVTSllod to preserve non-default value
+ mtchain_default_flag = 0;
+ if (mtchain < 1) error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ iarg += 2;
+ } else if (strcmp(arg[iarg],"pchain") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ mpchain = force->inumeric(FLERR,arg[iarg+1]);
+ if (mpchain < 0) error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ iarg += 2;
+ } else if (strcmp(arg[iarg],"mtk") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ if (strcmp(arg[iarg+1],"yes") == 0) mtk_flag = 1;
+ else if (strcmp(arg[iarg+1],"no") == 0) mtk_flag = 0;
+ else error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ iarg += 2;
+ } else if (strcmp(arg[iarg],"tloop") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ nc_tchain = force->inumeric(FLERR,arg[iarg+1]);
+ if (nc_tchain < 0) error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ iarg += 2;
+ } else if (strcmp(arg[iarg],"ploop") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ nc_pchain = force->inumeric(FLERR,arg[iarg+1]);
+ if (nc_pchain < 0) error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ iarg += 2;
+ } /*else if (strcmp(arg[iarg],"nreset") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ nreset_h0 = force->inumeric(FLERR,arg[iarg+1]);
+ if (nreset_h0 < 0) error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ iarg += 2;
+ } else if (strcmp(arg[iarg],"scalexy") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ if (strcmp(arg[iarg+1],"yes") == 0) scalexy = 1;
+ else if (strcmp(arg[iarg+1],"no") == 0) scalexy = 0;
+ else error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ iarg += 2;
+ } else if (strcmp(arg[iarg],"scalexz") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ if (strcmp(arg[iarg+1],"yes") == 0) scalexz = 1;
+ else if (strcmp(arg[iarg+1],"no") == 0) scalexz = 0;
+ else error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ iarg += 2;
+ } else if (strcmp(arg[iarg],"scaleyz") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ if (strcmp(arg[iarg+1],"yes") == 0) scaleyz = 1;
+ else if (strcmp(arg[iarg+1],"no") == 0) scaleyz = 0;
+ else error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ iarg += 2;
+ } else if (strcmp(arg[iarg],"flip") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ if (strcmp(arg[iarg+1],"yes") == 0) flipflag = 1;
+ else if (strcmp(arg[iarg+1],"no") == 0) flipflag = 0;
+ else error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ iarg += 2;
+ } else if (strcmp(arg[iarg],"update") == 0) {
+ if (iarg+2 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ if (strcmp(arg[iarg+1],"dipole") == 0) dipole_flag = 1;
+ else if (strcmp(arg[iarg+1],"dipole/dlm") == 0) {
+ dipole_flag = 1;
+ dlm_flag = 1;
+ } else error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ iarg += 2;
+ } else if (strcmp(arg[iarg],"fixedpoint") == 0) {
+ if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
+ fixedpoint[0] = force->numeric(FLERR,arg[iarg+1]);
+ fixedpoint[1] = force->numeric(FLERR,arg[iarg+2]);
+ fixedpoint[2] = force->numeric(FLERR,arg[iarg+3]);
+ iarg += 4;
+
+ // disc keyword is also parsed in fix/nh/sphere
+
+ } else if (strcmp(arg[iarg],"disc") == 0) {
+ iarg++;
+
+ }*/ else {
+ char * errmsg = (char *) calloc(80,sizeof(char));
+ sprintf(errmsg,"Illegal fix bocs command: unrecognized keyword %s"
+ ,arg[iarg]);
+ error->all(FLERR,errmsg);
+ }
+ }
+ // error checks
+
+ if (dimension != 3) // MRD NJD
+ error->all(FLERR,"Invalid fix bocs command. Must use 3 dimensions");
+
+/* if (dimension == 2 && (p_flag[2] || p_flag[3] || p_flag[4]))
+ error->all(FLERR,"Invalid fix nvt/npt/nph command for a 2d simulation");
+ if (dimension == 2 && (pcouple == YZ || pcouple == XZ))
+ error->all(FLERR,"Invalid fix nvt/npt/nph command for a 2d simulation");
+ if (dimension == 2 && (scalexz == 1 || scaleyz == 1 ))
+ error->all(FLERR,"Invalid fix nvt/npt/nph command for a 2d simulation");*/
+
+// With cgiso, p_flag[0] = p_flag[1] = p_flag[2] = 1
+/* if (pcouple == XYZ && (p_flag[0] == 0 || p_flag[1] == 0))
+ error->all(FLERR,"Invalid fix nvt/npt/nph command pressure settings");
+ if (pcouple == XYZ && dimension == 3 && p_flag[2] == 0)
+ error->all(FLERR,"Invalid fix nvt/npt/nph command pressure settings");
+ if (pcouple == XY && (p_flag[0] == 0 || p_flag[1] == 0))
+ error->all(FLERR,"Invalid fix nvt/npt/nph command pressure settings");
+ if (pcouple == YZ && (p_flag[1] == 0 || p_flag[2] == 0))
+ error->all(FLERR,"Invalid fix nvt/npt/nph command pressure settings");
+ if (pcouple == XZ && (p_flag[0] == 0 || p_flag[2] == 0))
+ error->all(FLERR,"Invalid fix nvt/npt/nph command pressure settings");*/
+
+ // require periodicity in tensile dimension
+
+ if (p_flag[0] && domain->xperiodic == 0)
+ error->all(FLERR,"Cannot use fix bocs on a non-periodic dimension");
+ if (p_flag[1] && domain->yperiodic == 0)
+ error->all(FLERR,"Cannot use fix bocs on a non-periodic dimension");
+ if (p_flag[2] && domain->zperiodic == 0)
+ error->all(FLERR,"Cannot use fix bocs on a non-periodic dimension");
+
+ // require periodicity in 2nd dim of off-diagonal tilt component
+
+/* if (p_flag[3] && domain->zperiodic == 0)
+ error->all(FLERR,
+ "Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension");
+ if (p_flag[4] && domain->zperiodic == 0)
+ error->all(FLERR,
+ "Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension");
+ if (p_flag[5] && domain->yperiodic == 0)
+ error->all(FLERR,
+ "Cannot use fix nvt/npt/nph on a 2nd non-periodic dimension");
+*/
+ if (scaleyz == 1 && domain->zperiodic == 0)
+ error->all(FLERR,"Cannot use fix bocs "
+ "with yz scaling when z is non-periodic dimension");
+ if (scalexz == 1 && domain->zperiodic == 0)
+ error->all(FLERR,"Cannot use fix bocs "
+ "with xz scaling when z is non-periodic dimension");
+ if (scalexy == 1 && domain->yperiodic == 0)
+ error->all(FLERR,"Cannot use fix bocs "
+ "with xy scaling when y is non-periodic dimension");
+
+/* if (p_flag[3] && scaleyz == 1)
+ error->all(FLERR,"Cannot use fix nvt/npt/nph with "
+ "both yz dynamics and yz scaling");
+ if (p_flag[4] && scalexz == 1)
+ error->all(FLERR,"Cannot use fix nvt/npt/nph with "
+ "both xz dynamics and xz scaling");
+ if (p_flag[5] && scalexy == 1)
+ error->all(FLERR,"Cannot use fix nvt/npt/nph with "
+ "both xy dynamics and xy scaling");*/
+
+//
+/* if (!domain->triclinic && (p_flag[3] || p_flag[4] || p_flag[5]))
+ error->all(FLERR,"Can not specify Pxy/Pxz/Pyz in "
+ "fix nvt/npt/nph with non-triclinic box");*/
+
+// This is all forced in cgiso
+/* if (pcouple == XYZ && dimension == 3 &&
+ (p_start[0] != p_start[1] || p_start[0] != p_start[2] ||
+ p_stop[0] != p_stop[1] || p_stop[0] != p_stop[2] ||
+ p_period[0] != p_period[1] || p_period[0] != p_period[2]))
+ error->all(FLERR,"Invalid fix nvt/npt/nph pressure settings");
+ if (pcouple == XYZ && dimension == 2 &&
+ (p_start[0] != p_start[1] || p_stop[0] != p_stop[1] ||
+ p_period[0] != p_period[1]))
+ error->all(FLERR,"Invalid fix nvt/npt/nph pressure settings");
+ if (pcouple == XY &&
+ (p_start[0] != p_start[1] || p_stop[0] != p_stop[1] ||
+ p_period[0] != p_period[1]))
+ error->all(FLERR,"Invalid fix nvt/npt/nph pressure settings");
+ if (pcouple == YZ &&
+ (p_start[1] != p_start[2] || p_stop[1] != p_stop[2] ||
+ p_period[1] != p_period[2]))
+ error->all(FLERR,"Invalid fix nvt/npt/nph pressure settings");
+ if (pcouple == XZ &&
+ (p_start[0] != p_start[2] || p_stop[0] != p_stop[2] ||
+ p_period[0] != p_period[2]))
+ error->all(FLERR,"Invalid fix nvt/npt/nph pressure settings");*/
+
+ if (dipole_flag) {
+ if (!atom->sphere_flag)
+ error->all(FLERR,"Using update dipole flag requires atom style sphere");
+ if (!atom->mu_flag)
+ error->all(FLERR,"Using update dipole flag requires atom attribute mu");
+ }
+
+ if ((tstat_flag && t_period <= 0.0) ||
+ (p_flag[0] && p_period[0] <= 0.0) ||
+ (p_flag[1] && p_period[1] <= 0.0) ||
+ (p_flag[2] && p_period[2] <= 0.0) ||
+ (p_flag[3] && p_period[3] <= 0.0) ||
+ (p_flag[4] && p_period[4] <= 0.0) ||
+ (p_flag[5] && p_period[5] <= 0.0))
+ error->all(FLERR,"Fix bocs damping parameters must be > 0.0");
+
+ // set pstat_flag and box change and restart_pbc variables
+
+ pre_exchange_flag = 0;
+ pstat_flag = 0;
+ pstyle = ISO;
+
+ for (int i = 0; i < 6; i++)
+ if (p_flag[i]) pstat_flag = 1;
+
+ if (pstat_flag) {
+ if (p_flag[0] || p_flag[1] || p_flag[2]) box_change_size = 1;
+ if (p_flag[3] || p_flag[4] || p_flag[5]) box_change_shape = 1;
+ no_change_box = 1;
+ if (allremap == 0) restart_pbc = 1;
+
+ // pstyle = TRICLINIC if any off-diagonal term is controlled -> 6 dof
+ // else pstyle = ISO if XYZ coupling or XY coupling in 2d -> 1 dof
+ // else pstyle = ANISO -> 3 dof
+
+/* if (p_flag[3] || p_flag[4] || p_flag[5]) pstyle = TRICLINIC;
+ else if (pcouple == XYZ || (dimension == 2 && pcouple == XY)) pstyle = ISO;
+ else pstyle = ANISO;*/
+ pstyle = ISO; // MRD this is the only one that can happen
+
+ // pre_exchange only required if flips can occur due to shape changes
+
+ if (flipflag && (p_flag[3] || p_flag[4] || p_flag[5]))
+ pre_exchange_flag = 1;
+ if (flipflag && (domain->yz != 0.0 || domain->xz != 0.0 ||
+ domain->xy != 0.0))
+ pre_exchange_flag = 1;
+ }
+
+ // convert input periods to frequencies
+
+ t_freq = 0.0;
+ p_freq[0] = p_freq[1] = p_freq[2] = p_freq[3] = p_freq[4] = p_freq[5] = 0.0;
+
+ if (tstat_flag) t_freq = 1.0 / t_period;
+ if (p_flag[0]) p_freq[0] = 1.0 / p_period[0];
+ if (p_flag[1]) p_freq[1] = 1.0 / p_period[1];
+ if (p_flag[2]) p_freq[2] = 1.0 / p_period[2];
+ if (p_flag[3]) p_freq[3] = 1.0 / p_period[3];
+ if (p_flag[4]) p_freq[4] = 1.0 / p_period[4];
+ if (p_flag[5]) p_freq[5] = 1.0 / p_period[5];
+
+ // Nose/Hoover temp and pressure init
+
+ size_vector = 0;
+
+ if (tstat_flag) {
+ int ich;
+ eta = new double[mtchain];
+
+ // add one extra dummy thermostat, set to zero
+
+ eta_dot = new double[mtchain+1];
+ eta_dot[mtchain] = 0.0;
+ eta_dotdot = new double[mtchain];
+ for (ich = 0; ich < mtchain; ich++) {
+ eta[ich] = eta_dot[ich] = eta_dotdot[ich] = 0.0;
+ }
+ eta_mass = new double[mtchain];
+ size_vector += 2*2*mtchain;
+ }
+
+ if (pstat_flag) {
+ omega[0] = omega[1] = omega[2] = 0.0;
+ omega_dot[0] = omega_dot[1] = omega_dot[2] = 0.0;
+ omega_mass[0] = omega_mass[1] = omega_mass[2] = 0.0;
+ omega[3] = omega[4] = omega[5] = 0.0;
+ omega_dot[3] = omega_dot[4] = omega_dot[5] = 0.0;
+ omega_mass[3] = omega_mass[4] = omega_mass[5] = 0.0;
+ if (pstyle == ISO) size_vector += 2*2*1;
+ else if (pstyle == ANISO) size_vector += 2*2*3;
+ else if (pstyle == TRICLINIC) size_vector += 2*2*6;
+
+ if (mpchain) {
+ int ich;
+ etap = new double[mpchain];
+
+ // add one extra dummy thermostat, set to zero
+
+ etap_dot = new double[mpchain+1];
+ etap_dot[mpchain] = 0.0;
+ etap_dotdot = new double[mpchain];
+ for (ich = 0; ich < mpchain; ich++) {
+ etap[ich] = etap_dot[ich] =
+ etap_dotdot[ich] = 0.0;
+ }
+ etap_mass = new double[mpchain];
+ size_vector += 2*2*mpchain;
+ }
+
+ if (deviatoric_flag) size_vector += 1;
+ }
+
+ nrigid = 0;
+ rfix = NULL;
+
+ if (pre_exchange_flag) irregular = new Irregular(lmp);
+ else irregular = NULL;
+
+ // initialize vol0,t0 to zero to signal uninitialized
+ // values then assigned in init(), if necessary
+
+ vol0 = t0 = 0.0;
+
+ /*~ MRD I copied this from fix_npt.cpp 8/17/17 ~*/
+
+ if (!tstat_flag)
+ error->all(FLERR,"Temperature control must be used with fix bocs");
+ if (!pstat_flag)
+ error->all(FLERR,"Pressure control must be used with fix bocs");
+
+ // create a new compute temp style
+ // id = fix-ID + temp
+ // compute group = all since pressure is always global (group all)
+ // and thus its KE/temperature contribution should use group all
+
+
+ int n = strlen(id) + 6;
+ id_temp = new char[n];
+ strcpy(id_temp,id);
+ strcat(id_temp,"_temp");
+
+ char **newarg = new char*[3];
+ newarg[0] = id_temp;
+ newarg[1] = (char *) "all";
+ newarg[2] = (char *) "temp";
+
+
+ modify->add_compute(3,newarg);
+ delete [] newarg;
+ tcomputeflag = 1;
+
+ // create a new compute pressure style
+ // id = fix-ID + press, compute group = all
+ // pass id_temp as 4th arg to pressure constructor
+
+ n = strlen(id) + 7;
+ id_press = new char[n];
+ strcpy(id_press,id);
+ strcat(id_press,"_press");
+
+ newarg = new char*[4];
+ newarg[0] = id_press;
+ newarg[1] = (char *) "all";
+ newarg[2] = (char *) "pressureBocs";
+ newarg[3] = id_temp;
+ modify->add_compute(4,newarg);
+ delete [] newarg;
+ pcomputeflag = 1;
+
+
+/*~ MRD End of stuff copied from fix_npt.cpp~*/
+
+}
+
+/* ---------------------------------------------------------------------- */
+
+FixBocs::~FixBocs()
+{
+ if (copymode) return;
+
+ delete [] id_dilate;
+ delete [] rfix;
+
+ delete irregular;
+
+ // delete temperature and pressure if fix created them
+
+ if (tcomputeflag) modify->delete_compute(id_temp);
+ delete [] id_temp;
+
+ if (tstat_flag) {
+ delete [] eta;
+ delete [] eta_dot;
+ delete [] eta_dotdot;
+ delete [] eta_mass;
+ }
+
+ if (pstat_flag) {
+ if (pcomputeflag) modify->delete_compute(id_press);
+ delete [] id_press;
+ if (mpchain) {
+ delete [] etap;
+ delete [] etap_dot;
+ delete [] etap_dotdot;
+ delete [] etap_mass;
+ }
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixBocs::setmask()
+{
+ int mask = 0;
+ mask |= INITIAL_INTEGRATE;
+ mask |= FINAL_INTEGRATE;
+ mask |= THERMO_ENERGY;
+ mask |= INITIAL_INTEGRATE_RESPA;
+ mask |= FINAL_INTEGRATE_RESPA;
+ if (pre_exchange_flag) mask |= PRE_EXCHANGE;
+ return mask;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixBocs::init()
+{
+ // recheck that dilate group has not been deleted
+ if (allremap == 0) {
+ int idilate = group->find(id_dilate);
+ if (idilate == -1)
+ error->all(FLERR,"Fix bocs dilate group ID does not exist");
+ dilate_group_bit = group->bitmask[idilate];
+ }
+
+ // ensure no conflict with fix deform
+
+ if (pstat_flag)
+ {
+ for (int i = 0; i < modify->nfix; i++)
+ if (strcmp(modify->fix[i]->style,"deform") == 0) {
+ int *dimflag = ((FixDeform *) modify->fix[i])->dimflag;
+ if ((p_flag[0] && dimflag[0]) || (p_flag[1] && dimflag[1]) ||
+ (p_flag[2] && dimflag[2]) || (p_flag[3] && dimflag[3]) ||
+ (p_flag[4] && dimflag[4]) || (p_flag[5] && dimflag[5]))
+ error->all(FLERR,"Cannot use fix npt and fix deform on "
+ "same component of stress tensor");
+ }
+ if (p_match_flag) // MRD NJD
+ {
+ if (pressure)
+ {
+ if (p_basis_type == 0)
+ {
+ pressure->send_cg_info(p_basis_type, N_p_match, p_match_coeffs,
+ N_mol, vavg);
+ }
+ else if ( p_basis_type == 1 || p_basis_type == 2 )
+ {
+ pressure->send_cg_info(p_basis_type, splines, spline_length);
+ }
+ }
+ else
+ {
+ error->all(FLERR,"Unable to find pressure. Are you sure you included"
+ " the compute bocsPress and fix_modify commands?");
+ }
+ }
+ }
+
+ // set temperature and pressure ptrs
+ int icompute = modify->find_compute(id_temp);
+ if (icompute < 0)
+ error->all(FLERR,"Temperature ID for fix bocs does not exist");
+ temperature = modify->compute[icompute];
+
+ if (temperature->tempbias) which = BIAS;
+ else which = NOBIAS;
+
+ if (pstat_flag) {
+ icompute = modify->find_compute(id_press);
+ if (icompute < 0)
+ error->all(FLERR,"Pressure ID for fix bocs does not exist");
+ pressure = modify->compute[icompute];
+ }
+
+ // set timesteps and frequencies
+
+ dtv = update->dt;
+ dtf = 0.5 * update->dt * force->ftm2v;
+ dthalf = 0.5 * update->dt;
+ dt4 = 0.25 * update->dt;
+ dt8 = 0.125 * update->dt;
+ dto = dthalf;
+
+ p_freq_max = 0.0;
+ if (pstat_flag) {
+ p_freq_max = MAX(p_freq[0],p_freq[1]);
+ p_freq_max = MAX(p_freq_max,p_freq[2]);
+ if (pstyle == TRICLINIC) {
+ p_freq_max = MAX(p_freq_max,p_freq[3]);
+ p_freq_max = MAX(p_freq_max,p_freq[4]);
+ p_freq_max = MAX(p_freq_max,p_freq[5]);
+ }
+ pdrag_factor = 1.0 - (update->dt * p_freq_max * drag / nc_pchain);
+ }
+
+ if (tstat_flag)
+ tdrag_factor = 1.0 - (update->dt * t_freq * drag / nc_tchain);
+
+ // tally the number of dimensions that are barostatted
+ // set initial volume and reference cell, if not already done
+
+ if (pstat_flag) {
+ pdim = p_flag[0] + p_flag[1] + p_flag[2];
+ if (vol0 == 0.0) {
+ if (dimension == 3) vol0 = domain->xprd * domain->yprd * domain->zprd;
+ else vol0 = domain->xprd * domain->yprd;
+ h0_inv[0] = domain->h_inv[0];
+ h0_inv[1] = domain->h_inv[1];
+ h0_inv[2] = domain->h_inv[2];
+ h0_inv[3] = domain->h_inv[3];
+ h0_inv[4] = domain->h_inv[4];
+ h0_inv[5] = domain->h_inv[5];
+ }
+ }
+
+ boltz = force->boltz;
+ nktv2p = force->nktv2p;
+
+ if (force->kspace) kspace_flag = 1;
+ else kspace_flag = 0;
+
+ if (strstr(update->integrate_style,"respa")) {
+ nlevels_respa = ((Respa *) update->integrate)->nlevels;
+ step_respa = ((Respa *) update->integrate)->step;
+ dto = 0.5*step_respa[0];
+ }
+
+ // detect if any rigid fixes exist so rigid bodies move when box is remapped
+ // rfix[] = indices to each fix rigid
+
+ delete [] rfix;
+ nrigid = 0;
+ rfix = NULL;
+
+ for (int i = 0; i < modify->nfix; i++)
+ if (modify->fix[i]->rigid_flag) nrigid++;
+ if (nrigid) {
+ rfix = new int[nrigid];
+ nrigid = 0;
+ for (int i = 0; i < modify->nfix; i++)
+ if (modify->fix[i]->rigid_flag) rfix[nrigid++] = i;
+ }
+}
+
+// NJD MRD 2 functions
+int FixBocs::read_F_table( char *filename, int p_basis_type )
+{
+ char separator = ',';
+ FILE *fpi;
+ int N_columns = 2, n_entries = 0, i;
+ float f1, f2;
+ double n1, n2;
+ int test_sscanf;
+ double **data = (double **) calloc(N_columns,sizeof(double *));
+ char * line = (char *) calloc(200,sizeof(char));
+
+ fpi = fopen(filename,"r");
+ if (fpi)
+ {
+ while (fgets(line,199,fpi)) { ++n_entries; }
+ fclose(fpi);
+ for (i = 0; i < N_columns; ++i)
+ {
+ data[i] = (double *) calloc(n_entries,sizeof(double));
+ }
+ }
+ else
+ {
+ char * errmsg = (char *) calloc(50,sizeof(char));
+ sprintf(errmsg,"Unable to open file: %s\n",filename);
+ error->all(FLERR,errmsg);
+ }
+
+ n_entries = 0;
+ fpi = fopen(filename,"r");
+ if (fpi)
+ {
+ while( fgets(line,199,fpi))
+ {
+ ++n_entries;
+ test_sscanf = sscanf(line," %f , %f ",&f1, &f2);
+ if (test_sscanf == 2)
+ {
+ data[0][n_entries-1] = (double) f1;
+ data[1][n_entries-1] = (double) f2;
+ }
+ else
+ {
+ fprintf(stderr,"WARNING: did not find 2 comma separated values in "
+ "line %d of file %s\n\tline: %s",n_entries,filename,line);
+ }
+ }
+ }
+ else
+ {
+ char * errmsg = (char *) calloc(50,sizeof(char));
+ sprintf(errmsg,"Unable to open file: %s\n",filename);
+ error->all(FLERR,errmsg);
+ }
+ fclose(fpi);
+
+ if (p_basis_type == 1)
+ {
+ splines = (double **) calloc(2,sizeof(double *));
+ splines[0] = (double *) calloc(n_entries,sizeof(double));
+ splines[1] = (double *) calloc(n_entries,sizeof(double));
+ int idxa, idxb;
+ for (idxa = 0; idxa < 2; ++idxa)
+ {
+ for (idxb = 0; idxb < n_entries; ++idxb)
+ {
+ splines[idxa][idxb] = data[idxa][idxb];
+ }
+ }
+ }
+ else if (p_basis_type == 2)
+ {
+ spline_length = n_entries;
+ build_cubic_splines(data);
+ n_entries -= 1;
+ }
+ else
+ {
+ char * errmsg = (char *) calloc(70,sizeof(char));
+ sprintf(errmsg,"ERROR: invalid p_basis_type value "
+ "of %d in read_F_table",p_basis_type);
+ error->all(FLERR,errmsg);
+ }
+ return n_entries;
+}
+
+void FixBocs::build_cubic_splines( double **data )
+{
+ double *a, *b, *d, *h, *alpha, *c, *l, *mu, *z;
+ int n = spline_length;
+ double alpha_i;
+ a = (double *) calloc(n,sizeof(double));
+ b = (double *) calloc(n+1,sizeof(double));
+ d = (double *) calloc(n+1,sizeof(double));
+ h = (double *) calloc(n,sizeof(double));
+ alpha = (double *) calloc(n,sizeof(double));
+ c = (double *) calloc(n+1,sizeof(double));
+ l = (double *) calloc(n,sizeof(double));
+ mu = (double *) calloc(n,sizeof(double));
+ z = (double *) calloc(n,sizeof(double));
+ int idx;
+ for (int i=0; i<n; i++)
+ {
+ a[i] = data[1][i];
+ b[i] = 0.0;
+ d[i] = 0.0;
+
+ if (i<(n-1))
+ {
+ h[i] = (data[0][i+1] - data[0][i]);
+ }
+
+ if (i>1 && i<(n-1))
+ {
+ alpha_i = (3.0 / h[i]) * ( data[1][i+1] - data[1][i]) - (3.0 / h[i-1] )
+ * ( data[1][i] - data[1][i-1] );
+ alpha[i-1] = alpha_i;
+ }
+ }
+ l[0] = 1.0;
+ mu[0] = 0.0;
+ z[0] = 0.0;
+
+ for (int i=1; i<n-1; i++)
+ {
+ l[i] = 2*(data[0][i+1] - data[0][i-1]) - h[i-1] * mu[i-1];
+ mu[i] = h[i]/l[i];
+ z[i] = (alpha[i] - h[i-1] * z[i-1]) / l[i];
+ }
+ l[n-1] = 1.0;
+ mu[n-1] = 0.0;
+ z[n-1] = 0.0;
+
+ c[n] = 0.0;
+ b[n] = 0.0;
+ d[n] = 0.0;
+
+ for(int j=n-1; j>=0; j--)
+ {
+ c[j] = z[j] - mu[j]*c[j+1];
+
+ b[j] = (a[j+1]-a[j])/h[j] - h[j]*(c[j+1] + 2.0 * c[j])/3.0;
+
+ d[j] = (c[j+1]-c[j])/(3.0 * h[j]);
+ }
+ splines = (double **) calloc(5,sizeof(double *));
+
+ for ( idx = 0; idx < 5; ++idx)
+ {
+ splines[idx] = (double *) calloc(n-1,sizeof(double));
+ }
+ idx = 0;
+ for ( idx = 0; idx < n - 1; ++idx)
+ {
+ splines[1][idx] = a[idx];
+ splines[2][idx] = b[idx];
+ splines[3][idx] = c[idx];
+ splines[4][idx] = d[idx];
+ splines[0][idx] = data[0][idx];
+ }
+}
+// END NJD MRD 2 functions
+
+/* ----------------------------------------------------------------------
+ compute T,P before integrator starts
+------------------------------------------------------------------------- */
+
+void FixBocs::setup(int vflag)
+{
+ // tdof needed by compute_temp_target()
+
+ t_current = temperature->compute_scalar();
+ tdof = temperature->dof;
+
+ // t_target is needed by NVT and NPT in compute_scalar()
+ // If no thermostat or using fix nphug,
+ // t_target must be defined by other means.
+
+ if (tstat_flag && strstr(style,"nphug") == NULL) {
+ compute_temp_target();
+ } else if (pstat_flag) {
+
+ // t0 = reference temperature for masses
+ // cannot be done in init() b/c temperature cannot be called there
+ // is b/c Modify::init() inits computes after fixes due to dof dependence
+ // guesstimate a unit-dependent t0 if actual T = 0.0
+ // if it was read in from a restart file, leave it be
+
+ if (t0 == 0.0) {
+ t0 = temperature->compute_scalar();
+ if (t0 == 0.0) {
+ if (strcmp(update->unit_style,"lj") == 0) t0 = 1.0;
+ else t0 = 300.0;
+ }
+ }
+ t_target = t0;
+ }
+
+ if (pstat_flag) compute_press_target();
+
+ if (pstat_flag) {
+ if (pstyle == ISO) pressure->compute_scalar();
+ else pressure->compute_vector();
+ couple();
+ pressure->addstep(update->ntimestep+1);
+ }
+
+ // masses and initial forces on thermostat variables
+
+ if (tstat_flag) {
+ eta_mass[0] = tdof * boltz * t_target / (t_freq*t_freq);
+ for (int ich = 1; ich < mtchain; ich++)
+ eta_mass[ich] = boltz * t_target / (t_freq*t_freq);
+ for (int ich = 1; ich < mtchain; ich++) {
+ eta_dotdot[ich] = (eta_mass[ich-1]*eta_dot[ich-1]*eta_dot[ich-1] -
+ boltz * t_target) / eta_mass[ich];
+ }
+ }
+
+ // masses and initial forces on barostat variables
+
+ if (pstat_flag) {
+ double kt = boltz * t_target;
+ double nkt = atom->natoms * kt;
+
+ for (int i = 0; i < 3; i++)
+ if (p_flag[i])
+ omega_mass[i] = nkt/(p_freq[i]*p_freq[i]);
+
+ if (pstyle == TRICLINIC) {
+ for (int i = 3; i < 6; i++)
+ if (p_flag[i]) omega_mass[i] = nkt/(p_freq[i]*p_freq[i]);
+ }
+
+ // masses and initial forces on barostat thermostat variables
+
+ if (mpchain) {
+ etap_mass[0] = boltz * t_target / (p_freq_max*p_freq_max);
+ for (int ich = 1; ich < mpchain; ich++)
+ etap_mass[ich] = boltz * t_target / (p_freq_max*p_freq_max);
+ for (int ich = 1; ich < mpchain; ich++)
+ etap_dotdot[ich] =
+ (etap_mass[ich-1]*etap_dot[ich-1]*etap_dot[ich-1] -
+ boltz * t_target) / etap_mass[ich];
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ 1st half of Verlet update
+------------------------------------------------------------------------- */
+
+void FixBocs::initial_integrate(int vflag)
+{
+ // update eta_press_dot
+
+ if (pstat_flag && mpchain) nhc_press_integrate();
+
+ // update eta_dot
+
+ if (tstat_flag) {
+ compute_temp_target();
+ nhc_temp_integrate();
+ }
+
+ // need to recompute pressure to account for change in KE
+ // t_current is up-to-date, but compute_temperature is not
+ // compute appropriately coupled elements of mvv_current
+
+ if (pstat_flag) {
+ if (pstyle == ISO) {
+ temperature->compute_scalar();
+ pressure->compute_scalar();
+ } else {
+ temperature->compute_vector();
+ pressure->compute_vector();
+ }
+ couple();
+ pressure->addstep(update->ntimestep+1);
+ }
+
+ if (pstat_flag) {
+ compute_press_target();
+ nh_omega_dot();
+ nh_v_press();
+ }
+
+ nve_v();
+
+ // remap simulation box by 1/2 step
+
+ if (pstat_flag) remap();
+
+ nve_x();
+
+ // remap simulation box by 1/2 step
+ // redo KSpace coeffs since volume has changed
+
+ if (pstat_flag) {
+ remap();
+ if (kspace_flag) force->kspace->setup();
+ }
+}
+
+/* ----------------------------------------------------------------------
+ 2nd half of Verlet update
+------------------------------------------------------------------------- */
+
+void FixBocs::final_integrate()
+{
+ nve_v();
+
+ // re-compute temp before nh_v_press()
+ // only needed for temperature computes with BIAS on reneighboring steps:
+ // b/c some biases store per-atom values (e.g. temp/profile)
+ // per-atom values are invalid if reneigh/comm occurred
+ // since temp->compute() in initial_integrate()
+
+ if (which == BIAS && neighbor->ago == 0)
+ t_current = temperature->compute_scalar();
+
+ if (pstat_flag) nh_v_press();
+
+ // compute new T,P after velocities rescaled by nh_v_press()
+ // compute appropriately coupled elements of mvv_current
+
+ t_current = temperature->compute_scalar();
+ tdof = temperature->dof;
+
+ if (pstat_flag) {
+ if (pstyle == ISO) pressure->compute_scalar();
+ else pressure->compute_vector();
+ couple();
+ pressure->addstep(update->ntimestep+1);
+ }
+
+ if (pstat_flag) nh_omega_dot();
+
+ // update eta_dot
+ // update eta_press_dot
+
+ if (tstat_flag) nhc_temp_integrate();
+ if (pstat_flag && mpchain) nhc_press_integrate();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixBocs::initial_integrate_respa(int vflag, int ilevel, int iloop)
+{
+ // set timesteps by level
+
+ dtv = step_respa[ilevel];
+ dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
+ dthalf = 0.5 * step_respa[ilevel];
+
+ // outermost level - update eta_dot and omega_dot, apply to v
+ // all other levels - NVE update of v
+ // x,v updates only performed for atoms in group
+
+ if (ilevel == nlevels_respa-1) {
+
+ // update eta_press_dot
+
+ if (pstat_flag && mpchain) nhc_press_integrate();
+
+ // update eta_dot
+
+ if (tstat_flag) {
+ compute_temp_target();
+ nhc_temp_integrate();
+ }
+
+ // recompute pressure to account for change in KE
+ // t_current is up-to-date, but compute_temperature is not
+ // compute appropriately coupled elements of mvv_current
+
+ if (pstat_flag) {
+ if (pstyle == ISO) {
+ temperature->compute_scalar();
+ pressure->compute_scalar();
+ } else {
+ temperature->compute_vector();
+ pressure->compute_vector();
+ }
+ couple();
+ pressure->addstep(update->ntimestep+1);
+ }
+
+ if (pstat_flag) {
+ compute_press_target();
+ nh_omega_dot();
+ nh_v_press();
+ }
+
+ nve_v();
+
+ } else nve_v();
+
+ // innermost level - also update x only for atoms in group
+ // if barostat, perform 1/2 step remap before and after
+
+ if (ilevel == 0) {
+ if (pstat_flag) remap();
+ nve_x();
+ if (pstat_flag) remap();
+ }
+
+ // if barostat, redo KSpace coeffs at outermost level,
+ // since volume has changed
+
+ if (ilevel == nlevels_respa-1 && kspace_flag && pstat_flag)
+ force->kspace->setup();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixBocs::final_integrate_respa(int ilevel, int iloop)
+{
+ // set timesteps by level
+
+ dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
+ dthalf = 0.5 * step_respa[ilevel];
+
+ // outermost level - update eta_dot and omega_dot, apply via final_integrate
+ // all other levels - NVE update of v
+
+ if (ilevel == nlevels_respa-1) final_integrate();
+ else nve_v();
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixBocs::couple()
+{
+ double *tensor = pressure->vector;
+
+ if (pstyle == ISO)
+ p_current[0] = p_current[1] = p_current[2] = pressure->scalar;
+ else if (pcouple == XYZ) {
+ double ave = 1.0/3.0 * (tensor[0] + tensor[1] + tensor[2]);
+ p_current[0] = p_current[1] = p_current[2] = ave;
+ } else if (pcouple == XY) {
+ double ave = 0.5 * (tensor[0] + tensor[1]);
+ p_current[0] = p_current[1] = ave;
+ p_current[2] = tensor[2];
+ } else if (pcouple == YZ) {
+ double ave = 0.5 * (tensor[1] + tensor[2]);
+ p_current[1] = p_current[2] = ave;
+ p_current[0] = tensor[0];
+ } else if (pcouple == XZ) {
+ double ave = 0.5 * (tensor[0] + tensor[2]);
+ p_current[0] = p_current[2] = ave;
+ p_current[1] = tensor[1];
+ } else {
+ p_current[0] = tensor[0];
+ p_current[1] = tensor[1];
+ p_current[2] = tensor[2];
+ }
+
+ if (!ISFINITE(p_current[0]) || !ISFINITE(p_current[1]) || !ISFINITE(p_current[2]))
+ error->all(FLERR,"Non-numeric pressure - simulation unstable");
+
+ // switch order from xy-xz-yz to Voigt
+
+ if (pstyle == TRICLINIC) {
+ p_current[3] = tensor[5];
+ p_current[4] = tensor[4];
+ p_current[5] = tensor[3];
+
+ if (!ISFINITE(p_current[3]) || !ISFINITE(p_current[4]) || !ISFINITE(p_current[5]))
+ error->all(FLERR,"Non-numeric pressure - simulation unstable");
+ }
+}
+
+/* ----------------------------------------------------------------------
+ change box size
+ remap all atoms or dilate group atoms depending on allremap flag
+ if rigid bodies exist, scale rigid body centers-of-mass
+------------------------------------------------------------------------- */
+
+void FixBocs::remap()
+{
+ int i;
+ double oldlo,oldhi;
+ double expfac;
+
+ double **x = atom->x;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ double *h = domain->h;
+
+ // omega is not used, except for book-keeping
+
+ for (int i = 0; i < 6; i++) omega[i] += dto*omega_dot[i];
+
+ // convert pertinent atoms and rigid bodies to lamda coords
+
+ if (allremap) domain->x2lamda(nlocal);
+ else {
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & dilate_group_bit)
+ domain->x2lamda(x[i],x[i]);
+ }
+
+ if (nrigid)
+ for (i = 0; i < nrigid; i++)
+ modify->fix[rfix[i]]->deform(0);
+
+ // reset global and local box to new size/shape
+
+ // this operation corresponds to applying the
+ // translate and scale operations
+ // corresponding to the solution of the following ODE:
+ //
+ // h_dot = omega_dot * h
+ //
+ // where h_dot, omega_dot and h are all upper-triangular
+ // 3x3 tensors. In Voigt notation, the elements of the
+ // RHS product tensor are:
+ // h_dot = [0*0, 1*1, 2*2, 1*3+3*2, 0*4+5*3+4*2, 0*5+5*1]
+ //
+ // Ordering of operations preserves time symmetry.
+
+ double dto2 = dto/2.0;
+ double dto4 = dto/4.0;
+ double dto8 = dto/8.0;
+
+ // off-diagonal components, first half
+
+ if (pstyle == TRICLINIC) {
+
+ if (p_flag[4]) {
+ expfac = exp(dto8*omega_dot[0]);
+ h[4] *= expfac;
+ h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
+ h[4] *= expfac;
+ }
+
+ if (p_flag[3]) {
+ expfac = exp(dto4*omega_dot[1]);
+ h[3] *= expfac;
+ h[3] += dto2*(omega_dot[3]*h[2]);
+ h[3] *= expfac;
+ }
+
+ if (p_flag[5]) {
+ expfac = exp(dto4*omega_dot[0]);
+ h[5] *= expfac;
+ h[5] += dto2*(omega_dot[5]*h[1]);
+ h[5] *= expfac;
+ }
+
+ if (p_flag[4]) {
+ expfac = exp(dto8*omega_dot[0]);
+ h[4] *= expfac;
+ h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
+ h[4] *= expfac;
+ }
+ }
+
+ // scale diagonal components
+ // scale tilt factors with cell, if set
+
+ if (p_flag[0]) {
+ oldlo = domain->boxlo[0];
+ oldhi = domain->boxhi[0];
+ expfac = exp(dto*omega_dot[0]);
+ domain->boxlo[0] = (oldlo-fixedpoint[0])*expfac + fixedpoint[0];
+ domain->boxhi[0] = (oldhi-fixedpoint[0])*expfac + fixedpoint[0];
+ }
+
+ if (p_flag[1]) {
+ oldlo = domain->boxlo[1];
+ oldhi = domain->boxhi[1];
+ expfac = exp(dto*omega_dot[1]);
+ domain->boxlo[1] = (oldlo-fixedpoint[1])*expfac + fixedpoint[1];
+ domain->boxhi[1] = (oldhi-fixedpoint[1])*expfac + fixedpoint[1];
+ if (scalexy) h[5] *= expfac;
+ }
+
+ if (p_flag[2]) {
+ oldlo = domain->boxlo[2];
+ oldhi = domain->boxhi[2];
+ expfac = exp(dto*omega_dot[2]);
+ domain->boxlo[2] = (oldlo-fixedpoint[2])*expfac + fixedpoint[2];
+ domain->boxhi[2] = (oldhi-fixedpoint[2])*expfac + fixedpoint[2];
+ if (scalexz) h[4] *= expfac;
+ if (scaleyz) h[3] *= expfac;
+ }
+
+ // off-diagonal components, second half
+
+ if (pstyle == TRICLINIC) {
+
+ if (p_flag[4]) {
+ expfac = exp(dto8*omega_dot[0]);
+ h[4] *= expfac;
+ h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
+ h[4] *= expfac;
+ }
+
+ if (p_flag[3]) {
+ expfac = exp(dto4*omega_dot[1]);
+ h[3] *= expfac;
+ h[3] += dto2*(omega_dot[3]*h[2]);
+ h[3] *= expfac;
+ }
+
+ if (p_flag[5]) {
+ expfac = exp(dto4*omega_dot[0]);
+ h[5] *= expfac;
+ h[5] += dto2*(omega_dot[5]*h[1]);
+ h[5] *= expfac;
+ }
+
+ if (p_flag[4]) {
+ expfac = exp(dto8*omega_dot[0]);
+ h[4] *= expfac;
+ h[4] += dto4*(omega_dot[5]*h[3]+omega_dot[4]*h[2]);
+ h[4] *= expfac;
+ }
+
+ }
+
+ domain->yz = h[3];
+ domain->xz = h[4];
+ domain->xy = h[5];
+
+ // tilt factor to cell length ratio can not exceed TILTMAX in one step
+
+ if (domain->yz < -TILTMAX*domain->yprd ||
+ domain->yz > TILTMAX*domain->yprd ||
+ domain->xz < -TILTMAX*domain->xprd ||
+ domain->xz > TILTMAX*domain->xprd ||
+ domain->xy < -TILTMAX*domain->xprd ||
+ domain->xy > TILTMAX*domain->xprd)
+ error->all(FLERR,"Fix bocs has tilted box too far in one step - "
+ "periodic cell is too far from equilibrium state");
+
+ domain->set_global_box();
+ domain->set_local_box();
+
+ // convert pertinent atoms and rigid bodies back to box coords
+
+ if (allremap) domain->lamda2x(nlocal);
+ else {
+ for (i = 0; i < nlocal; i++)
+ if (mask[i] & dilate_group_bit)
+ domain->lamda2x(x[i],x[i]);
+ }
+
+ if (nrigid)
+ for (i = 0; i < nrigid; i++)
+ modify->fix[rfix[i]]->deform(1);
+}
+
+/* ----------------------------------------------------------------------
+ pack entire state of Fix into one write
+------------------------------------------------------------------------- */
+
+void FixBocs::write_restart(FILE *fp)
+{
+ int nsize = size_restart_global();
+
+ double *list;
+ memory->create(list,nsize,"nh:list");
+
+ pack_restart_data(list);
+
+ if (comm->me == 0) {
+ int size = nsize * sizeof(double);
+ fwrite(&size,sizeof(int),1,fp);
+ fwrite(list,sizeof(double),nsize,fp);
+ }
+
+ memory->destroy(list);
+}
+
+/* ----------------------------------------------------------------------
+ calculate the number of data to be packed
+------------------------------------------------------------------------- */
+
+int FixBocs::size_restart_global()
+{
+ int nsize = 2;
+ if (tstat_flag) nsize += 1 + 2*mtchain;
+ if (pstat_flag) {
+ nsize += 16 + 2*mpchain;
+ if (deviatoric_flag) nsize += 6;
+ }
+
+ return nsize;
+}
+
+/* ----------------------------------------------------------------------
+ pack restart data
+------------------------------------------------------------------------- */
+
+int FixBocs::pack_restart_data(double *list)
+{
+ int n = 0;
+
+ list[n++] = tstat_flag;
+ if (tstat_flag) {
+ list[n++] = mtchain;
+ for (int ich = 0; ich < mtchain; ich++)
+ list[n++] = eta[ich];
+ for (int ich = 0; ich < mtchain; ich++)
+ list[n++] = eta_dot[ich];
+ }
+
+ list[n++] = pstat_flag;
+ if (pstat_flag) {
+ list[n++] = omega[0];
+ list[n++] = omega[1];
+ list[n++] = omega[2];
+ list[n++] = omega[3];
+ list[n++] = omega[4];
+ list[n++] = omega[5];
+ list[n++] = omega_dot[0];
+ list[n++] = omega_dot[1];
+ list[n++] = omega_dot[2];
+ list[n++] = omega_dot[3];
+ list[n++] = omega_dot[4];
+ list[n++] = omega_dot[5];
+ list[n++] = vol0;
+ list[n++] = t0;
+ list[n++] = mpchain;
+ if (mpchain) {
+ for (int ich = 0; ich < mpchain; ich++)
+ list[n++] = etap[ich];
+ for (int ich = 0; ich < mpchain; ich++)
+ list[n++] = etap_dot[ich];
+ }
+
+ list[n++] = deviatoric_flag;
+ if (deviatoric_flag) {
+ list[n++] = h0_inv[0];
+ list[n++] = h0_inv[1];
+ list[n++] = h0_inv[2];
+ list[n++] = h0_inv[3];
+ list[n++] = h0_inv[4];
+ list[n++] = h0_inv[5];
+ }
+ }
+
+ return n;
+}
+
+/* ----------------------------------------------------------------------
+ use state info from restart file to restart the Fix
+------------------------------------------------------------------------- */
+
+void FixBocs::restart(char *buf)
+{
+ int n = 0;
+ double *list = (double *) buf;
+ int flag = static_cast<int> (list[n++]);
+ if (flag) {
+ int m = static_cast<int> (list[n++]);
+ if (tstat_flag && m == mtchain) {
+ for (int ich = 0; ich < mtchain; ich++)
+ eta[ich] = list[n++];
+ for (int ich = 0; ich < mtchain; ich++)
+ eta_dot[ich] = list[n++];
+ } else n += 2*m;
+ }
+ flag = static_cast<int> (list[n++]);
+ if (flag) {
+ omega[0] = list[n++];
+ omega[1] = list[n++];
+ omega[2] = list[n++];
+ omega[3] = list[n++];
+ omega[4] = list[n++];
+ omega[5] = list[n++];
+ omega_dot[0] = list[n++];
+ omega_dot[1] = list[n++];
+ omega_dot[2] = list[n++];
+ omega_dot[3] = list[n++];
+ omega_dot[4] = list[n++];
+ omega_dot[5] = list[n++];
+ vol0 = list[n++];
+ t0 = list[n++];
+ int m = static_cast<int> (list[n++]);
+ if (pstat_flag && m == mpchain) {
+ for (int ich = 0; ich < mpchain; ich++)
+ etap[ich] = list[n++];
+ for (int ich = 0; ich < mpchain; ich++)
+ etap_dot[ich] = list[n++];
+ } else n+=2*m;
+ flag = static_cast<int> (list[n++]);
+ if (flag) {
+ h0_inv[0] = list[n++];
+ h0_inv[1] = list[n++];
+ h0_inv[2] = list[n++];
+ h0_inv[3] = list[n++];
+ h0_inv[4] = list[n++];
+ h0_inv[5] = list[n++];
+ }
+ }
+}
+
+/* ---------------------------------------------------------------------- */
+
+int FixBocs::modify_param(int narg, char **arg)
+{
+ if (strcmp(arg[0],"temp") == 0) {
+ if (narg < 2) error->all(FLERR,"Illegal fix_modify command");
+ if (tcomputeflag) {
+ modify->delete_compute(id_temp);
+ tcomputeflag = 0;
+ }
+ delete [] id_temp;
+ int n = strlen(arg[1]) + 1;
+ id_temp = new char[n];
+ strcpy(id_temp,arg[1]);
+
+ int icompute = modify->find_compute(arg[1]);
+ if (icompute < 0)
+ error->all(FLERR,"Could not find fix_modify temperature ID");
+ temperature = modify->compute[icompute];
+
+ if (temperature->tempflag == 0)
+ error->all(FLERR,
+ "Fix_modify temperature ID does not compute temperature");
+ if (temperature->igroup != 0 && comm->me == 0)
+ error->warning(FLERR,"Temperature for fix modify is not for group all");
+
+ // reset id_temp of pressure to new temperature ID
+
+ if (pstat_flag) {
+ icompute = modify->find_compute(id_press);
+ if (icompute < 0)
+ error->all(FLERR,"Pressure ID for fix modify does not exist");
+ modify->compute[icompute]->reset_extra_compute_fix(id_temp);
+ }
+
+ return 2;
+
+ } else if (strcmp(arg[0],"press") == 0) {
+ if (narg < 2) error->all(FLERR,"Illegal fix_modify command");
+ if (!pstat_flag) error->all(FLERR,"Illegal fix_modify command");
+ if (pcomputeflag) {
+ modify->delete_compute(id_press);
+ pcomputeflag = 0;
+ }
+ delete [] id_press;
+ int n = strlen(arg[1]) + 1;
+ id_press = new char[n];
+ strcpy(id_press,arg[1]);
+
+ int icompute = modify->find_compute(arg[1]);
+ if (icompute < 0) error->all(FLERR,"Could not find fix_modify pressure ID");
+ pressure = modify->compute[icompute];
+
+ if (p_match_flag) // NJD MRD
+ {
+ if ( p_basis_type == 0 )
+ {
+ pressure->send_cg_info(p_basis_type, N_p_match, p_match_coeffs,
+ N_mol, vavg);
+ }
+ else if ( p_basis_type == 1 || p_basis_type == 2 )
+ {
+ pressure->send_cg_info(p_basis_type, splines, spline_length );
+ }
+ }
+
+ if (pressure->pressflag == 0)
+ error->all(FLERR,"Fix_modify pressure ID does not compute pressure");
+ return 2;
+ }
+
+ return 0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+double FixBocs::compute_scalar()
+{
+ int i;
+ double volume;
+ double energy;
+ double kt = boltz * t_target;
+ double lkt_press = kt;
+ int ich;
+ if (dimension == 3) volume = domain->xprd * domain->yprd * domain->zprd;
+ else volume = domain->xprd * domain->yprd;
+
+ energy = 0.0;
+
+ // thermostat chain energy is equivalent to Eq. (2) in
+ // Martyna, Tuckerman, Tobias, Klein, Mol Phys, 87, 1117
+ // Sum(0.5*p_eta_k^2/Q_k,k=1,M) + L*k*T*eta_1 + Sum(k*T*eta_k,k=2,M),
+ // where L = tdof
+ // M = mtchain
+ // p_eta_k = Q_k*eta_dot[k-1]
+ // Q_1 = L*k*T/t_freq^2
+ // Q_k = k*T/t_freq^2, k > 1
+
+ if (tstat_flag) {
+ energy += ke_target * eta[0] + 0.5*eta_mass[0]*eta_dot[0]*eta_dot[0];
+ for (ich = 1; ich < mtchain; ich++)
+ energy += kt * eta[ich] + 0.5*eta_mass[ich]*eta_dot[ich]*eta_dot[ich];
+ }
+
+ // barostat energy is equivalent to Eq. (8) in
+ // Martyna, Tuckerman, Tobias, Klein, Mol Phys, 87, 1117
+ // Sum(0.5*p_omega^2/W + P*V),
+ // where N = natoms
+ // p_omega = W*omega_dot
+ // W = N*k*T/p_freq^2
+ // sum is over barostatted dimensions
+
+ if (pstat_flag) {
+ for (i = 0; i < 3; i++)
+ if (p_flag[i])
+ energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i] +
+ p_hydro*(volume-vol0) / (pdim*nktv2p);
+
+ if (pstyle == TRICLINIC) {
+ for (i = 3; i < 6; i++)
+ if (p_flag[i])
+ energy += 0.5*omega_dot[i]*omega_dot[i]*omega_mass[i];
+ }
+
+ // extra contributions from thermostat chain for barostat
+
+ if (mpchain) {
+ energy += lkt_press * etap[0] + 0.5*etap_mass[0]*etap_dot[0]*etap_dot[0];
+ for (ich = 1; ich < mpchain; ich++)
+ energy += kt * etap[ich] +
+ 0.5*etap_mass[ich]*etap_dot[ich]*etap_dot[ich];
+ }
+
+ // extra contribution from strain energy
+
+ if (deviatoric_flag) energy += compute_strain_energy();
+ }
+
+ return energy;
+}
+
+/* ----------------------------------------------------------------------
+ return a single element of the following vectors, in this order:
+ eta[tchain], eta_dot[tchain], omega[ndof], omega_dot[ndof]
+ etap[pchain], etap_dot[pchain], PE_eta[tchain], KE_eta_dot[tchain]
+ PE_omega[ndof], KE_omega_dot[ndof], PE_etap[pchain], KE_etap_dot[pchain]
+ PE_strain[1]
+ if no thermostat exists, related quantities are omitted from the list
+ if no barostat exists, related quantities are omitted from the list
+ ndof = 1,3,6 degrees of freedom for pstyle = ISO,ANISO,TRI
+------------------------------------------------------------------------- */
+
+double FixBocs::compute_vector(int n)
+{
+ int ilen;
+
+ if (tstat_flag) {
+ ilen = mtchain;
+ if (n < ilen) return eta[n];
+ n -= ilen;
+ ilen = mtchain;
+ if (n < ilen) return eta_dot[n];
+ n -= ilen;
+ }
+
+ if (pstat_flag) {
+ if (pstyle == ISO) {
+ ilen = 1;
+ if (n < ilen) return omega[n];
+ n -= ilen;
+ } else if (pstyle == ANISO) {
+ ilen = 3;
+ if (n < ilen) return omega[n];
+ n -= ilen;
+ } else {
+ ilen = 6;
+ if (n < ilen) return omega[n];
+ n -= ilen;
+ }
+
+ if (pstyle == ISO) {
+ ilen = 1;
+ if (n < ilen) return omega_dot[n];
+ n -= ilen;
+ } else if (pstyle == ANISO) {
+ ilen = 3;
+ if (n < ilen) return omega_dot[n];
+ n -= ilen;
+ } else {
+ ilen = 6;
+ if (n < ilen) return omega_dot[n];
+ n -= ilen;
+ }
+
+ if (mpchain) {
+ ilen = mpchain;
+ if (n < ilen) return etap[n];
+ n -= ilen;
+ ilen = mpchain;
+ if (n < ilen) return etap_dot[n];
+ n -= ilen;
+ }
+ }
+
+ double volume;
+ double kt = boltz * t_target;
+ double lkt_press = kt;
+ int ich;
+ if (dimension == 3) volume = domain->xprd * domain->yprd * domain->zprd;
+ else volume = domain->xprd * domain->yprd;
+
+ if (tstat_flag) {
+ ilen = mtchain;
+ if (n < ilen) {
+ ich = n;
+ if (ich == 0)
+ return ke_target * eta[0];
+ else
+ return kt * eta[ich];
+ }
+ n -= ilen;
+ ilen = mtchain;
+ if (n < ilen) {
+ ich = n;
+ if (ich == 0)
+ return 0.5*eta_mass[0]*eta_dot[0]*eta_dot[0];
+ else
+ return 0.5*eta_mass[ich]*eta_dot[ich]*eta_dot[ich];
+ }
+ n -= ilen;
+ }
+
+ if (pstat_flag) {
+ if (pstyle == ISO) {
+ ilen = 1;
+ if (n < ilen)
+ return p_hydro*(volume-vol0) / nktv2p;
+ n -= ilen;
+ } else if (pstyle == ANISO) {
+ ilen = 3;
+ if (n < ilen) {
+ if (p_flag[n])
+ return p_hydro*(volume-vol0) / (pdim*nktv2p);
+ else
+ return 0.0;
+ }
+ n -= ilen;
+ } else {
+ ilen = 6;
+ if (n < ilen) {
+ if (n > 2) return 0.0;
+ else if (p_flag[n])
+ return p_hydro*(volume-vol0) / (pdim*nktv2p);
+ else
+ return 0.0;
+ }
+ n -= ilen;
+ }
+
+ if (pstyle == ISO) {
+ ilen = 1;
+ if (n < ilen)
+ return pdim*0.5*omega_dot[n]*omega_dot[n]*omega_mass[n];
+ n -= ilen;
+ } else if (pstyle == ANISO) {
+ ilen = 3;
+ if (n < ilen) {
+ if (p_flag[n])
+ return 0.5*omega_dot[n]*omega_dot[n]*omega_mass[n];
+ else return 0.0;
+ }
+ n -= ilen;
+ } else {
+ ilen = 6;
+ if (n < ilen) {
+ if (p_flag[n])
+ return 0.5*omega_dot[n]*omega_dot[n]*omega_mass[n];
+ else return 0.0;
+ }
+ n -= ilen;
+ }
+
+ if (mpchain) {
+ ilen = mpchain;
+ if (n < ilen) {
+ ich = n;
+ if (ich == 0) return lkt_press * etap[0];
+ else return kt * etap[ich];
+ }
+ n -= ilen;
+ ilen = mpchain;
+ if (n < ilen) {
+ ich = n;
+ if (ich == 0)
+ return 0.5*etap_mass[0]*etap_dot[0]*etap_dot[0];
+ else
+ return 0.5*etap_mass[ich]*etap_dot[ich]*etap_dot[ich];
+ }
+ n -= ilen;
+ }
+
+ if (deviatoric_flag) {
+ ilen = 1;
+ if (n < ilen)
+ return compute_strain_energy();
+ n -= ilen;
+ }
+ }
+
+ return 0.0;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixBocs::reset_target(double t_new)
+{
+ t_target = t_start = t_stop = t_new;
+}
+
+/* ---------------------------------------------------------------------- */
+
+void FixBocs::reset_dt()
+{
+ dtv = update->dt;
+ dtf = 0.5 * update->dt * force->ftm2v;
+ dthalf = 0.5 * update->dt;
+ dt4 = 0.25 * update->dt;
+ dt8 = 0.125 * update->dt;
+ dto = dthalf;
+
+ // If using respa, then remap is performed in innermost level
+
+ if (strstr(update->integrate_style,"respa"))
+ dto = 0.5*step_respa[0];
+
+ if (pstat_flag)
+ pdrag_factor = 1.0 - (update->dt * p_freq_max * drag / nc_pchain);
+
+ if (tstat_flag)
+ tdrag_factor = 1.0 - (update->dt * t_freq * drag / nc_tchain);
+}
+
+/* ----------------------------------------------------------------------
+ extract thermostat properties
+------------------------------------------------------------------------- */
+
+void *FixBocs::extract(const char *str, int &dim)
+{
+ dim=0;
+ if (tstat_flag && strcmp(str,"t_target") == 0) {
+ return &t_target;
+ } else if (tstat_flag && strcmp(str,"t_start") == 0) {
+ return &t_start;
+ } else if (tstat_flag && strcmp(str,"t_stop") == 0) {
+ return &t_stop;
+ } else if (tstat_flag && strcmp(str,"mtchain") == 0) {
+ return &mtchain;
+ } else if (pstat_flag && strcmp(str,"mpchain") == 0) {
+ return &mtchain;
+ }
+ dim=1;
+ if (tstat_flag && strcmp(str,"eta") == 0) {
+ return η
+ } else if (pstat_flag && strcmp(str,"etap") == 0) {
+ return η
+ } else if (pstat_flag && strcmp(str,"p_flag") == 0) {
+ return &p_flag;
+ } else if (pstat_flag && strcmp(str,"p_start") == 0) {
+ return &p_start;
+ } else if (pstat_flag && strcmp(str,"p_stop") == 0) {
+ return &p_stop;
+ } else if (pstat_flag && strcmp(str,"p_target") == 0) {
+ return &p_target;
+ }
+ return NULL;
+}
+
+/* ----------------------------------------------------------------------
+ perform half-step update of chain thermostat variables
+------------------------------------------------------------------------- */
+
+void FixBocs::nhc_temp_integrate()
+{
+ int ich;
+ double expfac;
+ double kecurrent = tdof * boltz * t_current;
+
+ // Update masses, to preserve initial freq, if flag set
+
+ if (eta_mass_flag) {
+ eta_mass[0] = tdof * boltz * t_target / (t_freq*t_freq);
+ for (int ich = 1; ich < mtchain; ich++)
+ eta_mass[ich] = boltz * t_target / (t_freq*t_freq);
+ }
+
+ if (eta_mass[0] > 0.0)
+ eta_dotdot[0] = (kecurrent - ke_target)/eta_mass[0];
+ else eta_dotdot[0] = 0.0;
+
+ double ncfac = 1.0/nc_tchain;
+ for (int iloop = 0; iloop < nc_tchain; iloop++) {
+
+ for (ich = mtchain-1; ich > 0; ich--) {
+ expfac = exp(-ncfac*dt8*eta_dot[ich+1]);
+ eta_dot[ich] *= expfac;
+ eta_dot[ich] += eta_dotdot[ich] * ncfac*dt4;
+ eta_dot[ich] *= tdrag_factor;
+ eta_dot[ich] *= expfac;
+ }
+
+ expfac = exp(-ncfac*dt8*eta_dot[1]);
+ eta_dot[0] *= expfac;
+ eta_dot[0] += eta_dotdot[0] * ncfac*dt4;
+ eta_dot[0] *= tdrag_factor;
+ eta_dot[0] *= expfac;
+
+ factor_eta = exp(-ncfac*dthalf*eta_dot[0]);
+ nh_v_temp();
+
+ // rescale temperature due to velocity scaling
+ // should not be necessary to explicitly recompute the temperature
+
+ t_current *= factor_eta*factor_eta;
+ kecurrent = tdof * boltz * t_current;
+
+ if (eta_mass[0] > 0.0)
+ eta_dotdot[0] = (kecurrent - ke_target)/eta_mass[0];
+ else eta_dotdot[0] = 0.0;
+
+ for (ich = 0; ich < mtchain; ich++)
+ eta[ich] += ncfac*dthalf*eta_dot[ich];
+
+ eta_dot[0] *= expfac;
+ eta_dot[0] += eta_dotdot[0] * ncfac*dt4;
+ eta_dot[0] *= expfac;
+
+ for (ich = 1; ich < mtchain; ich++) {
+ expfac = exp(-ncfac*dt8*eta_dot[ich+1]);
+ eta_dot[ich] *= expfac;
+ eta_dotdot[ich] = (eta_mass[ich-1]*eta_dot[ich-1]*eta_dot[ich-1]
+ - boltz * t_target)/eta_mass[ich];
+ eta_dot[ich] += eta_dotdot[ich] * ncfac*dt4;
+ eta_dot[ich] *= expfac;
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ perform half-step update of chain thermostat variables for barostat
+ scale barostat velocities
+------------------------------------------------------------------------- */
+
+void FixBocs::nhc_press_integrate()
+{
+ int ich,i;
+ double expfac,factor_etap,kecurrent;
+ double kt = boltz * t_target;
+ double lkt_press = kt;
+
+ // Update masses, to preserve initial freq, if flag set
+
+ if (omega_mass_flag) {
+ double nkt = atom->natoms * kt;
+ for (int i = 0; i < 3; i++)
+ if (p_flag[i])
+ omega_mass[i] = nkt/(p_freq[i]*p_freq[i]);
+
+ if (pstyle == TRICLINIC) {
+ for (int i = 3; i < 6; i++)
+ if (p_flag[i]) omega_mass[i] = nkt/(p_freq[i]*p_freq[i]);
+ }
+ }
+
+ if (etap_mass_flag) {
+ if (mpchain) {
+ etap_mass[0] = boltz * t_target / (p_freq_max*p_freq_max);
+ for (int ich = 1; ich < mpchain; ich++)
+ etap_mass[ich] = boltz * t_target / (p_freq_max*p_freq_max);
+ for (int ich = 1; ich < mpchain; ich++)
+ etap_dotdot[ich] =
+ (etap_mass[ich-1]*etap_dot[ich-1]*etap_dot[ich-1] -
+ boltz * t_target) / etap_mass[ich];
+ }
+ }
+
+ kecurrent = 0.0;
+ for (i = 0; i < 3; i++)
+ if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
+
+ if (pstyle == TRICLINIC) {
+ for (i = 3; i < 6; i++)
+ if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
+ }
+
+ etap_dotdot[0] = (kecurrent - lkt_press)/etap_mass[0];
+
+ double ncfac = 1.0/nc_pchain;
+ for (int iloop = 0; iloop < nc_pchain; iloop++) {
+
+ for (ich = mpchain-1; ich > 0; ich--) {
+ expfac = exp(-ncfac*dt8*etap_dot[ich+1]);
+ etap_dot[ich] *= expfac;
+ etap_dot[ich] += etap_dotdot[ich] * ncfac*dt4;
+ etap_dot[ich] *= pdrag_factor;
+ etap_dot[ich] *= expfac;
+ }
+
+ expfac = exp(-ncfac*dt8*etap_dot[1]);
+ etap_dot[0] *= expfac;
+ etap_dot[0] += etap_dotdot[0] * ncfac*dt4;
+ etap_dot[0] *= pdrag_factor;
+ etap_dot[0] *= expfac;
+
+ for (ich = 0; ich < mpchain; ich++)
+ etap[ich] += ncfac*dthalf*etap_dot[ich];
+
+ factor_etap = exp(-ncfac*dthalf*etap_dot[0]);
+ for (i = 0; i < 3; i++)
+ if (p_flag[i]) omega_dot[i] *= factor_etap;
+
+ if (pstyle == TRICLINIC) {
+ for (i = 3; i < 6; i++)
+ if (p_flag[i]) omega_dot[i] *= factor_etap;
+ }
+
+ kecurrent = 0.0;
+ for (i = 0; i < 3; i++)
+ if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
+
+ if (pstyle == TRICLINIC) {
+ for (i = 3; i < 6; i++)
+ if (p_flag[i]) kecurrent += omega_mass[i]*omega_dot[i]*omega_dot[i];
+ }
+
+ etap_dotdot[0] = (kecurrent - lkt_press)/etap_mass[0];
+
+ etap_dot[0] *= expfac;
+ etap_dot[0] += etap_dotdot[0] * ncfac*dt4;
+ etap_dot[0] *= expfac;
+
+ for (ich = 1; ich < mpchain; ich++) {
+ expfac = exp(-ncfac*dt8*etap_dot[ich+1]);
+ etap_dot[ich] *= expfac;
+ etap_dotdot[ich] =
+ (etap_mass[ich-1]*etap_dot[ich-1]*etap_dot[ich-1] - boltz*t_target) /
+ etap_mass[ich];
+ etap_dot[ich] += etap_dotdot[ich] * ncfac*dt4;
+ etap_dot[ich] *= expfac;
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ perform half-step barostat scaling of velocities
+-----------------------------------------------------------------------*/
+
+void FixBocs::nh_v_press()
+{
+ double factor[3];
+ double **v = atom->v;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
+
+ factor[0] = exp(-dt4*(omega_dot[0]+mtk_term2));
+ factor[1] = exp(-dt4*(omega_dot[1]+mtk_term2));
+ factor[2] = exp(-dt4*(omega_dot[2]+mtk_term2));
+
+ if (which == NOBIAS) {
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ v[i][0] *= factor[0];
+ v[i][1] *= factor[1];
+ v[i][2] *= factor[2];
+ if (pstyle == TRICLINIC) {
+ v[i][0] += -dthalf*(v[i][1]*omega_dot[5] + v[i][2]*omega_dot[4]);
+ v[i][1] += -dthalf*v[i][2]*omega_dot[3];
+ }
+ v[i][0] *= factor[0];
+ v[i][1] *= factor[1];
+ v[i][2] *= factor[2];
+ }
+ }
+ } else if (which == BIAS) {
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ temperature->remove_bias(i,v[i]);
+ v[i][0] *= factor[0];
+ v[i][1] *= factor[1];
+ v[i][2] *= factor[2];
+ if (pstyle == TRICLINIC) {
+ v[i][0] += -dthalf*(v[i][1]*omega_dot[5] + v[i][2]*omega_dot[4]);
+ v[i][1] += -dthalf*v[i][2]*omega_dot[3];
+ }
+ v[i][0] *= factor[0];
+ v[i][1] *= factor[1];
+ v[i][2] *= factor[2];
+ temperature->restore_bias(i,v[i]);
+ }
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ perform half-step update of velocities
+-----------------------------------------------------------------------*/
+
+void FixBocs::nve_v()
+{
+ double dtfm;
+ double **v = atom->v;
+ double **f = atom->f;
+ double *rmass = atom->rmass;
+ double *mass = atom->mass;
+ int *type = atom->type;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
+
+ if (rmass) {
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ dtfm = dtf / rmass[i];
+ v[i][0] += dtfm*f[i][0];
+ v[i][1] += dtfm*f[i][1];
+ v[i][2] += dtfm*f[i][2];
+ }
+ }
+ } else {
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ dtfm = dtf / mass[type[i]];
+ v[i][0] += dtfm*f[i][0];
+ v[i][1] += dtfm*f[i][1];
+ v[i][2] += dtfm*f[i][2];
+ }
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ perform full-step update of positions
+-----------------------------------------------------------------------*/
+
+void FixBocs::nve_x()
+{
+ double **x = atom->x;
+ double **v = atom->v;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
+
+ // x update by full step only for atoms in group
+
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ x[i][0] += dtv * v[i][0];
+ x[i][1] += dtv * v[i][1];
+ x[i][2] += dtv * v[i][2];
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ perform half-step thermostat scaling of velocities
+-----------------------------------------------------------------------*/
+
+void FixBocs::nh_v_temp()
+{
+ double **v = atom->v;
+ int *mask = atom->mask;
+ int nlocal = atom->nlocal;
+ if (igroup == atom->firstgroup) nlocal = atom->nfirst;
+
+ if (which == NOBIAS) {
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ v[i][0] *= factor_eta;
+ v[i][1] *= factor_eta;
+ v[i][2] *= factor_eta;
+ }
+ }
+ } else if (which == BIAS) {
+ for (int i = 0; i < nlocal; i++) {
+ if (mask[i] & groupbit) {
+ temperature->remove_bias(i,v[i]);
+ v[i][0] *= factor_eta;
+ v[i][1] *= factor_eta;
+ v[i][2] *= factor_eta;
+ temperature->restore_bias(i,v[i]);
+ }
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ compute sigma tensor
+ needed whenever p_target or h0_inv changes
+-----------------------------------------------------------------------*/
+
+void FixBocs::compute_sigma()
+{
+ // if nreset_h0 > 0, reset vol0 and h0_inv
+ // every nreset_h0 timesteps
+
+ if (nreset_h0 > 0) {
+ int delta = update->ntimestep - update->beginstep;
+ if (delta % nreset_h0 == 0) {
+ if (dimension == 3) vol0 = domain->xprd * domain->yprd * domain->zprd;
+ else vol0 = domain->xprd * domain->yprd;
+ h0_inv[0] = domain->h_inv[0];
+ h0_inv[1] = domain->h_inv[1];
+ h0_inv[2] = domain->h_inv[2];
+ h0_inv[3] = domain->h_inv[3];
+ h0_inv[4] = domain->h_inv[4];
+ h0_inv[5] = domain->h_inv[5];
+ }
+ }
+
+ // generate upper-triangular half of
+ // sigma = vol0*h0inv*(p_target-p_hydro)*h0inv^t
+ // units of sigma are are PV/L^2 e.g. atm.A
+ //
+ // [ 0 5 4 ] [ 0 5 4 ] [ 0 5 4 ] [ 0 - - ]
+ // [ 5 1 3 ] = [ - 1 3 ] [ 5 1 3 ] [ 5 1 - ]
+ // [ 4 3 2 ] [ - - 2 ] [ 4 3 2 ] [ 4 3 2 ]
+
+ sigma[0] =
+ vol0*(h0_inv[0]*((p_target[0]-p_hydro)*h0_inv[0] +
+ p_target[5]*h0_inv[5]+p_target[4]*h0_inv[4]) +
+ h0_inv[5]*(p_target[5]*h0_inv[0] +
+ (p_target[1]-p_hydro)*h0_inv[5]+p_target[3]*h0_inv[4]) +
+ h0_inv[4]*(p_target[4]*h0_inv[0]+p_target[3]*h0_inv[5] +
+ (p_target[2]-p_hydro)*h0_inv[4]));
+ sigma[1] =
+ vol0*(h0_inv[1]*((p_target[1]-p_hydro)*h0_inv[1] +
+ p_target[3]*h0_inv[3]) +
+ h0_inv[3]*(p_target[3]*h0_inv[1] +
+ (p_target[2]-p_hydro)*h0_inv[3]));
+ sigma[2] =
+ vol0*(h0_inv[2]*((p_target[2]-p_hydro)*h0_inv[2]));
+ sigma[3] =
+ vol0*(h0_inv[1]*(p_target[3]*h0_inv[2]) +
+ h0_inv[3]*((p_target[2]-p_hydro)*h0_inv[2]));
+ sigma[4] =
+ vol0*(h0_inv[0]*(p_target[4]*h0_inv[2]) +
+ h0_inv[5]*(p_target[3]*h0_inv[2]) +
+ h0_inv[4]*((p_target[2]-p_hydro)*h0_inv[2]));
+ sigma[5] =
+ vol0*(h0_inv[0]*(p_target[5]*h0_inv[1]+p_target[4]*h0_inv[3]) +
+ h0_inv[5]*((p_target[1]-p_hydro)*h0_inv[1]+p_target[3]*h0_inv[3]) +
+ h0_inv[4]*(p_target[3]*h0_inv[1]+(p_target[2]-p_hydro)*h0_inv[3]));
+}
+
+/* ----------------------------------------------------------------------
+ compute strain energy
+-----------------------------------------------------------------------*/
+
+double FixBocs::compute_strain_energy()
+{
+ // compute strain energy = 0.5*Tr(sigma*h*h^t) in energy units
+
+ double* h = domain->h;
+ double d0,d1,d2;
+
+ d0 =
+ sigma[0]*(h[0]*h[0]+h[5]*h[5]+h[4]*h[4]) +
+ sigma[5]*( h[1]*h[5]+h[3]*h[4]) +
+ sigma[4]*( h[2]*h[4]);
+ d1 =
+ sigma[5]*( h[5]*h[1]+h[4]*h[3]) +
+ sigma[1]*( h[1]*h[1]+h[3]*h[3]) +
+ sigma[3]*( h[2]*h[3]);
+ d2 =
+ sigma[4]*( h[4]*h[2]) +
+ sigma[3]*( h[3]*h[2]) +
+ sigma[2]*( h[2]*h[2]);
+
+ double energy = 0.5*(d0+d1+d2)/nktv2p;
+ return energy;
+}
+
+/* ----------------------------------------------------------------------
+ compute deviatoric barostat force = h*sigma*h^t
+-----------------------------------------------------------------------*/
+
+void FixBocs::compute_deviatoric()
+{
+ // generate upper-triangular part of h*sigma*h^t
+ // units of fdev are are PV, e.g. atm*A^3
+ // [ 0 5 4 ] [ 0 5 4 ] [ 0 5 4 ] [ 0 - - ]
+ // [ 5 1 3 ] = [ - 1 3 ] [ 5 1 3 ] [ 5 1 - ]
+ // [ 4 3 2 ] [ - - 2 ] [ 4 3 2 ] [ 4 3 2 ]
+
+ double* h = domain->h;
+
+ fdev[0] =
+ h[0]*(sigma[0]*h[0]+sigma[5]*h[5]+sigma[4]*h[4]) +
+ h[5]*(sigma[5]*h[0]+sigma[1]*h[5]+sigma[3]*h[4]) +
+ h[4]*(sigma[4]*h[0]+sigma[3]*h[5]+sigma[2]*h[4]);
+ fdev[1] =
+ h[1]*( sigma[1]*h[1]+sigma[3]*h[3]) +
+ h[3]*( sigma[3]*h[1]+sigma[2]*h[3]);
+ fdev[2] =
+ h[2]*( sigma[2]*h[2]);
+ fdev[3] =
+ h[1]*( sigma[3]*h[2]) +
+ h[3]*( sigma[2]*h[2]);
+ fdev[4] =
+ h[0]*( sigma[4]*h[2]) +
+ h[5]*( sigma[3]*h[2]) +
+ h[4]*( sigma[2]*h[2]);
+ fdev[5] =
+ h[0]*( sigma[5]*h[1]+sigma[4]*h[3]) +
+ h[5]*( sigma[1]*h[1]+sigma[3]*h[3]) +
+ h[4]*( sigma[3]*h[1]+sigma[2]*h[3]);
+}
+
+/* ----------------------------------------------------------------------
+ compute target temperature and kinetic energy
+-----------------------------------------------------------------------*/
+
+void FixBocs::compute_temp_target()
+{
+ double delta = update->ntimestep - update->beginstep;
+ if (delta != 0.0) delta /= update->endstep - update->beginstep;
+
+ t_target = t_start + delta * (t_stop-t_start);
+ ke_target = tdof * boltz * t_target;
+}
+
+/* ----------------------------------------------------------------------
+ compute hydrostatic target pressure
+-----------------------------------------------------------------------*/
+
+void FixBocs::compute_press_target()
+{
+ double delta = update->ntimestep - update->beginstep;
+ if (delta != 0.0) delta /= update->endstep - update->beginstep;
+
+ p_hydro = 0.0;
+ for (int i = 0; i < 3; i++)
+ if (p_flag[i]) {
+ p_target[i] = p_start[i] + delta * (p_stop[i]-p_start[i]);
+ p_hydro += p_target[i];
+ }
+ if (pdim > 0) p_hydro /= pdim;
+
+ if (pstyle == TRICLINIC)
+ for (int i = 3; i < 6; i++)
+ p_target[i] = p_start[i] + delta * (p_stop[i]-p_start[i]);
+
+ // if deviatoric, recompute sigma each time p_target changes
+
+ if (deviatoric_flag) compute_sigma();
+}
+
+/* ----------------------------------------------------------------------
+ update omega_dot, omega
+-----------------------------------------------------------------------*/
+
+void FixBocs::nh_omega_dot()
+{
+ double f_omega,volume;
+
+ if (dimension == 3) volume = domain->xprd*domain->yprd*domain->zprd;
+ else volume = domain->xprd*domain->yprd;
+
+ if (deviatoric_flag) compute_deviatoric();
+
+ mtk_term1 = 0.0;
+ if (mtk_flag) {
+ if (pstyle == ISO) {
+ mtk_term1 = tdof * boltz * t_current;
+ mtk_term1 /= pdim * atom->natoms;
+ } else {
+ double *mvv_current = temperature->vector;
+ for (int i = 0; i < 3; i++)
+ if (p_flag[i])
+ mtk_term1 += mvv_current[i];
+ mtk_term1 /= pdim * atom->natoms;
+ }
+ }
+
+ for (int i = 0; i < 3; i++)
+ if (p_flag[i]) {
+ f_omega = (p_current[i]-p_hydro)*volume /
+ (omega_mass[i] * nktv2p) + mtk_term1 / omega_mass[i];
+ if (deviatoric_flag) f_omega -= fdev[i]/(omega_mass[i] * nktv2p);
+ omega_dot[i] += f_omega*dthalf;
+ omega_dot[i] *= pdrag_factor;
+ }
+
+ mtk_term2 = 0.0;
+ if (mtk_flag) {
+ for (int i = 0; i < 3; i++)
+ if (p_flag[i])
+ mtk_term2 += omega_dot[i];
+ if (pdim > 0) mtk_term2 /= pdim * atom->natoms;
+ }
+
+ if (pstyle == TRICLINIC) {
+ for (int i = 3; i < 6; i++) {
+ if (p_flag[i]) {
+ f_omega = p_current[i]*volume/(omega_mass[i] * nktv2p);
+ if (deviatoric_flag)
+ f_omega -= fdev[i]/(omega_mass[i] * nktv2p);
+ omega_dot[i] += f_omega*dthalf;
+ omega_dot[i] *= pdrag_factor;
+ }
+ }
+ }
+}
+
+/* ----------------------------------------------------------------------
+ if any tilt ratios exceed limits, set flip = 1 and compute new tilt values
+ do not flip in x or y if non-periodic (can tilt but not flip)
+ this is b/c the box length would be changed (dramatically) by flip
+ if yz tilt exceeded, adjust C vector by one B vector
+ if xz tilt exceeded, adjust C vector by one A vector
+ if xy tilt exceeded, adjust B vector by one A vector
+ check yz first since it may change xz, then xz check comes after
+ if any flip occurs, create new box in domain
+ image_flip() adjusts image flags due to box shape change induced by flip
+ remap() puts atoms outside the new box back into the new box
+ perform irregular on atoms in lamda coords to migrate atoms to new procs
+ important that image_flip comes before remap, since remap may change
+ image flags to new values, making eqs in doc of Domain:image_flip incorrect
+------------------------------------------------------------------------- */
+
+void FixBocs::pre_exchange()
+{
+ double xprd = domain->xprd;
+ double yprd = domain->yprd;
+
+ // flip is only triggered when tilt exceeds 0.5 by DELTAFLIP
+ // this avoids immediate re-flipping due to tilt oscillations
+
+ double xtiltmax = (0.5+DELTAFLIP)*xprd;
+ double ytiltmax = (0.5+DELTAFLIP)*yprd;
+
+ int flipxy,flipxz,flipyz;
+ flipxy = flipxz = flipyz = 0;
+
+ if (domain->yperiodic) {
+ if (domain->yz < -ytiltmax) {
+ domain->yz += yprd;
+ domain->xz += domain->xy;
+ flipyz = 1;
+ } else if (domain->yz >= ytiltmax) {
+ domain->yz -= yprd;
+ domain->xz -= domain->xy;
+ flipyz = -1;
+ }
+ }
+
+ if (domain->xperiodic) {
+ if (domain->xz < -xtiltmax) {
+ domain->xz += xprd;
+ flipxz = 1;
+ } else if (domain->xz >= xtiltmax) {
+ domain->xz -= xprd;
+ flipxz = -1;
+ }
+ if (domain->xy < -xtiltmax) {
+ domain->xy += xprd;
+ flipxy = 1;
+ } else if (domain->xy >= xtiltmax) {
+ domain->xy -= xprd;
+ flipxy = -1;
+ }
+ }
+
+ int flip = 0;
+ if (flipxy || flipxz || flipyz) flip = 1;
+
+ if (flip) {
+ domain->set_global_box();
+ domain->set_local_box();
+
+ domain->image_flip(flipxy,flipxz,flipyz);
+
+ double **x = atom->x;
+ imageint *image = atom->image;
+ int nlocal = atom->nlocal;
+ for (int i = 0; i < nlocal; i++) domain->remap(x[i],image[i]);
+
+ domain->x2lamda(atom->nlocal);
+ irregular->migrate_atoms();
+ domain->lamda2x(atom->nlocal);
+ }
+}
+
+/* ----------------------------------------------------------------------
+ memory usage of Irregular
+------------------------------------------------------------------------- */
+
+double FixBocs::memory_usage()
+{
+ double bytes = 0.0;
+ if (irregular) bytes += irregular->memory_usage();
+ return bytes;
+}
diff --git a/src/USER-BOCS/fix_bocs.h b/src/USER-BOCS/fix_bocs.h
new file mode 100644
index 0000000000..8e6eefdc69
--- /dev/null
+++ b/src/USER-BOCS/fix_bocs.h
@@ -0,0 +1,305 @@
+/* -*- 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.
+
+*/
--
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