patch 11Apr17

fix gcmc updates from Aidan, trimming of output for replica commands
Merge pull request #443 from Pakketeretet2/user-manifold-fix-every-keyword
2017-04-11 09:00:37 -06:00 · 2017-04-11 08:35:09 -06:00 · 2017-04-11 08:27:53 -06:00 · 2017-04-11 08:27:31 -06:00 · 2017-04-11 08:25:09 -06:00 · 2017-04-11 08:24:32 -06:00
70 changed files with 717 additions and 756 deletions
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@ -1,7 +1,7 @@
 <!-- HTML_ONLY -->
 <HEAD>
 <TITLE>LAMMPS Users Manual</TITLE>
-<META NAME="docnumber" CONTENT="31 Mar 2017 version">
+<META NAME="docnumber" CONTENT="11 Apr 2017 version">
 <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories">
 <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation.  This software and manual is distributed under the GNU General Public License.">
 </HEAD>
@ -21,7 +21,7 @@
 <H1></H1>

 LAMMPS Documentation :c,h3
-31 Mar 2017 version :c,h4
+11 Apr 2017 version :c,h4

 Version info: :h4

--- a/doc/src/Section_commands.txt
+++ b/doc/src/Section_commands.txt
@ -1155,7 +1155,7 @@ USER-OMP, t = OPT.
 "zero"_dihedral_zero.html,
 "hybrid"_dihedral_hybrid.html,
 "charmm (ko)"_dihedral_charmm.html,
-"charmmfsh"_dihedral_charmm.html,
+"charmmfsw"_dihedral_charmm.html,
 "class2 (ko)"_dihedral_class2.html,
 "harmonic (io)"_dihedral_harmonic.html,
 "helix (o)"_dihedral_helix.html,
--- a/doc/src/Section_howto.txt
+++ b/doc/src/Section_howto.txt
@ -215,7 +215,7 @@ documentation for the formula it computes.
 "special_bonds"_special_bonds.html charmm
 "special_bonds"_special_bonds.html amber :ul

-NOTE: For CHARMM, the newer {charmmfsw} or {charmmfsh} styles were
+NOTE: For CHARMM, newer {charmmfsw} or {charmmfsh} styles were
 released in March 2017.  We recommend they be used instead of the
 older {charmm} styles.  See discussion of the differences on the "pair
 charmm"_pair_charmm.html and "dihedral charmm"_dihedral_charmm.html
--- a/doc/src/Section_packages.txt
+++ b/doc/src/Section_packages.txt
@ -1308,8 +1308,8 @@ oxdna/..."_pair_oxdna.html, "pair_style
 oxdna2/..."_pair_oxdna2.html, "fix
 nve/dotc/langevin"_fix_nve_dotc_langevin.html

-Author: Oliver Henrich at the University of Strathclyde, Glasgow, UK and 
-University of Edinburgh (ohenrich@ph.ed.ac.uk).  
+Author: Oliver Henrich at the University of Strathclyde, Glasgow 
+(oliver.henrich at strath.ac.uk, also ohenrich at ph.ed.ac.uk). 
 Contact him directly if you have any questions.

 :line
--- a/doc/src/Section_start.txt
+++ b/doc/src/Section_start.txt
@ -455,8 +455,7 @@ and related PPPM operations are somewhat insensitive to floating point
 truncation errors and thus do not always need to be performed in
 double precision.  Using the -DFFT_SINGLE setting trades off a little
 accuracy for reduced memory use and parallel communication costs for
-transposing 3d FFT data.  Note that single precision FFTs have only
-been tested with the FFTW3, FFTW2, MKL, and KISS FFT options.
+transposing 3d FFT data.

 Step 7 :h6

--- a/doc/src/bond_oxdna.txt
+++ b/doc/src/bond_oxdna.txt
@ -46,9 +46,7 @@ for excluded volume interaction {oxdna/excv}, stacking {oxdna/stk}, cross-stacki
 and coaxial stacking interaction {oxdna/coaxstk} as well as hydrogen-bonding interaction {oxdna/hbond} (see also documentation of 
 "pair_style oxdna/excv"_pair_oxdna.html). For the oxDNA2 "(Snodin)"_#oxdna2 bond style the analogous pair styles and an additional Debye-Hueckel pair 
 style {oxdna2/dh} have to be defined.
-
-The coefficients 
-in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.
+The coefficients in the above example have to be kept fixed and cannot be changed without reparametrizing the entire model.

 Example input and data files for DNA duplexes can be found in examples/USER/cgdna/examples/oxDNA/ and /oxDNA2/.
 A simple python setup tool which creates single straight or helical DNA strands,
--- a/doc/src/dihedral_charmm.txt
+++ b/doc/src/dihedral_charmm.txt
@ -10,25 +10,25 @@ dihedral_style charmm command :h3
 dihedral_style charmm/intel command :h3
 dihedral_style charmm/kk command :h3
 dihedral_style charmm/omp command :h3
-dihedral_style charmmfsh command :h3
+dihedral_style charmmfsw command :h3

 [Syntax:]

 dihedral_style style :pre

-style = {charmm} or {charmmfsh} :ul
+style = {charmm} or {charmmfsw} :ul

 [Examples:]

 dihedral_style charmm
-dihedral_style charmmfsh
+dihedral_style charmmfsw
 dihedral_coeff  1 0.2 1 180 1.0
 dihedral_coeff  2 1.8 1   0 1.0
 dihedral_coeff  1 3.1 2 180 0.5 :pre

 [Description:]

-The {charmm} and {charmmfsh} dihedral styles use the potential
+The {charmm} and {charmmfsw} dihedral styles use the potential

 :c,image(Eqs/dihedral_charmm.jpg)

@ -38,10 +38,12 @@ field (see comment on weighting factors below).  See
 "(Cornell)"_#dihedral-Cornell for a description of the AMBER force
 field.

-NOTE: The newer {charmmfsh} style was released in March 2017.  We
+NOTE: The newer {charmmfsw} style was released in March 2017.  We
 recommend it be used instead of the older {charmm} style when running
-a simulation with the CHARMM force field and Coulomb cutoffs, via the
-"pair_style lj/charmmfsw/coul/charmmfsh"_pair_charmm.html command.
+a simulation with the CHARMM force field, either with long-range
+Coulombics or a Coulomb cutoff, via the "pair_style
+lj/charmmfsw/coul/long"_pair_charmm.html and "pair_style
+lj/charmmfsw/coul/charmmfsh"_pair_charmm.html commands respectively.
 Otherwise the older {charmm} style is fine to use.  See the discussion
 below and more details on the "pair_style charmm"_pair_charmm.html doc
 page.
@ -86,17 +88,18 @@ default). Otherwise 1-4 non-bonded interactions in dihedrals will be
 computed twice.

 For simulations using the CHARMM force field with a Coulomb cutoff,
-the difference between the {charmm} and {charmmfsh} styles is in the
+the difference between the {charmm} and {charmmfsw} styles is in the
 computation of the 1-4 non-bond interactions, though only if the
 distance between the two atoms is within the switching region of the
 pairwise potential defined by the corresponding CHARMM pair style,
 i.e. within the outer cutoff specified for the pair style.  The
-{charmmfsh} style should only be used when using the "pair_style
-lj/charmmfsw/coul/charmmfsh"_pair_charmm.html to make the Coulombic
-pairwise calculations consistent.  Use the {charmm} style with
-long-range Coulombics or the older "pair_style
-lj/charmm/coul/charmm"_pair_charmm.html command.  See the discussion
-on the "CHARMM pair_style"_pair_charmm.html doc page for details.
+{charmmfsw} style should only be used when using the corresponding
+"pair_style lj/charmmfsw/coul/charmmfsw"_pair_charmm.html or
+"pair_style lj/charmmfsw/coul/long"_pair_charmm.html commands.  Use
+the {charmm} style with the older "pair_style"_pair_charmm.html
+commands that have just "charmm" in their style name.  See the
+discussion on the "CHARMM pair_style"_pair_charmm.html doc page for
+details.

 Note that for AMBER force fields, which use pair styles with "lj/cut",
 the special_bonds 1-4 scaling factor should be set to the AMBER
@ -104,7 +107,7 @@ defaults (1/2 and 5/6) and all the dihedral weighting factors (4th
 coeff above) must be set to 0.0. In this case, you can use any pair
 style you wish, since the dihedral does not need any Lennard-Jones
 parameter information and will not compute any 1-4 non-bonded
-interactions.  Likewise the {charmm} or {charmmfsh} styles are
+interactions.  Likewise the {charmm} or {charmmfsw} styles are
 identical in this case since no 1-4 non-bonded interactions are
 computed.

--- a/doc/src/fix_adapt.txt
+++ b/doc/src/fix_adapt.txt
@ -22,6 +22,11 @@ attribute = {pair} or {kspace} or {atom} :l
    pparam = parameter to adapt over time
    I,J = type pair(s) to set parameter for
    v_name = variable with name that calculates value of pparam
+  {bond} args = bstyle bparam I v_name
+    bstyle = bond style name, e.g. harmonic
+    bparam = parameter to adapt over time
+    I = type bond to set parameter for
+    v_name = variable with name that calculates value of bparam
  {kspace} arg = v_name
    v_name = variable with name that calculates scale factor on K-space terms
  {atom} args = aparam v_name
@ -42,7 +47,10 @@ keyword = {scale} or {reset} :l
 fix 1 all adapt 1 pair soft a 1 1 v_prefactor
 fix 1 all adapt 1 pair soft a 2* 3 v_prefactor
 fix 1 all adapt 1 pair lj/cut epsilon * * v_scale1 coul/cut scale 3 3 v_scale2 scale yes reset yes
-fix 1 all adapt 10 atom diameter v_size :pre
+fix 1 all adapt 10 atom diameter v_size
+
+variable ramp_up equal "ramp(0.01,0.5)"
+fix stretch all adapt 1 bond harmonic r0 1 v_ramp_up :pre

 [Description:]

@ -192,6 +200,19 @@ fix 1 all adapt 1 pair soft a * * v_prefactor :pre

 :line

+The {bond} keyword uses the specified variable to change the value of
+a bond coefficient over time, very similar to how the {pair} keyword
+operates. The only difference is that now a bond coefficient for a
+given bond type is adapted.
+
+Currently {bond} does not support bond_style hybrid nor bond_style
+hybrid/overlay as bond styles. The only bonds that currently are
+working with fix_adapt are
+
+"harmonic"_bond_harmonic.html: k,r0: type bonds :tb(c=3,s=:)
+
+:line
+
 The {kspace} keyword used the specified variable as a scale factor on
 the energy, forces, virial calculated by whatever K-Space solver is
 defined by the "kspace_style"_kspace_style.html command.  If the
--- a/doc/src/kspace_modify.txt
+++ b/doc/src/kspace_modify.txt
@ -290,9 +290,10 @@ to be specified using the {gewald/disp}, {mesh/disp},
 {force/disp/real} or {force/disp/kspace} keywords, or
 the code will stop with an error message. When this option is set to
 {yes}, the error message will not appear and the simulation will start.
-For a typical application, using the automatic parameter generation will provide
-simulations that are either inaccurate or slow. Using this option is thus not
-recommended. For guidelines on how to obtain good parameters, see the "How-To"_Section_howto.html#howto_23 discussion.
+For a typical application, using the automatic parameter generation
+will provide simulations that are either inaccurate or slow. Using this
+option is thus not recommended. For guidelines on how to obtain good
+parameters, see the "How-To"_Section_howto.html#howto_24 discussion.

 [Restrictions:] none

--- a/doc/src/pair_buck.txt
+++ b/doc/src/pair_buck.txt
@ -120,6 +120,9 @@ cutoff (distance units)
 cutoff2 (distance units) :ul

 The second coefficient, rho, must be greater than zero.
+The coefficients A, rho, and C can be written as analytical expressions
+of epsilon and sigma, in analogy to the Lennard-Jones potential
+"(Khrapak)"_#Khrapak.

 The latter 2 coefficients are optional.  If not specified, the global
 A,C and Coulombic cutoffs are used.  If only one cutoff is specified,
@ -127,7 +130,6 @@ it is used as the cutoff for both A,C and Coulombic interactions for
 this type pair.  If both coefficients are specified, they are used as
 the A,C and Coulombic cutoffs for this type pair.  You cannot specify
 2 cutoffs for style {buck}, since it has no Coulombic terms.
-
 For {buck/coul/long} only the LJ cutoff can be specified since a
 Coulombic cutoff cannot be specified for an individual I,J type pair.
 All type pairs use the same global Coulombic cutoff specified in the
@ -194,3 +196,6 @@ only enabled if LAMMPS was built with that package.  See the
 "pair_coeff"_pair_coeff.html, "pair_style born"_pair_born.html

 [Default:] none
+
+:link(Khrapak)
+[(Khrapak)] Khrapak, Chaudhuri, and Morfill, J Chem Phys, 134, 054120 (2011).
--- a/doc/src/pair_charmm.txt
+++ b/doc/src/pair_charmm.txt
@ -99,9 +99,10 @@ artifacts.

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

 The general CHARMM formulas are as follows

--- a/examples/cmap/in.cmap
+++ b/examples/cmap/in.cmap
@ -9,11 +9,10 @@ boundary        p p p
 atom_style      full
 bond_style      harmonic
 angle_style     charmm
-dihedral_style  charmm
+dihedral_style  charmmfsw
 improper_style  harmonic

-pair_style      lj/charmm/coul/charmm 8 12
-#pair_style      lj/charmmfsw/coul/charmmfsh 8 12
+pair_style      lj/charmmfsw/coul/charmmfsh 8 12
 pair_modify     mix arithmetic

 fix             cmap all cmap charmm22.cmap
--- a/examples/cmap/log.5Oct16.cmap.g++.1
+++ b/examples/cmap/log.5Oct16.cmap.g++.1
@ -1,201 +0,0 @@
-LAMMPS (5 Oct 2016)
-# Created by charmm2lammps v1.8.2.6 beta on Thu Mar  3 20:56:57 EST 2016
-
-units           real
-neigh_modify    delay 2 every 1
-#newton          off
-
-boundary        p p p
-
-atom_style      full
-bond_style      harmonic
-angle_style     charmm
-dihedral_style  charmm
-improper_style  harmonic
-
-pair_style      lj/charmm/coul/charmm 8 12
-#pair_style      lj/charmmfsw/coul/charmmfsh 8 12
-pair_modify     mix arithmetic
-
-fix             cmap all cmap charmm22.cmap
-Reading potential file charmm22.cmap with DATE: 2016-09-26
-fix_modify      cmap energy yes
-
-read_data       gagg.data fix cmap crossterm CMAP
-  orthogonal box = (-34.4147 -36.1348 -39.3491) to (45.5853 43.8652 40.6509)
-  1 by 1 by 1 MPI processor grid
-  reading atoms ...
-  34 atoms
-  scanning bonds ...
-  4 = max bonds/atom
-  scanning angles ...
-  6 = max angles/atom
-  scanning dihedrals ...
-  12 = max dihedrals/atom
-  scanning impropers ...
-  1 = max impropers/atom
-  reading bonds ...
-  33 bonds
-  reading angles ...
-  57 angles
-  reading dihedrals ...
-  75 dihedrals
-  reading impropers ...
-  7 impropers
-  4 = max # of 1-2 neighbors
-  7 = max # of 1-3 neighbors
-  13 = max # of 1-4 neighbors
-  16 = max # of special neighbors
-
-special_bonds   charmm
-fix             1 all nve
-
-#fix             1 all nvt temp 300 300 100.0
-#fix             2 all shake 1e-9 500 0 m 1.0
-
-velocity        all create 0.0 12345678 dist uniform
-
-thermo          1000
-thermo_style    custom step ecoul evdwl ebond eangle edihed f_cmap eimp
-timestep        2.0
-
-run             100000
-Neighbor list info ...
-  1 neighbor list requests
-  update every 1 steps, delay 2 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 14
-  ghost atom cutoff = 14
-  binsize = 7 -> bins = 12 12 12
-Memory usage per processor = 14.6355 Mbytes
-Step E_coul E_vdwl E_bond E_angle E_dihed f_cmap E_impro 
-       0    26.542777  -0.93822087    1.2470497    4.8441789    4.5432816    -1.473352   0.10453023 
-    1000    28.673005  -0.47724367   0.80029132     3.151679    4.4684446   -2.3928648   0.18604953 
-    2000     27.67955    -1.170342   0.72018905    4.0400131    4.4713764   -2.5490207   0.21834436 
-    3000    29.256656  -0.35856055   0.73303546    3.7411606    4.4710568   -2.8939692   0.37728884 
-    4000    30.097549   -1.1353905   0.79007053    3.0688444    4.4091469   -2.3383587   0.20743631 
-    5000    28.357525   -1.0723742    0.9180297    3.6579424    4.8792664   -2.3185572  0.088366962 
-    6000    29.214175  -0.95299225   0.81926009    3.6805429    4.6742897   -2.9343577   0.26697813 
-    7000    27.018614  -0.52423475   0.72502764    3.8840137    4.7780956   -2.3916009   0.24952584 
-    8000    29.682167   -1.0939711   0.76111486    3.1090116    4.9359719   -2.5662984    0.1411154 
-    9000    27.909695  -0.80905986   0.78952533     4.203187    4.1301204    -2.000402  0.088859259 
-   10000    27.480298  -0.86273377    1.1293962    4.3857421     4.899282   -3.3895621   0.12126215 
-   11000    28.303203   -1.0221152   0.62762348     4.055414    4.5863024   -2.5842816   0.17996907 
-   12000    28.311127  -0.94227367   0.91859012    3.6673926    4.7018632    -3.902715   0.30065704 
-   13000    30.818607   -1.5220116   0.95710386    3.3364371     4.543427   -3.0423067   0.16712905 
-   14000    27.643736   -1.0144117   0.95806952    4.1046912     4.800236   -4.0534389   0.29293405 
-   15000    27.660491   -1.0390086   0.78061056    4.1139174    4.7197202   -2.3670379   0.22126985 
-   16000    27.845157  -0.63654502   0.78007478    3.9365994     4.949418   -3.1470214   0.22335355 
-   17000     28.44772   -1.0255112   0.70402007    4.0573343    4.2887527   -2.2099596  0.048050962 
-   18000    27.128323  -0.96218536    1.1327159    4.3222585     4.326607   -2.2881766   0.13491257 
-   19000    27.337633  -0.78999574   0.80152298    4.2239689    4.7073478   -2.2924164   0.12710292 
-   20000    27.780537  -0.46458072   0.79707671    3.7232618     4.943417   -2.5290628   0.26191223 
-   21000    26.435484   -0.7803224    1.0753217    4.4196051    5.9945933   -2.3340925   0.16448475 
-   22000    28.619429   -1.1623149    0.9401731    3.8508844    5.1636737   -2.5551846   0.25318434 
-   23000    28.399338  -0.79700962   0.85575503     4.488526    4.5975422   -2.5663549   0.13601693 
-   24000    29.645532    -1.158744   0.83180313    3.8193399      4.60319   -2.6847864   0.24260466 
-   25000    28.695339   -1.4802204   0.76583757    3.6786272    4.8959496   -2.3627896  0.080867326 
-   26000    28.149711    -1.029689   0.79383806    3.7885067    4.3345813   -2.1041553   0.14598209 
-   27000    29.580373   -1.0525813    1.0262723    3.7767318    4.6119758   -2.2802386  0.088556038 
-   28000     28.44308  -0.93411225    0.8794395     3.948079     4.780246   -2.1814583   0.14340149 
-   29000    29.335621   -1.6087988   0.71803091    3.7819186    4.6688385   -2.4282242   0.16061111 
-   30000    28.706138   -1.3938241   0.67713818     4.031275    4.4756505   -2.1807056   0.11461356 
-   31000    27.451944  0.010297225   0.65064883    3.6402029    4.3607811   -2.5511516   0.12637237 
-   32000    27.070878    -1.103158    1.1932199    5.1329709    4.5201653   -2.2224479   0.11215427 
-   33000    29.889976   -1.6228316   0.69407996    3.5361991    4.3502767   -1.9847454   0.09089949 
-   34000    28.223151    -0.927208     1.043253    3.4650939    5.1028142   -2.8127219   0.10648823 
-   35000    27.985986  -0.48153861   0.63878449    3.3724641    4.9551679   -2.6565919   0.12123115 
-   36000    28.580688   -1.4500694     1.055762    4.0490064     4.423782   -2.3103578  0.072747638 
-   37000    29.192947  -0.49678176    1.1146731    2.9233947    4.5738603   -2.4376144   0.22874047 
-   38000    26.954594  -0.53812359   0.79230685    4.3356989    5.0284656   -2.3791255    0.0486081 
-   39000    27.567555  -0.57870028   0.73614374     4.191991    4.9209556   -2.6122044   0.08635571 
-   40000    28.494172  -0.79057135   0.79072816    4.1893209    4.4826919   -2.4179635   0.14612898 
-   41000     28.44904   -1.1002948   0.93405654    4.3586358    4.4338415   -2.2950944   0.15705834 
-   42000     28.95725   -1.0297067    1.1632348     4.274711    4.9979487   -2.7611464   0.15944725 
-   43000    28.640394  -0.70938882   0.68100893    3.1844315    5.1817454   -2.2837487   0.14189233 
-   44000    27.997558   -1.0115099   0.59125208    4.0883422    4.6033907   -2.2775964  0.094273258 
-   45000     27.67163  -0.67992747    1.1225552    3.9020703    4.8171056   -2.1952679  0.041418433 
-   46000    28.822607   -0.6687953   0.74160059    3.3193715    4.5546965   -2.3024572  0.047569065 
-   47000     29.20147   -1.4456785   0.79223353    3.8288813    4.5811826   -2.5154936  0.061230141 
-   48000    27.843026   -1.0222301   0.87322137    4.3432743    4.4266307   -2.1414153   0.06802794 
-   49000    28.199573   -1.1887794    1.2781088    4.0779644    4.5881353    -2.319775  0.094803547 
-   50000    28.759212    -1.354416   0.68534569    3.8394841    4.2308134   -2.1281844    0.1395951 
-   51000    27.876455   -1.5705462   0.76557156    4.5335223     4.523708    -2.203702   0.14679803 
-   52000    27.930587   -1.2277489   0.96071516     3.960953    5.1152188   -2.4101451  0.060949521 
-   53000    27.031236   -1.4746477    1.2341141    5.0540975    4.3656865   -2.1288513  0.092725656 
-   54000    28.809394   -1.1162427   0.94350207    3.4013958    4.4755547   -2.3342811   0.18855912 
-   55000    28.948415   -1.1560418    0.6260139    3.5386373    4.5244978    -2.340212   0.17474657 
-   56000    28.048368  -0.95784532   0.76432571    4.1404665    4.4570033   -2.0899628  0.045693628 
-   57000    28.707642    -1.366574    0.9907873     3.729903    4.3131997   -2.2777698  0.065420213 
-   58000    26.361663   -1.0424403    1.0452563    5.0977108    4.7035231   -2.3101244   0.13671642 
-   59000    29.218218   -1.2210564   0.62435875    3.4236327    4.5481681   -2.1575943  0.037984042 
-   60000    27.655546   -1.1053224   0.86323501    3.7641375    4.8946898   -2.2422249  0.077725979 
-   61000    27.252108   -1.3744824    1.1150806    5.0444848    4.4878135   -2.2743829  0.058331257 
-   62000    27.163469   -1.1715781   0.72099321    4.5295501    4.9509918   -2.2993961  0.050401105 
-   63000    29.581575   -1.2238537   0.86303245    3.1194038    5.2218965   -2.5002427  0.055032632 
-   64000    27.897822   -1.1011516   0.74540883    4.2869228    4.3394269   -2.2552393    0.1403321 
-   65000    27.083245   -1.0633392   0.92771724    5.0805224    4.2747962   -2.2388039  0.064196692 
-   66000    29.072723   -1.5514209   0.89798805    4.2600224    4.4261812   -2.3524752   0.15067414 
-   67000    27.308181  -0.72224802   0.97109517    4.5074578    4.4559352   -2.1381121  0.089297603 
-   68000    27.505686  -0.43855431   0.80785812    4.1917251    5.0157721   -2.3382145   0.11105164 
-   69000    29.041681  -0.64735378   0.89874684    3.3891579    4.3753361   -2.2320941   0.14716747 
-   70000    29.735756   -1.7061457    0.9206878    3.5767878    4.3851664   -2.2516304  0.097196062 
-   71000    28.224352  -0.92217702   0.86093586    3.9507157    4.5596589   -2.2173397  0.089116669 
-   72000    29.282336    -1.056142   0.65185725    3.8735742    4.4839333   -2.4314756  0.071909704 
-   73000    26.257283  -0.64273826   0.98300685     5.063943     5.045958   -2.5544375    0.2180275 
-   74000    28.825119  -0.97736616   0.87201848      3.55875    4.3653309   -2.2303567  0.098963875 
-   75000    29.239507  -0.96508809   0.74517323    3.4306236    4.7651921   -2.6077732   0.17883654 
-   76000    27.349841  -0.50990238    1.1183613    4.4252451    4.4097775   -2.4125794   0.18483606 
-   77000    28.130197   -1.4081219   0.94921357    4.2572132    4.5162849   -2.4013797  0.073744606 
-   78000    28.235774   -0.9214321    0.6324981    3.8697686    4.8092154   -2.2272847  0.092108346 
-   79000    26.732846  -0.55949486    1.0989617    5.0088609    4.4930687    -2.277945   0.03855146 
-   80000    28.529208  -0.94244671   0.79407482     3.961106    4.3930011   -2.3127726  0.091124948 
-   81000    29.603852   -1.6116062     1.060847    3.7824932     4.151001   -1.9139868   0.19875986 
-   82000    28.232876   -1.1833011    1.0182713    3.4195758    5.1394333   -2.4632697   0.28501012 
-   83000    29.565482   -1.3479552   0.99056973    3.7851802    4.4781011   -2.7872481    0.2031991 
-   84000    28.780274   -1.3073882    1.0512637     4.004638     4.502282   -2.3789146  0.015656202 
-   85000    27.262312   -1.1305346     1.203524    4.7938623    4.1747105   -2.0952844  0.054240361 
-   86000    28.157348   -1.0662817   0.81163796    3.9912709    4.8320213    -2.255237   0.14698333 
-   87000    28.445543   -1.3365026   0.78156195    4.4767689    4.4457575   -2.5008786   0.13879386 
-   88000    27.656717   -1.1490599   0.87974869    4.4629952    4.7023033   -2.3258145  0.081904139 
-   89000    28.838821    -1.020709   0.85587929    3.7110705    4.4938307   -2.4914483   0.11447952 
-   90000    27.356497  -0.59107077   0.81879666    4.5209332    4.4703836   -2.3806717  0.071307775 
-   91000    27.780445  -0.80564513   0.94752313    3.8468943    4.2924253   -2.1011134    0.1118672 
-   92000    28.555276   -1.3514732   0.80826674    3.9590742    4.5775954   -2.4891232  0.054254978 
-   93000    28.747267   -1.2133243   0.75507246    4.1319789    4.9048611   -2.4913887   0.13045693 
-   94000    27.479343  -0.69973695   0.99696121    3.5966229     4.549025   -2.4155312   0.41745762 
-   95000    27.726945   -1.1905026    1.1120842    4.7433275    4.5386861   -2.7947142   0.33671682 
-   96000    28.021114   -1.0341645    0.6663033    4.2397505    4.6203984   -1.9904034   0.10972565 
-   97000    28.382022   -1.3916008     1.180588    4.0729621    4.6741792    -2.554927   0.13462346 
-   98000    27.895969   -0.7496449    1.3072185    4.2611888    4.3726077   -2.1320701   0.15376665 
-   99000    28.517889   -1.2183957     1.279778     3.957647    4.2638434   -2.2888407  0.042705003 
-  100000    28.109211   -1.2538948   0.83671785    4.3734766     4.544545   -2.3076497  0.042189096 
-Loop time of 2.84552 on 1 procs for 100000 steps with 34 atoms
-
-Performance: 6072.706 ns/day, 0.004 hours/ns, 35142.973 timesteps/s
-99.9% CPU use with 1 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
-Pair    | 0.94207    | 0.94207    | 0.94207    |   0.0 | 33.11
-Bond    | 1.6125     | 1.6125     | 1.6125     |   0.0 | 56.67
-Neigh   | 0.0073986  | 0.0073986  | 0.0073986  |   0.0 |  0.26
-Comm    | 0.012739   | 0.012739   | 0.012739   |   0.0 |  0.45
-Output  | 0.00075531 | 0.00075531 | 0.00075531 |   0.0 |  0.03
-Modify  | 0.21483    | 0.21483    | 0.21483    |   0.0 |  7.55
-Other   |            | 0.05524    |            |       |  1.94
-
-Nlocal:    34 ave 34 max 34 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Nghost:    0 ave 0 max 0 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-Neighs:    395 ave 395 max 395 min
-Histogram: 1 0 0 0 0 0 0 0 0 0
-
-Total # of neighbors = 395
-Ave neighs/atom = 11.6176
-Ave special neighs/atom = 9.52941
-Neighbor list builds = 237
-Dangerous builds = 0
-Total wall time: 0:00:02
--- a/examples/cmap/log.5Oct16.cmap.g++.4
+++ b/examples/cmap/log.5Oct16.cmap.g++.4
@ -1,201 +0,0 @@
-LAMMPS (5 Oct 2016)
-# Created by charmm2lammps v1.8.2.6 beta on Thu Mar  3 20:56:57 EST 2016
-
-units           real
-neigh_modify    delay 2 every 1
-#newton          off
-
-boundary        p p p
-
-atom_style      full
-bond_style      harmonic
-angle_style     charmm
-dihedral_style  charmm
-improper_style  harmonic
-
-pair_style      lj/charmm/coul/charmm 8 12
-#pair_style      lj/charmmfsw/coul/charmmfsh 8 12
-pair_modify     mix arithmetic
-
-fix             cmap all cmap charmm22.cmap
-Reading potential file charmm22.cmap with DATE: 2016-09-26
-fix_modify      cmap energy yes
-
-read_data       gagg.data fix cmap crossterm CMAP
-  orthogonal box = (-34.4147 -36.1348 -39.3491) to (45.5853 43.8652 40.6509)
-  1 by 2 by 2 MPI processor grid
-  reading atoms ...
-  34 atoms
-  scanning bonds ...
-  4 = max bonds/atom
-  scanning angles ...
-  6 = max angles/atom
-  scanning dihedrals ...
-  12 = max dihedrals/atom
-  scanning impropers ...
-  1 = max impropers/atom
-  reading bonds ...
-  33 bonds
-  reading angles ...
-  57 angles
-  reading dihedrals ...
-  75 dihedrals
-  reading impropers ...
-  7 impropers
-  4 = max # of 1-2 neighbors
-  7 = max # of 1-3 neighbors
-  13 = max # of 1-4 neighbors
-  16 = max # of special neighbors
-
-special_bonds   charmm
-fix             1 all nve
-
-#fix             1 all nvt temp 300 300 100.0
-#fix             2 all shake 1e-9 500 0 m 1.0
-
-velocity        all create 0.0 12345678 dist uniform
-
-thermo          1000
-thermo_style    custom step ecoul evdwl ebond eangle edihed f_cmap eimp
-timestep        2.0
-
-run             100000
-Neighbor list info ...
-  1 neighbor list requests
-  update every 1 steps, delay 2 steps, check yes
-  max neighbors/atom: 2000, page size: 100000
-  master list distance cutoff = 14
-  ghost atom cutoff = 14
-  binsize = 7 -> bins = 12 12 12
-Memory usage per processor = 15.9307 Mbytes
-Step E_coul E_vdwl E_bond E_angle E_dihed f_cmap E_impro 
-       0    26.542777  -0.93822087    1.2470497    4.8441789    4.5432816    -1.473352   0.10453023 
-    1000    28.673005  -0.47724367   0.80029132     3.151679    4.4684446   -2.3928648   0.18604953 
-    2000     27.67955    -1.170342   0.72018905    4.0400131    4.4713764   -2.5490207   0.21834436 
-    3000    29.256656  -0.35856055   0.73303546    3.7411606    4.4710568   -2.8939692   0.37728884 
-    4000    30.097549   -1.1353905   0.79007053    3.0688444    4.4091469   -2.3383587   0.20743631 
-    5000    28.357525   -1.0723742    0.9180297    3.6579424    4.8792663   -2.3185572  0.088366962 
-    6000    29.214175  -0.95299239   0.81926011    3.6805428    4.6742897   -2.9343578   0.26697816 
-    7000    27.018614  -0.52423469   0.72502751    3.8840141    4.7780958   -2.3916014   0.24952572 
-    8000    29.682494   -1.0940368   0.76113051    3.1089345    4.9357863   -2.5662256   0.14112613 
-    9000    27.853918   -0.7913741   0.79503268    4.2177256     4.146792     -2.00475  0.090585666 
-   10000     27.13754  -0.80551128    1.1325023    4.4718283    5.2460631   -3.4947725   0.11893125 
-   11000    28.277434   -1.4897448   0.90075953    4.1895717    4.3594269   -1.9553119  0.090222212 
-   12000    28.630973    -1.222206   0.67796385    3.3905661    4.9691334   -2.9052721   0.13897658 
-   13000    28.593007  -0.95684026   0.75585196    3.7242568    4.7417932   -2.3893117    0.2074121 
-   14000    26.147115   -0.6026921   0.93591488    5.1292829    4.9821952   -2.2571835   0.11872421 
-   15000     26.29432  -0.82424162     1.048979    4.5569495    5.1189308   -2.9750422   0.16195676 
-   16000    29.189992  -0.80998247   0.74093508    3.8299275    4.4536688   -2.5497538   0.19155639 
-   17000    25.878012   -0.3519646    1.0988924    4.7359591    5.3923098   -2.7211029   0.13405223 
-   18000    27.726135  -0.28229987   0.63072344    4.1777888    4.7237271   -2.2177157   0.15939372 
-   19000    27.153504  -0.66477422   0.77910129    4.2036117     5.113851   -2.3494315  0.094793307 
-   20000    28.044833   -1.2835827   0.88745367    3.9955526    4.5077788   -3.0116467   0.17197859 
-   21000    27.205696  -0.74090037    1.0023251    4.3421733     4.912671   -2.3473271   0.26089356 
-   22000    27.385785  -0.93740972   0.84554838     4.562743     4.883866   -2.2110955   0.11573301 
-   23000     27.05534  -0.95605442   0.96719024    3.9277618    5.0359014   -2.6135949   0.21368061 
-   24000    28.273378  -0.97543103    0.8983443    4.2067985    4.4782971   -2.4230505   0.30311692 
-   25000    27.477789  -0.20383849    0.8380706    3.8037992    4.8312504   -2.5831791  0.093843746 
-   26000    30.344199   -1.9773473   0.92882437    3.7821405    4.5176677   -2.3020968    0.2194307 
-   27000     27.32767   -0.9803839   0.92988865    3.7611603    5.0328211   -2.4647656   0.18213622 
-   28000     27.34208    -1.037938   0.74488346    4.1727342    4.7056812   -2.2718346   0.17741362 
-   29000    27.682777  -0.51006495   0.57074224    4.7332237    4.7080462   -2.0491512    0.2130517 
-   30000    24.925731   0.13670248   0.84976065    4.4143762    6.0677158   -3.5479173   0.28059419 
-   31000    28.623419  -0.90725708    1.0710501    3.6930688    4.6639301   -2.2225373   0.20988139 
-   32000    27.732286   -1.1948367   0.89230134    4.4398373    4.8923907   -3.5849327   0.49167488 
-   33000    28.800772   -1.5319589   0.93455495    4.1634728    4.6107706   -2.3503486   0.22636535 
-   34000    27.374398   -1.0957453   0.89450276    3.9829508     4.991786   -2.3548834   0.15869465 
-   35000     28.38753  -0.89261166   0.90000776     3.536864    4.4293294   -2.4218118   0.10640557 
-   36000    27.713974  0.088038031   0.85190574    3.8969601    4.6256355   -2.7935475   0.34671662 
-   37000     29.13007    -1.378597   0.74412556     3.131538    4.6458653   -2.9373734   0.38035616 
-   38000    28.556573   -1.4055344     1.139984    4.0035753    4.2938358    -2.489329   0.25338326 
-   39000    26.447036   -1.1829705   0.87032438    5.0804461    4.5772023   -2.7346466   0.32165802 
-   40000    27.991454  -0.64295679   0.61020872     4.165871    4.4623087   -2.2244194   0.13826991 
-   41000    29.483296   -1.2400745   0.66926627    3.3473666    4.5766617   -2.3051145   0.12171554 
-   42000    26.948627   -1.2162288    1.1440628    4.3993073    5.1176533   -2.4734485   0.15497709 
-   43000     28.04459  -0.26543193   0.83647367    3.5160747    4.6964397   -2.2805068   0.12618821 
-   44000    28.213608    -1.216128    0.9132792    4.0206483    4.9483599   -2.3387049   0.10132022 
-   45000    28.283506   -1.0390766   0.86113772     4.504509    4.7209088   -2.3043085   0.14588362 
-   46000    27.433853  -0.57912107   0.78448334    4.5998579    5.1181394   -2.6165094   0.18722528 
-   47000    27.552939   -1.1128925   0.80087638    4.3448001    4.8062869   -2.4296883    0.2702479 
-   48000    28.874034   -1.3242519   0.71770727    3.5648565    4.4671824   -2.2608958   0.16115978 
-   49000    29.216186   -1.2210307   0.76937497    3.9260628    4.7550577   -2.7316081  0.085505664 
-   50000    28.065856   -1.1545547   0.86953819    4.4137666     4.732157   -2.4450867   0.23320539 
-   51000    26.308975  -0.99728352   0.90408444    4.2400186    5.6340425   -2.2090554  0.079882158 
-   52000    28.517571   -1.5027398   0.83520278    3.8176552    4.3001251   -2.0731682    0.1665375 
-   53000     28.77579   -1.3564268   0.97253881    3.6866407    4.8532347   -2.5330776   0.17668411 
-   54000    29.135315   -1.0994106   0.67605671    3.6819254    4.3134408   -1.9796929  0.076951331 
-   55000    26.168938  -0.76247492   0.88784685    4.6533473    6.0484793   -2.1334561  0.036876985 
-   56000    27.471775  -0.68648837    1.0576168    4.0354311    4.4767052   -2.2368959   0.24950568 
-   57000    29.787083   -1.4914384    1.0702944    3.5388133    4.5173097   -2.6694464   0.27937092 
-   58000    28.705448   -1.3016617   0.63337853    3.9552713    4.4119825   -1.8774657   0.17540021 
-   59000    29.130155  -0.91647363   0.84384883    3.1076903    4.5346348   -2.3457338   0.16674486 
-   60000    26.874199  -0.81598034    1.3432151    5.1322624    4.9545484   -2.9566615   0.25950486 
-   61000    27.401306  -0.82895856    1.1636949     4.020154    4.5745928    -2.601466   0.18061051 
-   62000    28.930313   -1.5231967   0.85173243    4.3517328    4.4878662   -2.5859205    0.1755493 
-   63000     26.56874  0.026147233   0.60836216    4.4231618    4.4390677   -2.1721849   0.08594237 
-   64000    26.729023  -0.76953985   0.76734633    4.5104288    5.0886456   -2.2118551   0.11339216 
-   65000    28.900471   -1.3901477   0.86194657    4.2774976     4.498325   -2.3672362   0.20668335 
-   66000    26.884253  -0.21198879   0.98509625    4.0843117    4.4344172   -2.3289416   0.23631017 
-   67000    27.210888  -0.84075559    1.0396559    4.7253607    4.4314589   -2.2985702   0.19326507 
-   68000    28.042102   -1.1898715     1.053534    3.8748712    4.4358449   -2.3998723    0.2431659 
-   69000    28.939141   -1.6968936   0.98155912    4.0460838    5.0075204   -2.5547087   0.28645131 
-   70000     27.15577  -0.85202797    1.1469079    4.7645212    4.6133209   -2.3410451  0.086576572 
-   71000    25.507417  -0.27780727   0.95157881    4.8759406     4.853401   -2.9598705   0.41011008 
-   72000    29.804703   -1.4847015   0.96345767    3.6797304    4.3678377   -2.4594626   0.14480206 
-   73000    28.602798   -1.4906143   0.72497266    4.2442974    4.5360598   -2.3621638   0.14385651 
-   74000      28.4928  -0.91319873    1.0377472    3.8033127    4.3991601   -2.4051911  0.095567428 
-   75000     26.38168  -0.70733237    1.1557817     5.697939    4.5935618   -2.4285007  0.058980519 
-   76000     27.16626  -0.83631031   0.84844246    4.7460887    4.5801472   -2.1260014   0.12845946 
-   77000    29.040661   -1.3089499   0.80285084     4.664804    4.5215895   -2.6861939   0.13215598 
-   78000    27.477871   -1.0600977   0.88595045    4.6264017    5.4095605    -2.474411   0.10987174 
-   79000    26.151797  -0.55779685   0.91382436      4.99964    4.9184022   -2.2547241   0.22854038 
-   80000     28.14523  -0.54460026    0.8982411    3.5374555    4.3785673   -2.3196807  0.088567964 
-   81000    29.029941   -1.6467789   0.79042284    3.7269899    4.7407998   -2.3795824    0.1408727 
-   82000    27.920287  -0.72798032    1.0076975    3.4449461    4.5621371   -2.8239074   0.25103454 
-   83000    29.131054    -1.114367   0.76887285     3.459639    4.5163922    -2.607825   0.19991648 
-   84000    28.249768  -0.69944068    1.0510846    4.0436296    4.6430538   -2.4213355  0.077299966 
-   85000     28.06888  -0.62132922   0.91829312    4.1294147    4.3099557    -2.354063   0.15866186 
-   86000    28.664264   -1.1022906   0.87831695    4.5773522    4.6045802   -2.9206875   0.33950063 
-   87000    27.960967   -1.2852756   0.77694253    3.9011301    4.9114139   -3.2374868    0.3068138 
-   88000    27.190678   -1.2803268    1.1545301    4.5769709    5.2404761   -2.3825838   0.10356039 
-   89000    26.792931  -0.44516641    1.0236244    4.2007253    4.7098685   -2.3608551  0.034447062 
-   90000    27.173991  -0.87185611     1.065719    4.1953618    4.6856408   -2.6539232   0.16957757 
-   91000    28.626528    -1.239257   0.89524651    4.7048012    4.6344201   -2.7367901   0.43534143 
-   92000    27.661812    -1.109044   0.92817391    5.0294489    4.3890711   -2.4108669   0.12570139 
-   93000    28.156793   -1.0820907   0.92812693     4.938385    4.4901426   -2.4023366   0.30135781 
-   94000    28.842149   -1.3524969    1.1451109    4.3125908    4.6959035   -2.6747199    0.2254607 
-   95000    27.862247   -1.2119045    1.0218976    4.2614082    4.4931316   -2.6902934   0.16345201 
-   96000    27.084973  -0.93738328    1.3984324    4.5647189    4.4232205   -2.2834097   0.11217888 
-   97000    27.587078  -0.89397255   0.78218462    3.8944421    4.3981479   -2.4205318   0.16570942 
-   98000    27.981746   -1.2380545   0.84847869     4.311441    4.7340377   -2.4270441  0.023565612 
-   99000    27.476625   -0.8569146   0.82550381    4.1656963    4.4064921   -2.4169708     0.160814 
-  100000    26.121325  -0.63610855    1.0803389    4.9257118    4.7073263   -2.4010334  0.066303044 
-Loop time of 2.693 on 4 procs for 100000 steps with 34 atoms
-
-Performance: 6416.646 ns/day, 0.004 hours/ns, 37133.367 timesteps/s
-98.4% CPU use with 4 MPI tasks x no OpenMP threads
-
-MPI task timing breakdown:
-Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
-Pair    | 0.065478   | 0.2501     | 0.63682    |  45.6 |  9.29
-Bond    | 0.066944   | 0.44772    | 0.88814    |  53.7 | 16.63
-Neigh   | 0.0076509  | 0.0077319  | 0.0078275  |   0.1 |  0.29
-Comm    | 0.57917    | 1.4166     | 1.9823     |  46.9 | 52.60
-Output  | 0.0033755  | 0.0035856  | 0.0037644  |   0.2 |  0.13
-Modify  | 0.03866    | 0.1366     | 0.23978    |  24.6 |  5.07
-Other   |            | 0.4306     |            |       | 15.99
-
-Nlocal:    8.5 ave 15 max 2 min
-Histogram: 1 1 0 0 0 0 0 0 1 1
-Nghost:    25.5 ave 32 max 19 min
-Histogram: 1 1 0 0 0 0 0 0 1 1
-Neighs:    98.75 ave 257 max 18 min
-Histogram: 1 1 1 0 0 0 0 0 0 1
-
-Total # of neighbors = 395
-Ave neighs/atom = 11.6176
-Ave special neighs/atom = 9.52941
-Neighbor list builds = 294
-Dangerous builds = 0
-Total wall time: 0:00:02
--- a/lib/voronoi/Install.py
+++ b/lib/voronoi/Install.py
@ -0,0 +1,116 @@
+#!/usr/bin/env python
+
+# install.py tool to download, unpack, build, and link to the Voro++ library
+# used to automate the steps described in the README file in this dir
+
+import sys,os,re,urllib,commands
+
+# help message
+
+help = """
+Syntax: install.py -v version -g gdir [gname] -b bdir -l ldir
+  specify one or more options, order does not matter
+  gdir,bdir,ldir can be paths relative to lib/latte, full paths, or contain ~
+  -v = version of Voro++ to download and build
+       default = voro++-0.4.6 (current as of Jan 2015)
+  -g = grab (download) from math.lbl.gov/voro++ website
+       unpack tarfile in gdir to produce version dir (e.g. voro++-0.4.6)
+       if optional gname specified, rename version dir to gname within gdir
+  -b = build Voro++, bdir = Voro++ home directory
+       note that bdir must include the version suffix unless renamed
+  -l = create 2 softlinks (includelink,liblink)
+         in lib/voronoi to src dir of ldir = Voro++ home directory
+       note that ldir must include the version suffix unless renamed
+"""
+
+# settings
+
+version = "voro++-0.4.6"
+url = "http://math.lbl.gov/voro++/download/dir/%s.tar.gz" % version
+
+# print error message or help
+
+def error(str=None):
+  if not str: print help
+  else: print "ERROR",str
+  sys.exit()
+
+# expand to full path name
+# process leading '~' or relative path
+  
+def fullpath(path):
+  return os.path.abspath(os.path.expanduser(path))
+  
+# parse args
+
+args = sys.argv[1:]
+nargs = len(args)
+if nargs == 0: error()
+
+grabflag = 0
+buildflag = 0
+linkflag = 0
+
+iarg = 0
+while iarg < nargs:
+  if args[iarg] == "-v":
+    if iarg+2 > nargs: error()
+    version = args[iarg+1]
+    iarg += 2  
+  elif args[iarg] == "-g":
+    if iarg+2 > nargs: error()
+    grabflag = 1
+    grabdir = args[iarg+1]
+    grabname = None
+    if iarg+2 < nargs and args[iarg+2][0] != '-':
+      grabname = args[iarg+2]
+      iarg += 1
+    iarg += 2
+  elif args[iarg] == "-b":
+    if iarg+2 > nargs: error()
+    buildflag = 1
+    builddir = args[iarg+1]
+    iarg += 2
+  elif args[iarg] == "-l":
+    if iarg+2 > nargs: error()
+    linkflag = 1
+    linkdir = args[iarg+1]
+    iarg += 2
+  else: error()
+
+# download and unpack Voro++ tarball
+
+if grabflag:
+  print "Downloading Voro++ ..."
+  grabdir = fullpath(grabdir)
+  if not os.path.isdir(grabdir): error("Grab directory does not exist")
+  urllib.urlretrieve(url,"%s/%s.tar.gz" % (grabdir,version))
+  
+  print "Unpacking Voro++ tarball ..."
+  tardir = "%s/%s" % (grabdir,version)
+  if os.path.exists(tardir): commands.getoutput("rm -rf %s" % tardir)
+  cmd = "cd %s; tar zxvf %s.tar.gz" % (grabdir,version)
+  txt = commands.getoutput(cmd)
+  print tardir,grabdir,grabname
+  if grabname: os.rename(tardir,"%s/%s" % (grabdir,grabname))
+
+# build Voro++
+
+if buildflag:
+  print "Building Voro++ ..."
+  cmd = "cd %s; make" % builddir
+  txt = commands.getoutput(cmd)
+  print txt
+
+# create 2 links in lib/voronoi to Voro++ src dir
+
+if linkflag:
+  print "Creating links to Voro++ include and lib files"
+  if os.path.isfile("includelink") or os.path.islink("includelink"):
+    os.remove("includelink")
+  if os.path.isfile("liblink") or os.path.islink("liblink"):
+    os.remove("liblink")
+  cmd = "ln -s %s/src includelink" % linkdir
+  commands.getoutput(cmd)
+  cmd = "ln -s %s/src liblink" % linkdir
+  commands.getoutput(cmd)
--- a/lib/voronoi/README
+++ b/lib/voronoi/README
@ -9,8 +9,8 @@ Laboratory.
 -----------------

 You must perform the following steps yourself, or you can use the
-install.py Python script to automate any or all steps of the process.
-Type "python install.py" for instructions.
+Install.py Python script to automate any or all steps of the process.
+Type "python Install.py" for instructions.

 1.  Download Voro++ at http://math.lbl.gov/voro++/download
    either as a tarball or via SVN, and unpack the
--- a/lib/voronoi/install.py
+++ b/lib/voronoi/install.py
@ -1,163 +0,0 @@
-#!usr/local/python
-
-# install.py tool to download, unpack, build, and link to the Voro++ library
-# used to automate the steps described in the README file in this dir
-
-import sys,os,re,urllib,commands
-
-help = """
-Syntax: install.py -d dir -v version -g -b -i installdir -l incdir libdir
-        specify one or more options, order does not matter
-        -d = dir to download tarball to, unpack tarball in, perform build in
-             dir will be created if it doesn't exist (only last level)
-             default = this dir
-        -v = version of Voro++ to download and work with
-             default = voro++-0.4.6 (current as of Jan 2015)
-        -g = download (grab) tarball from
-             http://math.lbl.gov/voro++/download/dir/version
-        -b = build Voro++ by invoking "make" in its home dir
-             no default
-        -i = install Voro++ by invoking "make install" in its home dir
-             installdir arg is optional:
-               if not specified, installs at PREFIX defined in config.mk file
-               if specified, will overwrite PREFIX and install there
-             if PREFIX starts with /usr, will invoke "sudo make install"
-        -l = create two links to incdir and libdir
-             incdir and libdir are optional (specify neither or both):
-               if specified, includelink and liblink are to those two dirs
-                 these are dirs where Voro++ include files and lib file are
-               if not specified and no install, links are to Voro++ src dir
-               if not specified and install performed,
-                 links are to include and lib dirs under PREFIX
-"""
-
-def error():
-  print help
-  sys.exit()
-  
-# parse args
-
-args = sys.argv
-
-if len(args) == 1: error()
-
-dir = "."
-version = "voro++-0.4.6"
-grabflag = 0
-buildflag = 0
-installflag = 0
-linkflag = 0
-
-iarg = 1
-while iarg < len(args):
-  if args[iarg] == "-d":
-    if iarg+2 > len(args): error()
-    dir = args[iarg+1]
-    iarg += 2  
-  elif args[iarg] == "-v":
-    if iarg+2 > len(args): error()
-    version = args[iarg+1]
-    iarg += 2  
-  elif args[iarg] == "-g":
-    grabflag = 1
-    iarg += 1
-  elif args[iarg] == "-b":
-    buildflag = 1
-    iarg += 1
-  elif args[iarg] == "-i":
-    installflag = 1
-    if iarg+1 == len(args) or args[iarg+1][0] == '-':
-      installdir = ""
-      iarg += 1
-    else:
-      if iarg+2 > len(args): error()
-      installdir = args[iarg+1]
-      iarg += 2  
-  elif args[iarg] == "-l":
-    linkflag = 1
-    if iarg+1 == len(args) or args[iarg+1][0] == '-' or \
-          iarg+2 == len(args) or args[iarg+2][0] == '-':
-      includedir = libdir = ""
-      iarg += 1
-    else:
-      if iarg+3 > len(args): error()
-      includedir = args[iarg+1]
-      libdir = args[iarg+2]
-      iarg += 3
-  else: error()
-
-dir = os.path.abspath(dir)
-url = "http://math.lbl.gov/voro++/download/dir/%s.tar.gz" % version
-
-# create dir if does not exist
-
-if not os.path.isdir(dir):
-  if os.path.isfile(dir):
-    print "ERROR: Dir already exists as file"
-    sys.exit()
-  os.mkdir(dir)
-  if not os.path.isdir(dir):
-    print "ERROR: Unable to create dir"
-    sys.exit()
-
-# download and unpack tarball
-
-if grabflag:
-  print "Downloading Voro++ tarball ..."
-  urllib.urlretrieve(url,"%s/%s.tar.gz" % (dir,version))
-  print "Unpacking Voro++ tarball ..."
-  cmd = "cd %s; tar zxvf %s.tar.gz" % (dir,version)
-  txt = commands.getoutput(cmd)
-
-# build Voro++ in its dir
-
-if buildflag:
-  print "Building Voro++ ..."
-  cmd = "cd %s/%s; make" % (dir,version)
-  txt = commands.getoutput(cmd)
-  print txt
-
-# install Voro++
-# if installdir set, overwrite PREFIX var in its config.mk file
-# if PREFIX var starts with /usr, invoke sudo make install, else make install
-  
-if installflag:
-  print "Installing Voro++ ..."
-  if installdir:
-    txt = open("%s/%s/config.mk" % (dir,version),'r').read()
-    txt = re.sub("PREFIX=.*?\n","PREFIX=%s\n" % installdir,txt)
-    open("%s/%s/config.mk" % (dir,version),'w').write(txt)
-    print "TXT:",txt
-  txt = open("%s/%s/config.mk" % (dir,version),'r').read()
-  var = re.findall("PREFIX=.*?\n",txt)
-  prefix = var[0].split('=')[1].strip()
-  if prefix.startswith("/usr"):
-    cmd = "cd %s/%s; sudo make install" % (dir,version)
-  else:
-    cmd = "cd %s/%s; make install" % (dir,version)
-  txt = commands.getoutput(cmd)
-  print txt
-  
-# create links in this dir to Voro++ include and lib files
-
-if linkflag:
-  print "Creating links to Voro++ include and lib files"
-  if os.path.isfile("includelink") or os.path.islink("includelink"):
-    os.remove("includelink")
-  if os.path.isfile("liblink") or os.path.islink("liblink"):
-    os.remove("liblink")
-  if includedir:
-    cmd = "ln -s %s includelink" % includedir
-    txt = commands.getoutput(cmd)
-    cmd = "ln -s %s liblink" % linkdir
-    txt = commands.getoutput(cmd)
-  elif not installflag:
-    cmd = "ln -s %s/%s/src includelink" % (dir,version)
-    txt = commands.getoutput(cmd)
-    cmd = "ln -s %s/%s/src liblink" % (dir,version)
-    txt = commands.getoutput(cmd)
-  else:
-    cmd = "ln -s %s/include includelink" % prefix
-    txt = commands.getoutput(cmd)
-    cmd = "ln -s %s/lib liblink" % prefix
-    txt = commands.getoutput(cmd)
--- a/src/ASPHERE/compute_temp_asphere.cpp
+++ b/src/ASPHERE/compute_temp_asphere.cpp
@ -73,6 +73,11 @@ ComputeTempAsphere::ComputeTempAsphere(LAMMPS *lmp, int narg, char **arg) :
    } else error->all(FLERR,"Illegal compute temp/asphere command");
  }

+  // when computing only the rotational temperature,
+  // do not remove DOFs for translation as set by default
+
+  if (mode == ROTATE) extra_dof = 0;
+
  vector = new double[6];

 }
--- a/src/COMPRESS/Install.sh
+++ b/src/COMPRESS/Install.sh
@ -29,7 +29,7 @@ action () {
 # all package files with no dependencies

 for file in *.cpp *.h; do
-  action $file
+  test -f ${file} && action $file
 done

 # edit 2 Makefile.package files to include/exclude package info
--- a/src/Install.sh
+++ b/src/Install.sh
@ -33,5 +33,5 @@ action () {
 # all package files with no dependencies

 for file in *.cpp *.h; do
-  action $file
+  test -f ${file} && action $file
 done
--- a/src/KIM/Install.sh
+++ b/src/KIM/Install.sh
@ -29,7 +29,7 @@ action () {
 # all package files with no dependencies

 for file in *.cpp *.h; do
-  action $file
+  test -f ${file} && action $file
 done

 # edit 2 Makefile.package files to include/exclude package info
--- a/src/MC/fix_gcmc.cpp
+++ b/src/MC/fix_gcmc.cpp
@ -60,7 +60,7 @@ using namespace MathConst;
 // this must be lower than MAXENERGYSIGNAL
 // by a large amount, so that it is still
 // less than total energy when negative
-// energy changes are added to MAXENERGYSIGNAL
+// energy contributions are added to MAXENERGYSIGNAL

 #define MAXENERGYTEST 1.0e50

@ -701,6 +701,9 @@ void FixGCMC::pre_exchange()

  if (full_flag) {
    energy_stored = energy_full();
+    if (overlap_flag && energy_stored > MAXENERGYTEST)
+        error->warning(FLERR,"Energy of old configuration in "
+                       "fix gcmc is > MAXENERGYTEST.");

    if (mode == MOLECULE) {
      for (int i = 0; i < ncycles; i++) {
@ -778,6 +781,9 @@ void FixGCMC::attempt_atomic_translation()
  if (i >= 0) {
    double **x = atom->x;
    double energy_before = energy(i,ngcmc_type,-1,x[i]);
+    if (overlap_flag && energy_before > MAXENERGYTEST)
+        error->warning(FLERR,"Energy of old configuration in "
+                       "fix gcmc is > MAXENERGYTEST.");
    double rsq = 1.1;
    double rx,ry,rz;
    rx = ry = rz = 0.0;
@ -998,6 +1004,9 @@ void FixGCMC::attempt_molecule_translation()
  if (translation_molecule == -1) return;

  double energy_before_sum = molecule_energy(translation_molecule);
+  if (overlap_flag && energy_before_sum > MAXENERGYTEST)
+    error->warning(FLERR,"Energy of old configuration in "
+                   "fix gcmc is > MAXENERGYTEST.");

  double **x = atom->x;
  double rx,ry,rz;
@ -1095,6 +1104,9 @@ void FixGCMC::attempt_molecule_rotation()
  if (rotation_molecule == -1) return;

  double energy_before_sum = molecule_energy(rotation_molecule);
+  if (overlap_flag && energy_before_sum > MAXENERGYTEST)
+    error->warning(FLERR,"Energy of old configuration in "
+                   "fix gcmc is > MAXENERGYTEST.");

  int nlocal = atom->nlocal;
  int *mask = atom->mask;
@ -2170,6 +2182,8 @@ double FixGCMC::molecule_energy(tagint gas_molecule_id)

 double FixGCMC::energy_full()
 {
+  int imolecule;
+  
  if (triclinic) domain->x2lamda(atom->nlocal);
  domain->pbc();
  comm->exchange();
@ -2185,14 +2199,15 @@ double FixGCMC::energy_full()
  // return signal value for energy 

  if (overlap_flag) {
+    int overlaptestall;
+    int overlaptest = 0;
    double delx,dely,delz,rsq;
    double **x = atom->x;
    tagint *molecule = atom->molecule;
    int nall = atom->nlocal + atom->nghost;
    for (int i = 0; i < atom->nlocal; i++) {
-      int imolecule = molecule[i];
+      if (mode == MOLECULE) imolecule = molecule[i];
      for (int j = i+1; j < nall; j++) {
-
        if (mode == MOLECULE)
          if (imolecule == molecule[j]) continue;
      
@ -2201,9 +2216,16 @@ double FixGCMC::energy_full()
        delz = x[i][2] - x[j][2];
        rsq = delx*delx + dely*dely + delz*delz;
      
-        if (rsq < overlap_cutoff) return MAXENERGYSIGNAL;
+        if (rsq < overlap_cutoff) {
+          overlaptest = 1;
+          break;
        }
      }
+      if (overlaptest) break;
+    }
+    MPI_Allreduce(&overlaptest, &overlaptestall, 1,
+                  MPI_INT, MPI_MAX, world);
+    if (overlaptestall) return MAXENERGYSIGNAL;
  }

  // clear forces so they don't accumulate over multiple
--- a/src/MC/fix_gcmc.h
+++ b/src/MC/fix_gcmc.h
@ -106,7 +106,7 @@ class FixGCMC : public Fix {
  double xlo,xhi,ylo,yhi,zlo,zhi;
  double region_xlo,region_xhi,region_ylo,region_yhi,region_zlo,region_zhi;
  double region_volume;
-  double energy_stored;
+  double energy_stored;  // full energy of old/current configuration
  double *sublo,*subhi;
  int *local_gas_list;
  double **cutsq;
@ -214,9 +214,14 @@ W: Fix gcmc using full_energy option

 Fix gcmc has automatically turned on the full_energy option since it
 is required for systems like the one specified by the user. User input
-included one or more of the following: kspace, triclinic, a hybrid
-pair style, an eam pair style, or no "single" function for the pair
-style.
+included one or more of the following: kspace, a hybrid
+pair style, an eam pair style, tail correction, 
+or no "single" function for the pair style.
+
+W: Energy of old configuration in fix gcmc is > MAXENERGYTEST. 
+
+This probably means that a pair of atoms are closer than the 
+overlap cutoff distance for keyword overlap_cutoff.

 E: Invalid atom type in fix gcmc command

--- a/src/MEAM/Install.sh
+++ b/src/MEAM/Install.sh
@ -29,7 +29,7 @@ action () {
 # all package files with no dependencies

 for file in *.cpp *.h; do
-  action $file
+  test -f ${file} && action $file
 done

 # edit 2 Makefile.package files to include/exclude package info
--- a/src/MOLECULE/bond_harmonic.cpp
+++ b/src/MOLECULE/bond_harmonic.cpp
@ -13,6 +13,7 @@

 #include <math.h>
 #include <stdlib.h>
+#include <string.h>
 #include "bond_harmonic.h"
 #include "atom.h"
 #include "neighbor.h"
@ -26,7 +27,10 @@ using namespace LAMMPS_NS;

 /* ---------------------------------------------------------------------- */

-BondHarmonic::BondHarmonic(LAMMPS *lmp) : Bond(lmp) {}
+BondHarmonic::BondHarmonic(LAMMPS *lmp) : Bond(lmp)
+{
+  reinitflag = 1;
+}

 /* ---------------------------------------------------------------------- */

@ -196,3 +200,16 @@ double BondHarmonic::single(int type, double rsq, int i, int j,
  if (r > 0.0) fforce = -2.0*rk/r;
  return rk*dr;
 }
+
+/* ----------------------------------------------------------------------
+    Return ptr to internal members upon request.
+------------------------------------------------------------------------ */
+void *BondHarmonic::extract( char *str, int &dim )
+{
+  dim = 1;
+  if( strcmp(str,"kappa")==0) return (void*) k;
+  if( strcmp(str,"r0")==0) return (void*) r0;
+  return NULL;
+}
+
+
--- a/src/MOLECULE/bond_harmonic.h
+++ b/src/MOLECULE/bond_harmonic.h
@ -36,6 +36,7 @@ class BondHarmonic : public Bond {
  void read_restart(FILE *);
  void write_data(FILE *);
  double single(int, double, int, int, double &);
+  virtual void *extract(char *, int &);

 protected:
  double *k,*r0;
--- a/src/MOLECULE/dihedral_charmmfsw.cpp
+++ b/src/MOLECULE/dihedral_charmmfsw.cpp
@ -21,7 +21,7 @@
 #include <mpi.h>
 #include <math.h>
 #include <stdlib.h>
-#include "dihedral_charmmfsh.h"
+#include "dihedral_charmmfsw.h"
 #include "atom.h"
 #include "comm.h"
 #include "neighbor.h"
@ -40,7 +40,7 @@ using namespace MathConst;

 /* ---------------------------------------------------------------------- */

-DihedralCharmmfsh::DihedralCharmmfsh(LAMMPS *lmp) : Dihedral(lmp)
+DihedralCharmmfsw::DihedralCharmmfsw(LAMMPS *lmp) : Dihedral(lmp)
 {
  weightflag = 0;
  writedata = 1;
@ -48,7 +48,7 @@ DihedralCharmmfsh::DihedralCharmmfsh(LAMMPS *lmp) : Dihedral(lmp)

 /* ---------------------------------------------------------------------- */

-DihedralCharmmfsh::~DihedralCharmmfsh()
+DihedralCharmmfsw::~DihedralCharmmfsw()
 {
  if (allocated && !copymode) {
    memory->destroy(setflag);
@ -63,7 +63,7 @@ DihedralCharmmfsh::~DihedralCharmmfsh()

 /* ---------------------------------------------------------------------- */

-void DihedralCharmmfsh::compute(int eflag, int vflag)
+void DihedralCharmmfsw::compute(int eflag, int vflag)
 {
  int i1,i2,i3,i4,i,m,n,type;
  double vb1x,vb1y,vb1z,vb2x,vb2y,vb2z,vb3x,vb3y,vb3z,vb2xm,vb2ym,vb2zm;
@ -322,7 +322,7 @@ void DihedralCharmmfsh::compute(int eflag, int vflag)

 /* ---------------------------------------------------------------------- */

-void DihedralCharmmfsh::allocate()
+void DihedralCharmmfsw::allocate()
 {
  allocated = 1;
  int n = atom->ndihedraltypes;
@ -342,7 +342,7 @@ void DihedralCharmmfsh::allocate()
   set coeffs for one type
 ------------------------------------------------------------------------- */

-void DihedralCharmmfsh::coeff(int narg, char **arg)
+void DihedralCharmmfsw::coeff(int narg, char **arg)
 {
  if (narg != 5) error->all(FLERR,"Incorrect args for dihedral coefficients");
  if (!allocated) allocate();
@ -384,7 +384,7 @@ void DihedralCharmmfsh::coeff(int narg, char **arg)
   error check and initialize all values needed for force computation
 ------------------------------------------------------------------------- */

-void DihedralCharmmfsh::init_style()
+void DihedralCharmmfsw::init_style()
 {
  // insure use of CHARMM pair_style if any weight factors are non-zero
  // set local ptrs to LJ 14 arrays setup by Pair
@ -392,14 +392,14 @@ void DihedralCharmmfsh::init_style()
  if (weightflag) {
    int itmp;
    if (force->pair == NULL)
-      error->all(FLERR,"Dihedral charmmfsh is incompatible with Pair style");
+      error->all(FLERR,"Dihedral charmmfsw is incompatible with Pair style");
    lj14_1 = (double **) force->pair->extract("lj14_1",itmp);
    lj14_2 = (double **) force->pair->extract("lj14_2",itmp);
    lj14_3 = (double **) force->pair->extract("lj14_3",itmp);
    lj14_4 = (double **) force->pair->extract("lj14_4",itmp);
    int *ptr = (int *) force->pair->extract("implicit",itmp);
    if (!lj14_1 || !lj14_2 || !lj14_3 || !lj14_4 || !ptr)
-      error->all(FLERR,"Dihedral charmmfsh is incompatible with Pair style");
+      error->all(FLERR,"Dihedral charmmfsw is incompatible with Pair style");
    implicit = *ptr;
  }

@ -414,7 +414,7 @@ void DihedralCharmmfsh::init_style()
  
  if (p_cutcoul == NULL || p_cutljinner == NULL || 
      p_cutlj == NULL || p_dihedflag == NULL)
-    error->all(FLERR,"Dihedral charmmfsh is incompatible with Pair style");
+    error->all(FLERR,"Dihedral charmmfsw is incompatible with Pair style");
  
  dihedflag = *p_dihedflag;
  cut_coul14 = *p_cutcoul;
@ -433,7 +433,7 @@ void DihedralCharmmfsh::init_style()
   proc 0 writes out coeffs to restart file
 ------------------------------------------------------------------------- */

-void DihedralCharmmfsh::write_restart(FILE *fp)
+void DihedralCharmmfsw::write_restart(FILE *fp)
 {
  fwrite(&k[1],sizeof(double),atom->ndihedraltypes,fp);
  fwrite(&multiplicity[1],sizeof(int),atom->ndihedraltypes,fp);
@ -446,7 +446,7 @@ void DihedralCharmmfsh::write_restart(FILE *fp)
   proc 0 reads coeffs from restart file, bcasts them
 ------------------------------------------------------------------------- */

-void DihedralCharmmfsh::read_restart(FILE *fp)
+void DihedralCharmmfsw::read_restart(FILE *fp)
 {
  allocate();

@ -474,7 +474,7 @@ void DihedralCharmmfsh::read_restart(FILE *fp)
   proc 0 writes to data file
 ------------------------------------------------------------------------- */

-void DihedralCharmmfsh::write_data(FILE *fp)
+void DihedralCharmmfsw::write_data(FILE *fp)
 {
  for (int i = 1; i <= atom->ndihedraltypes; i++)
    fprintf(fp,"%d %g %d %d %g\n",i,k[i],multiplicity[i],shift[i],weight[i]);
--- a/src/MOLECULE/dihedral_charmmfsw.h
+++ b/src/MOLECULE/dihedral_charmmfsw.h
@ -13,22 +13,22 @@

 #ifdef DIHEDRAL_CLASS

-DihedralStyle(charmmfsh,DihedralCharmmfsh)
+DihedralStyle(charmmfsw,DihedralCharmmfsw)

 #else

-#ifndef LMP_DIHEDRAL_CHARMMFSH_H
-#define LMP_DIHEDRAL_CHARMMFSH_H
+#ifndef LMP_DIHEDRAL_CHARMMFSW_H
+#define LMP_DIHEDRAL_CHARMMFSW_H

 #include <stdio.h>
 #include "dihedral.h"

 namespace LAMMPS_NS {

-class DihedralCharmmfsh : public Dihedral {
+class DihedralCharmmfsw : public Dihedral {
 public:
-  DihedralCharmmfsh(class LAMMPS *);
-  virtual ~DihedralCharmmfsh();
+  DihedralCharmmfsw(class LAMMPS *);
+  virtual ~DihedralCharmmfsw();
  virtual void compute(int, int);
  virtual void coeff(int, char **);
  virtual void init_style();
@ -73,9 +73,9 @@ E: Incorrect weight arg for dihedral coefficients

 Self-explanatory.  Check the input script or data file.

-E: Dihedral charmmfsh is incompatible with Pair style
+E: Dihedral charmmfsw is incompatible with Pair style

-Dihedral style charmmfsh must be used with a pair style charmm
+Dihedral style charmmfsw must be used with a pair style charmm
 in order for the 1-4 epsilon/sigma parameters to be defined.

 */
--- a/src/MPIIO/Install.sh
+++ b/src/MPIIO/Install.sh
@ -36,7 +36,7 @@ touch ../write_restart.cpp
 # all package files with no dependencies

 for file in *.cpp *.h; do
-  action $file
+  test -f ${file} && action $file
 done

 # edit 2 Makefile.package to include/exclude LMP_MPIIO setting
--- a/src/MSCG/Install.sh
+++ b/src/MSCG/Install.sh
@ -25,7 +25,7 @@ action () {
 # all package files with no dependencies

 for file in *.cpp *.h; do
-  action $file
+  test -f ${file} && action $file
 done

 # edit 2 Makefile.package files to include/exclude package info
--- a/src/Makefile
+++ b/src/Makefile
@ -43,6 +43,15 @@ endif

 # Package variables

+# PACKAGE    = standard packages
+# PACKUSER   = user packagse
+# PACKLIB    = all packages that require an additional lib
+# PACKSYS    = subset that reqiure a common system library
+# PACKINT    = subset that require an internal (provided) library
+# PACKEXT    = subset that require an external (downloaded) library
+# PACKLIB    = PACKSYS + PACKING + PACKEXT
+# PACKSCRIPT = libs under lammps/lib that have an Install.py script
+
 PACKAGE = asphere body class2 colloid compress coreshell dipole gpu \
 	  granular kim kokkos kspace manybody mc meam misc molecule \
 	  mpiio mscg opt peri poems \
@ -55,10 +64,21 @@ PACKUSER = user-atc user-awpmd user-cg-cmm user-cgdna user-colvars \
 	   user-quip user-reaxc user-smd user-smtbq user-sph user-tally \
 	   user-vtk

-PACKLIB = compress gpu kim kokkos meam mpiio mscg poems python reax voronoi \
-	  user-atc user-awpmd user-colvars user-h5md user-lb user-molfile \
+PACKLIB = compress gpu kim kokkos meam mpiio mscg poems \
+	  python reax voronoi \
+	  user-atc user-awpmd user-colvars user-h5md user-molfile \
 	  user-nc-dump user-qmmm user-quip user-smd user-vtk

+PACKSYS = compress mpiio python
+
+PACKINT = gpu kokkos meam poems reax user-atc user-awpmd user-colvars
+
+PACKEXT = kim mscg voronoi \
+	  user-h5md user-molfile user-nc-dump user-qmmm user-quip \
+	  user-smd user-vtk
+
+PACKSCRIPT = voronoi
+
 PACKALL = $(PACKAGE) $(PACKUSER)

 PACKAGEUC = $(shell echo $(PACKAGE) | tr a-z A-Z)
@ -66,6 +86,7 @@ PACKUSERUC = $(shell echo $(PACKUSER) | tr a-z A-Z)

 YESDIR = $(shell echo $(@:yes-%=%) | tr a-z A-Z)
 NODIR  = $(shell echo $(@:no-%=%) | tr a-z A-Z)
+LIBDIR = $(shell echo $(@:lib-%=%))

 # List of all targets

@ -75,9 +96,9 @@ help:
 	@echo 'make clean-machine       delete object files for one machine'
 	@echo 'make mpi-stubs           build dummy MPI library in STUBS'
 	@echo 'make install-python      install LAMMPS wrapper in Python'
-	@echo 'make tar                 create lmp_src.tar.gz of src dir and packages'
+	@echo 'make tar                 create lmp_src.tar.gz for src dir and packages'
 	@echo ''
-	@echo 'make package                 list available packages'
+	@echo 'make package                 list available packages and their dependencies'
 	@echo 'make package-status (ps)     status of all packages'
 	@echo 'make yes-package             install a single pgk in src dir'
 	@echo 'make no-package              remove a single pkg from src dir'
@ -87,11 +108,16 @@ help:
 	@echo 'make no-standard (no-std)    remove all standard pkgs'
 	@echo 'make yes-user                install all user pkgs'
 	@echo 'make no-user                 remove all user pkgs'
-	@echo 'make no-lib                  remove all pkgs with external libs'
+	@echo 'make yes-lib       install all pkgs with libs (incldued or ext)'
+	@echo 'make no-lib        remove all pkgs with libs (included or ext)'
+	@echo 'make yes-ext                 install all pkgs with external libs'
+	@echo 'make no-ext                  remove all pkgs with external libs'
 	@echo ''
 	@echo 'make package-update (pu) replace src files with updated package files'
 	@echo 'make package-overwrite   replace package files with src files'
 	@echo 'make package-diff (pd)   diff src files against package files'
+	@echo ''
+	@echo 'make lib-package         download/build/install a package library'
 	@echo 'make purge               purge obsolete copies of source files'
 	@echo ''
 	@echo 'make machine             build LAMMPS for machine'
@ -221,6 +247,13 @@ package:
 	@echo ''
 	@echo 'User-contributed packages:' $(PACKUSER)
 	@echo ''
+	@echo 'Packages that need system libraries:' $(PACKSYS)
+	@echo ''
+	@echo 'Packages that need provided libraries:' $(PACKINT)
+	@echo ''
+	@echo 'Packages that need external libraries:' $(PACKEXT)
+	@echo ''
+	@echo 'make package                 list available packages'
 	@echo 'make package                 list available packages'
 	@echo 'make package-status (ps)     status of all packages'
 	@echo 'make yes-package             install a single pgk in src dir'
@ -229,13 +262,18 @@ package:
 	@echo 'make no-all                  remove all pkgs from src dir'
 	@echo 'make yes-standard (yes-std)  install all standard pkgs'
 	@echo 'make no-standard (no-srd)    remove all standard pkgs'
-	@echo ''
 	@echo 'make yes-user                install all user pkgs'
 	@echo 'make no-user                 remove all user pkgs'
-	@echo 'make no-lib                  remove all pkgs with external libs'
+	@echo 'make yes-lib       install all pkgs with libs (included or ext)'
+	@echo 'make no-lib        remove all pkgs with libs (included or ext)'
+	@echo 'make yes-ext                 install all pkgs with external libs'
+	@echo 'make no-ext                  remove all pkgs with external libs'
+	@echo ''
 	@echo 'make package-update (pu)  replace src files with package files'
 	@echo 'make package-overwrite    replace package files with src files'
 	@echo 'make package-diff (pd)    diff src files against package file'
+	@echo ''
+	@echo 'make lib-package      download/build/install a package library'

 yes-all:
 	@for p in $(PACKALL); do $(MAKE) yes-$$p; done
@ -255,9 +293,18 @@ yes-user:
 no-user:
 	@for p in $(PACKUSER); do $(MAKE) no-$$p; done

+yes-lib:
+	@for p in $(PACKLIB); do $(MAKE) yes-$$p; done
+
 no-lib:
 	@for p in $(PACKLIB); do $(MAKE) no-$$p; done

+yes-ext:
+	@for p in $(PACKEXT); do $(MAKE) yes-$$p; done
+
+no-ext:
+	@for p in $(PACKEXT); do $(MAKE) no-$$p; done
+
 yes-%:
 	@if [ ! -e Makefile.package ]; \
 	  then cp Makefile.package.empty Makefile.package; fi
@ -288,6 +335,16 @@ no-%:
 		$(SHELL) Depend.sh $(NODIR) 0; \
        fi;

+# download/build/install a package library
+
+lib-%:
+	@if [ ! -e ../lib/$(LIBDIR)/Install.py ]; then \
+	  echo "Install script for lib $(@:lib-%=%) does not exist"; \
+	else \
+	  echo "Installing lib for package $(@:lib-%=%)"; \
+	  cd ../lib/$(LIBDIR); python Install.py $(args); \
+	fi;
+
 # status = list src files that differ from package files
 # update = replace src files with newer package files
 # overwrite = overwrite package files with newer src files
--- a/src/POEMS/Install.sh
+++ b/src/POEMS/Install.sh
@ -29,7 +29,7 @@ action () {
 # all package files with no dependencies

 for file in *.cpp *.h; do
-  action $file
+  test -f ${file} && action $file
 done

 # edit 2 Makefile.package files to include/exclude package info
--- a/src/PYTHON/Install.sh
+++ b/src/PYTHON/Install.sh
@ -35,7 +35,7 @@ touch ../variable.cpp
 # all package files with no dependencies

 for file in *.cpp *.h; do
-  action $file
+  test -f ${file} && action $file
 done

 # edit 2 Makefile.package files to include/exclude package info
--- a/src/PYTHON/python.cpp
+++ b/src/PYTHON/python.cpp
@ -37,6 +37,8 @@ Python::Python(LAMMPS *lmp) : Pointers(lmp)

  nfunc = 0;
  pfuncs = NULL;
+
+  external_interpreter = false;
 }

 /* ---------------------------------------------------------------------- */
@ -44,6 +46,7 @@ Python::Python(LAMMPS *lmp) : Pointers(lmp)
 Python::~Python()
 {
  // clean up
+  PyGILState_STATE gstate = PyGILState_Ensure();

  for (int i = 0; i < nfunc; i++) {
    delete [] pfuncs[i].name;
@ -54,7 +57,12 @@ Python::~Python()

  // shutdown Python interpreter

-  if (pyMain) Py_Finalize();
+  if (pyMain && !external_interpreter) {
+    Py_Finalize();
+  }
+  else {
+    PyGILState_Release(gstate);
+  }

  memory->sfree(pfuncs);
 }
@ -147,27 +155,20 @@ void Python::command(int narg, char **arg)
  int ifunc = create_entry(arg[0]);

  // one-time initialization of Python interpreter
-  // Py_SetArgv() enables finding of *.py module files in current dir
-  //   only needed for module load, not for direct file read into __main__
  // pymain stores pointer to main module
+  PyGILState_STATE gstate;

  if (pyMain == NULL) {
-    if (Py_IsInitialized())
-      error->all(FLERR,"Cannot embed Python when also "
-                 "extending Python with LAMMPS");
+    external_interpreter = Py_IsInitialized();
    Py_Initialize();
-
-    //char *arg = (char *) "./lmp";
-    //PySys_SetArgv(1,&arg);
-
-    //PyObject *pName = PyString_FromString("__main__");
-    //if (!pName) errorX->all(FLERR,"Bad pName");
-    //PyObject *pModule = PyImport_Import(pName);
-    //Py_DECREF(pName);
+    PyEval_InitThreads();
+    gstate = PyGILState_Ensure();

    PyObject *pModule = PyImport_AddModule("__main__");
    if (!pModule) error->all(FLERR,"Could not initialize embedded Python");
    pyMain = (void *) pModule;
+  } else {
+    gstate = PyGILState_Ensure();
  }

  // send Python code to Python interpreter
@ -177,22 +178,44 @@ void Python::command(int narg, char **arg)

  if (pyfile) {
    FILE *fp = fopen(pyfile,"r");
-    if (fp == NULL) error->all(FLERR,"Could not open Python file");
+
+    if (fp == NULL) {
+      PyGILState_Release(gstate);
+      error->all(FLERR,"Could not open Python file");
+    }
+
    int err = PyRun_SimpleFile(fp,pyfile);
-    if (err) error->all(FLERR,"Could not process Python file");
+
+    if (err) {
+      PyGILState_Release(gstate);
+      error->all(FLERR,"Could not process Python file");
+    }
+
    fclose(fp);
  } else if (herestr) {
    int err = PyRun_SimpleString(herestr);
-    if (err) error->all(FLERR,"Could not process Python string");
+
+    if (err) {
+      PyGILState_Release(gstate);
+      error->all(FLERR,"Could not process Python string");
+    }
  }

  // pFunc = function object for requested function

  PyObject *pModule = (PyObject *) pyMain;
  PyObject *pFunc = PyObject_GetAttrString(pModule,pfuncs[ifunc].name);
-  if (!pFunc) error->all(FLERR,"Could not find Python function");
-  if (!PyCallable_Check(pFunc))
+
+  if (!pFunc) {
+    PyGILState_Release(gstate);
+    error->all(FLERR,"Could not find Python function");
+  }
+
+  if (!PyCallable_Check(pFunc)) {
+    PyGILState_Release(gstate);
    error->all(FLERR,"Python function is not callable");
+  }
+
  pfuncs[ifunc].pFunc = (void *) pFunc;

  // clean-up input storage
@ -200,12 +223,14 @@ void Python::command(int narg, char **arg)
  delete [] istr;
  delete [] format;
  delete [] pyfile;
+  PyGILState_Release(gstate);
 }

 /* ------------------------------------------------------------------ */

 void Python::invoke_function(int ifunc, char *result)
 {
+  PyGILState_STATE gstate = PyGILState_Ensure();
  PyObject *pValue;
  char *str;

@ -215,29 +240,43 @@ void Python::invoke_function(int ifunc, char *result)

  int ninput = pfuncs[ifunc].ninput;
  PyObject *pArgs = PyTuple_New(ninput);
-  if (!pArgs) error->all(FLERR,"Could not create Python function arguments");
+
+  if (!pArgs) {
+    PyGILState_Release(gstate);
+    error->all(FLERR,"Could not create Python function arguments");
+  }

  for (int i = 0; i < ninput; i++) {
    int itype = pfuncs[ifunc].itype[i];
    if (itype == INT) {
      if (pfuncs[ifunc].ivarflag[i]) {
        str = input->variable->retrieve(pfuncs[ifunc].svalue[i]);
-        if (!str)
+
+        if (!str) {
+          PyGILState_Release(gstate);
          error->all(FLERR,"Could not evaluate Python function input variable");
+        }
+
        pValue = PyInt_FromLong(atoi(str));
      } else pValue = PyInt_FromLong(pfuncs[ifunc].ivalue[i]);
    } else if (itype == DOUBLE) {
      if (pfuncs[ifunc].ivarflag[i]) {
        str = input->variable->retrieve(pfuncs[ifunc].svalue[i]);
-        if (!str)
+
+        if (!str) {
+          PyGILState_Release(gstate);
          error->all(FLERR,"Could not evaluate Python function input variable");
+        }
+
        pValue = PyFloat_FromDouble(atof(str));
      } else pValue = PyFloat_FromDouble(pfuncs[ifunc].dvalue[i]);
    } else if (itype == STRING) {
      if (pfuncs[ifunc].ivarflag[i]) {
        str = input->variable->retrieve(pfuncs[ifunc].svalue[i]);
-        if (!str)
+        if (!str) {
+          PyGILState_Release(gstate);
          error->all(FLERR,"Could not evaluate Python function input variable");
+        }
        pValue = PyString_FromString(str);
      } else pValue = PyString_FromString(pfuncs[ifunc].svalue[i]);
    } else if (itype == PTR) {
@ -250,7 +289,12 @@ void Python::invoke_function(int ifunc, char *result)
  // error check with one() since only some procs may fail

  pValue = PyObject_CallObject(pFunc,pArgs);
-  if (!pValue) error->one(FLERR,"Python function evaluation failed");
+
+  if (!pValue) {
+    PyGILState_Release(gstate);
+    error->one(FLERR,"Python function evaluation failed");
+  }
+
  Py_DECREF(pArgs);

  // function returned a value
@ -271,6 +315,8 @@ void Python::invoke_function(int ifunc, char *result)
    }
    Py_DECREF(pValue);
  }
+
+  PyGILState_Release(gstate);
 }

 /* ------------------------------------------------------------------ */
--- a/src/PYTHON/python.h
+++ b/src/PYTHON/python.h
@ -21,6 +21,7 @@ namespace LAMMPS_NS {
 class Python : protected Pointers {
 public:
  int python_exists;
+  bool external_interpreter;

  Python(class LAMMPS *);
  ~Python();
--- a/src/REAX/Install.sh
+++ b/src/REAX/Install.sh
@ -29,7 +29,7 @@ action () {
 # all package files with no dependencies

 for file in *.cpp *.h; do
-  action $file
+  test -f ${file} && action $file
 done

 # edit 2 Makefile.package files to include/exclude package info
--- a/src/REPLICA/compute_event_displace.cpp
+++ b/src/REPLICA/compute_event_displace.cpp
@ -84,7 +84,7 @@ void ComputeEventDisplace::init()
 }

 /* ----------------------------------------------------------------------
-   return non-zero if an atom has moved > displace_dist since last event
+   return non-zero if any atom has moved > displace_dist since last event
 ------------------------------------------------------------------------- */

 double ComputeEventDisplace::compute_scalar()
@ -145,6 +145,62 @@ double ComputeEventDisplace::compute_scalar()
  return scalar;
 }

+/* ----------------------------------------------------------------------
+   return count of atoms that have moved > displace_dist since last event
+------------------------------------------------------------------------- */
+
+int ComputeEventDisplace::all_events()
+{
+  invoked_scalar = update->ntimestep;
+
+  if (id_event == NULL) return 0.0;
+
+  int event = 0;
+  double **xevent = fix_event->array_atom;
+
+  double **x = atom->x;
+  int *mask = atom->mask;
+  imageint *image = atom->image;
+  int nlocal = atom->nlocal;
+
+  double *h = domain->h;
+  double xprd = domain->xprd;
+  double yprd = domain->yprd;
+  double zprd = domain->zprd;
+  int xbox,ybox,zbox;
+  double dx,dy,dz,rsq;
+
+  if (triclinic == 0) {
+    for (int i = 0; i < nlocal; i++)
+      if (mask[i] & groupbit) {
+        xbox = (image[i] & IMGMASK) - IMGMAX;
+        ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
+        zbox = (image[i] >> IMG2BITS) - IMGMAX;
+        dx = x[i][0] + xbox*xprd - xevent[i][0];
+        dy = x[i][1] + ybox*yprd - xevent[i][1];
+        dz = x[i][2] + zbox*zprd - xevent[i][2];
+        rsq = dx*dx + dy*dy + dz*dz;
+        if (rsq >= displace_distsq) event++;
+      }
+  } else {
+    for (int i = 0; i < nlocal; i++)
+      if (mask[i] & groupbit) {
+        xbox = (image[i] & IMGMASK) - IMGMAX;
+        ybox = (image[i] >> IMGBITS & IMGMASK) - IMGMAX;
+        zbox = (image[i] >> IMG2BITS) - IMGMAX;
+        dx = x[i][0] + h[0]*xbox + h[5]*ybox + h[4]*zbox - xevent[i][0];
+        dy = x[i][1] + h[1]*ybox + h[3]*zbox - xevent[i][1];
+        dz = x[i][2] + h[2]*zbox - xevent[i][2];
+        rsq = dx*dx + dy*dy + dz*dz;
+        if (rsq >= displace_distsq) event++;
+      }
+  }
+
+  int allevents;
+  MPI_Allreduce(&event,&allevents,1,MPI_INT,MPI_SUM,world);
+
+  return allevents;
+}

 /* ---------------------------------------------------------------------- */

--- a/src/REPLICA/compute_event_displace.h
+++ b/src/REPLICA/compute_event_displace.h
@ -30,8 +30,11 @@ class ComputeEventDisplace : public Compute {
  ~ComputeEventDisplace();
  void init();
  double compute_scalar();
+
+  int all_events();
  void reset_extra_compute_fix(const char *);

+  
 private:
  int triclinic;
  double displace_distsq;
--- a/src/USER-ATC/Install.sh
+++ b/src/USER-ATC/Install.sh
@ -29,7 +29,7 @@ action () {
 # all package files with no dependencies

 for file in *.cpp *.h; do
-  action $file
+  test -f ${file} && action $file
 done

 # edit 2 Makefile.package files to include/exclude package info
--- a/src/USER-AWPMD/Install.sh
+++ b/src/USER-AWPMD/Install.sh
@ -29,7 +29,7 @@ action () {
 # all package files with no dependencies

 for file in *.cpp *.h; do
-  action $file
+  test -f ${file} && action $file
 done

 # edit 2 Makefile.package files to include/exclude package info
--- a/src/USER-COLVARS/Install.sh
+++ b/src/USER-COLVARS/Install.sh
@ -29,7 +29,7 @@ action () {
 # all package files with no dependencies

 for file in *.cpp *.h; do
-  action $file
+  test -f ${file} && action $file
 done

 # edit 2 Makefile.package files to include/exclude package info
--- a/src/USER-H5MD/Install.sh
+++ b/src/USER-H5MD/Install.sh
@ -27,7 +27,7 @@ action () {
 }

 for file in *.cpp *.h; do
-  action $file
+  test -f ${file} && action $file
 done

 # edit 2 Makefile.package files to include/exclude package info
--- a/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp
+++ b/src/USER-MANIFOLD/fix_nve_manifold_rattle.cpp
@ -94,6 +94,7 @@ FixNVEManifoldRattle::FixNVEManifoldRattle( LAMMPS *lmp, int &narg, char **arg,
  dof_flag = 1;

  nevery = 0;
+  next_output = 0;
  dtv = dtf = 0;

  tolerance = force->numeric( FLERR, arg[3] );
@ -145,6 +146,11 @@ FixNVEManifoldRattle::FixNVEManifoldRattle( LAMMPS *lmp, int &narg, char **arg,
  while( argi < narg ){
    if( strcmp(arg[argi], "every") == 0 ){
      nevery = force->inumeric(FLERR,arg[argi+1]);
+      next_output = update->ntimestep + nevery;
+      if( comm->me == 0 ){
+        fprintf(screen,"Outputing every %d steps, next is %d\n",
+			nevery, next_output);
+      }
      argi += 2;
    }else if( error_on_unknown_keyword ){
      char msg[2048];
@ -220,6 +226,11 @@ void FixNVEManifoldRattle::print_stats( const char *header )
            x_iters * inv_tdiff, v_iters * inv_tdiff, stats.dofs_removed);
    fprintf(screen,"\n");
  }
+
+  stats.x_iters_per_atom = 0;
+  stats.v_iters_per_atom = 0;
+  stats.x_iters = 0;
+  stats.v_iters = 0;
 }


@ -263,14 +274,6 @@ void FixNVEManifoldRattle::init()
 void FixNVEManifoldRattle::update_var_params()
 {
 
-  if( nevery > 0 ){
-    stats.x_iters = 0;
-    stats.v_iters = 0;
-    stats.natoms  = 0;
-    stats.x_iters_per_atom = 0.0;
-    stats.v_iters_per_atom = 0.0;
-  }
-
  double *ptr_params = ptr_m->params;
  
  for( int i = 0; i < nvars; ++i ){
@ -358,7 +361,12 @@ void FixNVEManifoldRattle::final_integrate()
   ---------------------------------------------------------------------------*/
 void FixNVEManifoldRattle::end_of_step()
 {
+  if (nevery && (update->ntimestep == next_output)){
+    if( comm->me == 0 ){
      print_stats( "nve/manifold/rattle" );
+      next_output += nevery;
+    }
+  }
 }

 /* -----------------------------------------------------------------------------
--- a/src/USER-MANIFOLD/fix_nve_manifold_rattle.h
+++ b/src/USER-MANIFOLD/fix_nve_manifold_rattle.h
@ -81,7 +81,7 @@ namespace LAMMPS_NS {

   protected:

-    int nevery;
+    int nevery, next_output;

    double dtv, dtf;
    double tolerance;
--- a/src/USER-MISC/Install.sh
+++ b/src/USER-MISC/Install.sh
@ -35,6 +35,6 @@ for file in *.cpp *.h; do
  elif (test $file = "pair_cdeam.h") then
    action pair_cdeam.h pair_eam_alloy.cpp
  else
-    action $file
+    test -f ${file} && action $file
  fi
 done
--- a/src/USER-MOLFILE/Install.sh
+++ b/src/USER-MOLFILE/Install.sh
@ -29,7 +29,7 @@ action () {
 # all package files with no dependencies

 for file in *.cpp *.h; do
-  action $file
+  test -f ${file} && action $file
 done

 # edit 2 Makefile.package files to include/exclude package info
--- a/src/USER-NC-DUMP/Install.sh
+++ b/src/USER-NC-DUMP/Install.sh
@ -27,7 +27,7 @@ action () {
 }

 for file in *.cpp *.h; do
-  action $file
+  test -f ${file} && action $file
 done

 # edit 2 Makefile.package files to include/exclude package info
--- a/src/USER-QMMM/Install.sh
+++ b/src/USER-QMMM/Install.sh
@ -29,7 +29,7 @@ action () {
 # all package files with no dependencies

 for file in *.cpp *.h; do
-  action $file
+  test -f ${file} && action $file
 done

 # edit 2 Makefile.package files to include/exclude package info
--- a/src/USER-QUIP/Install.sh
+++ b/src/USER-QUIP/Install.sh
@ -29,7 +29,7 @@ action () {
 # all package files with no dependencies

 for file in *.cpp *.h; do
-  action $file
+  test -f ${file} && action $file
 done

 # edit 2 Makefile.package files to include/exclude package info
--- a/src/USER-SMD/Install.sh
+++ b/src/USER-SMD/Install.sh
@ -29,7 +29,7 @@ action () {
 # all package files with no dependencies

 for file in *.cpp *.h; do
-  action $file
+  test -f ${file} && action $file
 done

 # edit 2 Makefile.package files to include/exclude package info
--- a/src/USER-VTK/Install.sh
+++ b/src/USER-VTK/Install.sh
@ -27,7 +27,7 @@ action () {
 }

 for file in *.cpp *.h; do
-  action $file
+  test -f ${file} && action $file
 done

 # edit 2 Makefile.package files to include/exclude package info
--- a/src/VORONOI/Install.sh
+++ b/src/VORONOI/Install.sh
@ -29,7 +29,7 @@ action () {
 # all package files with no dependencies

 for file in *.cpp *.h; do
-  action $file
+  test -f ${file} && action $file
 done

 # edit 2 Makefile.package files to include/exclude package info
--- a/src/bond.cpp
+++ b/src/bond.cpp
@ -292,3 +292,14 @@ double Bond::memory_usage()
  bytes += comm->nthreads*maxvatom*6 * sizeof(double);
  return bytes;
 }
+
+/* -----------------------------------------------------------------------
+   Reset all type-based bond params via init.
+-------------------------------------------------------------------------- */
+void Bond::reinit()
+{
+  if (!reinitflag)
+    error->all(FLERR,"Fix adapt interface to this bond style not supported");
+
+  init();
+}
--- a/src/bond.h
+++ b/src/bond.h
@ -30,6 +30,8 @@ class Bond : protected Pointers {
  double virial[6];               // accumulated virial
  double *eatom,**vatom;          // accumulated per-atom energy/virial

+  int reinitflag;                // 1 if compatible with fix adapt and alike
+
  // KOKKOS host/device flag and data masks

  ExecutionSpace execution_space;
@ -49,6 +51,8 @@ class Bond : protected Pointers {
  virtual void write_data(FILE *) {}
  virtual double single(int, double, int, int, double &) = 0;
  virtual double memory_usage();
+  virtual void *extract(char *, int &) {return NULL;}
+  virtual void reinit();

  void write_file(int, char**);

--- a/src/compute_temp_sphere.cpp
+++ b/src/compute_temp_sphere.cpp
@ -67,6 +67,11 @@ ComputeTempSphere::ComputeTempSphere(LAMMPS *lmp, int narg, char **arg) :
    } else error->all(FLERR,"Illegal compute temp/sphere command");
  }

+  // when computing only the rotational temperature,
+  // do not remove DOFs for translation as set by default
+
+  if (mode == ROTATE) extra_dof = 0;
+
  vector = new double[6];

  // error checks
--- a/src/finish.cpp
+++ b/src/finish.cpp
@ -162,6 +162,7 @@ void Finish::end(int flag)

      // CPU use on MPI tasks and OpenMP threads
      
+      if (timeflag) {
        if (lmp->kokkos) {
          const char fmt2[] =
            "%.1f%% CPU use with %d MPI tasks x %d OpenMP threads\n";
@ -184,6 +185,7 @@ void Finish::end(int flag)
        }
      }
    }
+  }

  // avoid division by zero for very short runs

--- a/src/fix_adapt.cpp
+++ b/src/fix_adapt.cpp
@ -16,6 +16,7 @@
 #include <stdlib.h>
 #include "fix_adapt.h"
 #include "atom.h"
+#include "bond.h"
 #include "update.h"
 #include "group.h"
 #include "modify.h"
@ -35,7 +36,7 @@ using namespace LAMMPS_NS;
 using namespace FixConst;
 using namespace MathConst;

-enum{PAIR,KSPACE,ATOM};
+enum{PAIR,KSPACE,ATOM,BOND};
 enum{DIAMETER,CHARGE};

 /* ---------------------------------------------------------------------- */
@ -68,6 +69,10 @@ nadapt(0), id_fix_diam(NULL), id_fix_chg(NULL), adapt(NULL)
      if (iarg+3 > narg) error->all(FLERR,"Illegal fix adapt command");
      nadapt++;
      iarg += 3;
+    } else if (strcmp(arg[iarg],"bond") == 0 ){
+      if (iarg+5 > narg) error->all(FLERR,"Illegal fix adapt command");
+      nadapt++;
+      iarg += 5;
    } else break;
  }

@ -103,6 +108,25 @@ nadapt(0), id_fix_diam(NULL), id_fix_chg(NULL), adapt(NULL)
      } else error->all(FLERR,"Illegal fix adapt command");
      nadapt++;
      iarg += 6;
+    } else if (strcmp(arg[iarg],"bond") == 0 ){
+      if (iarg+5 > narg) error->all(FLERR, "Illegal fix adapt command");
+      adapt[nadapt].which = BOND;
+      int n = strlen(arg[iarg+1]) + 1;
+      adapt[nadapt].bstyle = new char[n];
+      strcpy(adapt[nadapt].bstyle,arg[iarg+1]);
+      n = strlen(arg[iarg+2]) + 1;
+      adapt[nadapt].bparam = new char[n];
+      adapt[nadapt].bond = NULL;
+      strcpy(adapt[nadapt].bparam,arg[iarg+2]);
+      force->bounds(FLERR,arg[iarg+3],atom->ntypes,
+                    adapt[nadapt].ilo,adapt[nadapt].ihi);
+      if (strstr(arg[iarg+4],"v_") == arg[iarg+4]) {
+        n = strlen(&arg[iarg+4][2]) + 1;
+        adapt[nadapt].var = new char[n];
+        strcpy(adapt[nadapt].var,&arg[iarg+4][2]);
+      } else error->all(FLERR,"Illegal fix adapt command");
+      nadapt++;
+      iarg += 5;
    } else if (strcmp(arg[iarg],"kspace") == 0) {
      if (iarg+2 > narg) error->all(FLERR,"Illegal fix adapt command");
      adapt[nadapt].which = KSPACE;
@ -160,6 +184,13 @@ nadapt(0), id_fix_diam(NULL), id_fix_chg(NULL), adapt(NULL)
  for (int m = 0; m < nadapt; m++)
    if (adapt[m].which == PAIR)
      memory->create(adapt[m].array_orig,n+1,n+1,"adapt:array_orig");
+
+  // allocate bond style arrays:
+
+  n = atom->nbondtypes;
+  for (int m = 0; m < nadapt; ++m)
+    if (adapt[m].which == BOND)
+      memory->create(adapt[m].vector_orig,n+1,"adapt:vector_orig");
 }

 /* ---------------------------------------------------------------------- */
@ -172,6 +203,10 @@ FixAdapt::~FixAdapt()
      delete [] adapt[m].pstyle;
      delete [] adapt[m].pparam;
      memory->destroy(adapt[m].array_orig);
+    } else if (adapt[m].which == BOND) {
+      delete [] adapt[m].bstyle;
+      delete [] adapt[m].bparam;
+      memory->destroy(adapt[m].vector_orig);
    }
  }
  delete [] adapt;
@ -282,6 +317,7 @@ void FixAdapt::init()
  // setup and error checks

  anypair = 0;
+  anybond = 0;

  for (int m = 0; m < nadapt; m++) {
    Adapt *ad = &adapt[m];
@ -350,6 +386,41 @@ void FixAdapt::init()
      }

      delete [] pstyle;
+    } else if (ad->which == BOND){
+      ad->bond = NULL;
+      anybond = 1;
+      
+      int n = strlen(ad->bstyle) + 1;
+      char *bstyle = new char[n];
+      strcpy(bstyle,ad->bstyle);
+
+      if (lmp->suffix_enable) {
+        int len = 2 + strlen(bstyle) + strlen(lmp->suffix);
+        char *bsuffix = new char[len];
+        strcpy(bsuffix,bstyle);
+        strcat(bsuffix,"/");
+        strcat(bsuffix,lmp->suffix);
+        ad->bond = force->bond_match(bsuffix);
+        delete [] bsuffix;
+      }
+      if (ad->bond == NULL) ad->bond = force->bond_match(bstyle);
+      if (ad->bond == NULL )
+        error->all(FLERR,"Fix adapt bond style does not exist");
+
+      void *ptr = ad->bond->extract(ad->bparam,ad->bdim);
+      
+      if (ptr == NULL)
+        error->all(FLERR,"Fix adapt bond style param not supported");
+
+      // for bond styles, use a vector
+
+      if (ad->bdim == 1) ad->vector = (double *) ptr;
+
+      if (strcmp(force->bond_style,"hybrid") == 0 ||
+          strcmp(force->bond_style,"hybrid_overlay") == 0)
+        error->all(FLERR,"Fix adapt does not support bond_style hybrid");
+
+      delete [] bstyle;
        
    } else if (ad->which == KSPACE) {
      if (force->kspace == NULL)
@ -368,7 +439,7 @@ void FixAdapt::init()
    }
  }

-  // make copy of original pair array values
+  // make copy of original pair/bond array values

  for (int m = 0; m < nadapt; m++) {
    Adapt *ad = &adapt[m];
@ -378,7 +449,12 @@ void FixAdapt::init()
          ad->array_orig[i][j] = ad->array[i][j];
    } else if (ad->which == PAIR && ad->pdim == 0){
      ad->scalar_orig = *ad->scalar;
+      
+    } else if (ad->which == BOND && ad->bdim == 1){
+      for (i = ad->ilo; i <= ad->ihi; ++i )
+        ad->vector_orig[i] = ad->vector[i];
    }
+    
  }

  // fixes that store initial per-atom values
@ -470,6 +546,18 @@ void FixAdapt::change_settings()
              ad->array[i][j] = value;
      }

+    // set bond type array values:
+      
+    } else if (ad->which == BOND) {
+      if (ad->bdim == 1){
+        if (scaleflag)
+          for (i = ad->ilo; i <= ad->ihi; ++i )
+            ad->vector[i] = value*ad->vector_orig[i];
+        else
+          for (i = ad->ilo; i <= ad->ihi; ++i )
+            ad->vector[i] = value;
+      }
+      
    // set kspace scale factor

    } else if (ad->which == KSPACE) {
@ -522,8 +610,10 @@ void FixAdapt::change_settings()
  modify->addstep_compute(update->ntimestep + nevery);

  // re-initialize pair styles if any PAIR settings were changed
+  // ditto for bond styles if any BOND setitings were changes
  // this resets other coeffs that may depend on changed values,
  //   and also offset and tail corrections
+
  if (anypair) {
    for (int m = 0; m < nadapt; m++) {
      Adapt *ad = &adapt[m];
@ -532,6 +622,14 @@ void FixAdapt::change_settings()
      }
    }
  }
+  if (anybond) {
+    for (int m = 0; m < nadapt; ++m ) {
+      Adapt *ad = &adapt[m];
+      if (ad->which == BOND) {
+        ad->bond->reinit();
+      }
+    }
+  }

  // reset KSpace charges if charges have changed

@ -554,6 +652,12 @@ void FixAdapt::restore_settings()
            ad->array[i][j] = ad->array_orig[i][j];
      }

+    } else if (ad->which == BOND) {
+      if (ad->pdim == 1) {
+        for (int i = ad->ilo; i <= ad->ihi; i++)
+          ad->vector[i] = ad->vector_orig[i];
+      }
+      
    } else if (ad->which == KSPACE) {
      *kspace_scale = 1.0;

@ -588,6 +692,7 @@ void FixAdapt::restore_settings()
  }

  if (anypair) force->pair->reinit();
+  if (anybond) force->bond->reinit();
  if (chgflag && force->kspace) force->kspace->qsum_qsq();
 }

--- a/src/fix_adapt.h
+++ b/src/fix_adapt.h
@ -43,7 +43,7 @@ class FixAdapt : public Fix {

 private:
  int nadapt,resetflag,scaleflag;
-  int anypair;
+  int anypair, anybond;
  int nlevels_respa;
  char *id_fix_diam,*id_fix_chg;
  class FixStore *fix_diam,*fix_chg;
@ -52,12 +52,15 @@ class FixAdapt : public Fix {
    int which,ivar;
    char *var;
    char *pstyle,*pparam;
+    char *bstyle,*bparam;
    int ilo,ihi,jlo,jhi;
-    int pdim;
+    int pdim,bdim;
    double *scalar,scalar_orig;
+    double *vector,*vector_orig;
    double **array,**array_orig;
    int aparam;
    class Pair *pair;
+    class Bond *bond;
  };

  Adapt *adapt;
--- a/src/fix_ave_histo.cpp
+++ b/src/fix_ave_histo.cpp
@ -205,14 +205,18 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) :
  for (int i = 0; i < nvalues; i++) {
    if (which[i] == X || which[i] == V || which[i] == F) kindflag = PERATOM;
    else if (which[i] == COMPUTE) {
-      Compute *compute = modify->compute[modify->find_compute(ids[i])];
+      int c_id = modify->find_compute(ids[i]);
+      if (c_id < 0) error->all(FLERR,"Fix ave/histo input is invalid compute");
+      Compute *compute = modify->compute[c_id];
      if (compute->scalar_flag || compute->vector_flag || compute->array_flag)
        kindflag = GLOBAL;
      else if (compute->peratom_flag) kindflag = PERATOM;
      else if (compute->local_flag) kindflag = LOCAL;
      else error->all(FLERR,"Fix ave/histo input is invalid compute");
    } else if (which[i] == FIX) {
-      Fix *fix = modify->fix[modify->find_fix(ids[i])];
+      int f_id = modify->find_fix(ids[i]);
+      if (f_id < 0) error->all(FLERR,"Fix ave/histo input is invalid fix");
+      Fix *fix = modify->fix[f_id];
      if (fix->scalar_flag || fix->vector_flag || fix->array_flag)
        kindflag = GLOBAL;
      else if (fix->peratom_flag) kindflag = PERATOM;
@ -220,6 +224,7 @@ FixAveHisto::FixAveHisto(LAMMPS *lmp, int narg, char **arg) :
      else error->all(FLERR,"Fix ave/histo input is invalid fix");
    } else if (which[i] == VARIABLE) {
      int ivariable = input->variable->find(ids[i]);
+      if (ivariable < 0) error->all(FLERR,"Fix ave/histo input is invalid variable");
      if (input->variable->equalstyle(ivariable)) kindflag = GLOBAL;
      else if (input->variable->atomstyle(ivariable)) kindflag = PERATOM;
      else error->all(FLERR,"Fix ave/histo input is invalid variable");
--- a/src/integrate.h
+++ b/src/integrate.h
@ -23,7 +23,7 @@ class Integrate : protected Pointers {
  Integrate(class LAMMPS *, int, char **);
  virtual ~Integrate();
  virtual void init();
-  virtual void setup() = 0;
+  virtual void setup(int flag=1) = 0;
  virtual void setup_minimal(int) = 0;
  virtual void run(int) = 0;
  virtual void cleanup() {}
--- a/src/min.cpp
+++ b/src/min.cpp
@ -180,14 +180,16 @@ void Min::init()
   setup before run
 ------------------------------------------------------------------------- */

-void Min::setup()
+void Min::setup(int flag)
 {
  if (comm->me == 0 && screen) {
    fprintf(screen,"Setting up %s style minimization ...\n",
            update->minimize_style);
+    if (flag) {
      fprintf(screen,"  Unit style    : %s\n", update->unit_style);
      timer->print_timeout(screen);
    }
+  }
  update->setupflag = 1;

  // setup extra global dof due to fixes
@ -294,7 +296,7 @@ void Min::setup()
      requestor[m]->min_xf_get(m);

  modify->setup(vflag);
-  output->setup();
+  output->setup(flag);
  update->setupflag = 0;

  // stats for initial thermo output
--- a/src/min.h
+++ b/src/min.h
@ -31,7 +31,7 @@ class Min : protected Pointers {
  Min(class LAMMPS *);
  virtual ~Min();
  virtual void init();
-  void setup();
+  void setup(int flag=1);
  void setup_minimal(int);
  void run(int);
  void cleanup();
--- a/src/output.cpp
+++ b/src/output.cpp
@ -652,6 +652,21 @@ void Output::delete_dump(char *id)
  ndump--;
 }

+/* ----------------------------------------------------------------------
+   find a dump by ID
+   return index of dump or -1 if not found
+------------------------------------------------------------------------- */
+
+int Output::find_dump(const char *id)
+{
+  if (id == NULL) return -1;
+  int idump;
+  for (idump = 0; idump < ndump; idump++)
+    if (strcmp(id,dump[idump]->id) == 0) break;
+  if (idump == ndump) return -1;
+  return idump;
+}
+
 /* ----------------------------------------------------------------------
   set thermo output frequency from input script
 ------------------------------------------------------------------------- */
--- a/src/output.h
+++ b/src/output.h
@ -76,6 +76,7 @@ class Output : protected Pointers {
  void add_dump(int, char **);       // add a Dump to Dump list
  void modify_dump(int, char **);    // modify a Dump
  void delete_dump(char *);          // delete a Dump from Dump list
+  int find_dump(const char *);       // find a Dump ID

  void set_thermo(int, char **);     // set thermo output freqquency
  void create_thermo(int, char **);  // create a thermo style
--- a/src/respa.cpp
+++ b/src/respa.cpp
@ -398,12 +398,14 @@ void Respa::init()
   setup before run
 ------------------------------------------------------------------------- */

-void Respa::setup()
+void Respa::setup(int flag)
 {
  if (comm->me == 0 && screen) {
    fprintf(screen,"Setting up r-RESPA run ...\n");
+    if (flag) {
      fprintf(screen,"  Unit style    : %s\n", update->unit_style);
-    fprintf(screen,"  Current step  : " BIGINT_FORMAT "\n", update->ntimestep);
+      fprintf(screen,"  Current step  : " BIGINT_FORMAT "\n",
+              update->ntimestep);
      fprintf(screen,"  Time steps    :");
      for (int ilevel=0; ilevel < nlevels; ++ilevel)
        fprintf(screen," %d:%g",ilevel+1, step[ilevel]);
@ -417,6 +419,7 @@ void Respa::setup()
      fprintf(screen,"\n");
      timer->print_timeout(screen);
    }
+  }

  update->setupflag = 1;

@ -482,7 +485,7 @@ void Respa::setup()

  sum_flevel_f();
  modify->setup(vflag);
-  output->setup();
+  output->setup(flag);
  update->setupflag = 0;
 }

--- a/src/respa.h
+++ b/src/respa.h
@ -48,7 +48,7 @@ class Respa : public Integrate {
  Respa(class LAMMPS *, int, char **);
  virtual ~Respa();
  virtual void init();
-  virtual void setup();
+  virtual void setup(int flag=1);
  virtual void setup_minimal(int);
  virtual void run(int);
  virtual void cleanup();
--- a/src/verlet.cpp
+++ b/src/verlet.cpp
@ -85,15 +85,18 @@ void Verlet::init()
   setup before run
 ------------------------------------------------------------------------- */

-void Verlet::setup()
+void Verlet::setup(int flag)
 {
  if (comm->me == 0 && screen) {
    fprintf(screen,"Setting up Verlet run ...\n");
+    if (flag) {
      fprintf(screen,"  Unit style    : %s\n", update->unit_style);
-    fprintf(screen,"  Current step  : " BIGINT_FORMAT "\n", update->ntimestep);
+      fprintf(screen,"  Current step  : " BIGINT_FORMAT "\n",
+              update->ntimestep);
      fprintf(screen,"  Time step     : %g\n", update->dt);
      timer->print_timeout(screen);
    }
+  }

  if (lmp->kokkos)
    error->all(FLERR,"KOKKOS package requires run_style verlet/kk");
@ -148,7 +151,7 @@ void Verlet::setup()
  if (force->newton) comm->reverse_comm();

  modify->setup(vflag);
-  output->setup();
+  output->setup(flag);
  update->setupflag = 0;
 }

--- a/src/verlet.h
+++ b/src/verlet.h
@ -29,7 +29,7 @@ class Verlet : public Integrate {
  Verlet(class LAMMPS *, int, char **);
  virtual ~Verlet() {}
  virtual void init();
-  virtual void setup();
+  virtual void setup(int flag=1);
  virtual void setup_minimal(int);
  virtual void run(int);
  void cleanup();
--- a/src/version.h
+++ b/src/version.h
@ -1 +1 @@
-#define LAMMPS_VERSION "31 Mar 2017"
+#define LAMMPS_VERSION "11 Apr 2017"
--- a/src/write_restart.cpp
+++ b/src/write_restart.cpp
@ -297,6 +297,9 @@ void WriteRestart::write(char *file)

  // communication buffer for my atom info
  // max_size = largest buffer needed by any proc
+  // NOTE: are assuming size_restart() returns 32-bit int
+  //   for a huge one-proc problem, nlocal could be 32-bit
+  //   but nlocal * doubles-peratom could oveflow

  int max_size;
  int send_size = atom->avec->size_restart();
Author	SHA1	Message	Date
Steve Plimpton	4da8c1c4e2	patch 11Apr17	2017-04-11 09:00:37 -06:00
Steve Plimpton	49dd9449b8	fix gcmc updates from Aidan, trimming of output for replica commands	2017-04-11 08:35:09 -06:00
sjplimp	76fd936972	Merge pull request #443 from Pakketeretet2/user-manifold-fix-every-keyword User manifold fix every keyword	2017-04-11 08:27:53 -06:00
sjplimp	06cebb9fb4	Merge pull request #445 from Pakketeretet2/extract_for_bond Extract for bond	2017-04-11 08:27:31 -06:00
sjplimp	b9d844ca8d	Merge pull request #444 from ohenrich/user-cgdna Minor updates to docu of USER-CGDNA package	2017-04-11 08:25:09 -06:00
sjplimp	ccc9367de7	Merge pull request #442 from akohlmey/small-updates-and-bugfixes collected small updates and bugfixes	2017-04-11 08:24:32 -06:00
sjplimp	4c4a3fe5d1	Merge pull request #439 from rbberger/python_mixed_use_support Support mixed Python use by honoring Python GIL	2017-04-11 08:24:06 -06:00
Axel Kohlmeyer	84ea8a79e6	correct link for dispersion parameter how-to and reformat	2017-04-10 20:43:24 -04:00
Stefan Paquay	f19f558220	Removed changed bond_harmonic from wrong position.	2017-04-10 10:06:03 -04:00
Stefan Paquay	1ad7d856fe	Added forgotten #include string to bond_harmonic.cpp	2017-04-10 09:57:54 -04:00
Axel Kohlmeyer	d6357420ae	propagate global package installation bugfix to explicit package scripts	2017-04-07 15:29:56 -04:00
Axel Kohlmeyer	62b9fa22b8	when computing only rotational temperature, we must not subtract the default n-dim extra DOFs	2017-04-07 15:11:26 -04:00
Axel Kohlmeyer	1725832b6c	address issue where uninstalling an empty package will erase all code in src	2017-04-06 11:08:57 -04:00
Stefan Paquay	874944f2ec	Made fix adapt support bond harmonic.	2017-04-04 19:37:17 -04:00
Oliver Henrich	497a5d88af	Merge branch 'master' into user-cgdna	2017-04-04 20:03:57 +01:00
Oliver Henrich	8993daaa31	Minor update to docu	2017-04-04 19:54:22 +01:00
Axel Kohlmeyer	e190eb15f5	remove debug printf	2017-04-04 17:54:33 +00:00
Stefan Paquay	b6bc33bac6	Merge branch 'user_manifold_fix' into user-manifold-fix-every-keyword	2017-04-04 13:31:22 -04:00
Stefan Paquay	03a6f5237f	Made every keyword for user-manifold work as advertised.	2017-04-04 13:30:49 -04:00
Stefan Paquay	28e86917a0	Made fix adapt work with bond_harmonic.	2017-04-04 12:35:26 -04:00
Axel Kohlmeyer	6f1bbd3cec	protect fix ave/histo from segfaulting on non-existing computes, fixes or variables	2017-04-03 18:08:15 -04:00
Richard Berger	1544b51dcb	Support mixed Python use by honoring Python GIL This enables support to both drive LAMMPS with a Python interpreter and evaluating Python expressions inside of LAMMPS using that same interpreter. Previously this has been avoided through an error message because the binding code did not ensure that the necessary GIL (global interpreter lock) structures exist (see issue #438). All code paths which call Python C API functions must first acquire the GIL through a call PyGILState_Ensure and release it with PyGILState_Release.	2017-03-29 01:49:15 -04:00