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 
+Author: Oliver Henrich at the University of Strathclyde, Glasgow 
-University of Edinburgh (ohenrich@ph.ed.ac.uk).  
+(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
+transposing 3d FFT data.
 been tested with the FFTW3, FFTW2, MKL, and KISS FFT options.
 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
+a simulation with the CHARMM force field, either with long-range
-"pair_style lj/charmmfsw/coul/charmmfsh"_pair_charmm.html command.
+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
+{charmmfsw} style should only be used when using the corresponding
-lj/charmmfsw/coul/charmmfsh"_pair_charmm.html to make the Coulombic
+"pair_style lj/charmmfsw/coul/charmmfsw"_pair_charmm.html or
-pairwise calculations consistent.  Use the {charmm} style with
+"pair_style lj/charmmfsw/coul/long"_pair_charmm.html commands.  Use
-long-range Coulombics or the older "pair_style
+the {charmm} style with the older "pair_style"_pair_charmm.html
-lj/charmm/coul/charmm"_pair_charmm.html command.  See the discussion
+commands that have just "charmm" in their style name.  See the
-on the "CHARMM pair_style"_pair_charmm.html doc page for details.
+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
+For a typical application, using the automatic parameter generation
-simulations that are either inaccurate or slow. Using this option is thus not
+will provide simulations that are either inaccurate or slow. Using this
-recommended. For guidelines on how to obtain good parameters, see the "How-To"_Section_howto.html#howto_23 discussion.
+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
+styles.  This includes the newer "dihedral_style
-related pair styles (e.g. implicit, accelerator, free energy
+charmmfsw"_dihedral_charmm.html command.  Eventually code from the new
-variants).
+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.
+Install.py Python script to automate any or all steps of the process.
-Type "python install.py" for instructions.
+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
+included one or more of the following: kspace, a hybrid
-pair style, an eam pair style, or no "single" function for the pair
+pair style, an eam pair style, tail correction, 
-style.
+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
+#ifndef LMP_DIHEDRAL_CHARMMFSW_H
-#define LMP_DIHEDRAL_CHARMMFSH_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 *);
+  DihedralCharmmfsw(class LAMMPS *);
-  virtual ~DihedralCharmmfsh();
+  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 \
+PACKLIB = compress gpu kim kokkos meam mpiio mscg poems \
-	  user-atc user-awpmd user-colvars user-h5md user-lb user-molfile \
+	  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())
+    external_interpreter = Py_IsInitialized();
      error->all(FLERR,"Cannot embed Python when also "
                 "extending Python with LAMMPS");
    Py_Initialize();
-
+    PyEval_InitThreads();
-    //char *arg = (char *) "./lmp";
+    gstate = PyGILState_Ensure();
    //PySys_SetArgv(1,&arg);
    //PyObject *pName = PyString_FromString("__main__");
    //if (!pName) errorX->all(FLERR,"Bad pName");
    //PyObject *pModule = PyImport_Import(pName);
    //Py_DECREF(pName);
    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
`@ -1 +1 @@`
	`#define LAMMPS_VERSION "31 Mar 2017"`	`#define LAMMPS_VERSION "11 Apr 2017"`