patch 16Jul18

Merge pull request #1003 from akohlmey/restart_extra_flags
include support for 'extra/XXX/per/atom' info in restart files
2018-07-16 18:12:15 -06:00 · 2018-07-16 15:07:43 -06:00 · 2018-07-16 15:21:52 -04:00 · 2018-07-16 08:50:15 -06:00 · 2018-07-16 08:49:30 -06:00 · 2018-07-16 08:49:13 -06:00
43 changed files with 704 additions and 119 deletions
--- a/cmake/README.md
+++ b/cmake/README.md
@ -1421,11 +1421,11 @@ target API.
  <td>CUDA SM architecture targeted by GPU package</td>
  <td>
  <dl>
-    <dt><code>sm20</code> (Fermi)</dt>
-    <dt><code>sm30</code> (Kepler)</dt>
-    <dt><code>sm50</code> (Maxwell)</dt>
-    <dt><code>sm60</code> (Pascal)</dt>
-    <dt><code>sm70</code> (Volta)</dt>
+    <dt><code>sm_20</code> (Fermi)</dt>
+    <dt><code>sm_30</code> (Kepler)</dt>
+    <dt><code>sm_50</code> (Maxwell)</dt>
+    <dt><code>sm_60</code> (Pascal)</dt>
+    <dt><code>sm_70</code> (Volta)</dt>
  </dl>
  </td>
 </tr>
--- a/doc/src/Developer/developer.tex
+++ b/doc/src/Developer/developer.tex
@ -476,7 +476,7 @@ is the name of the class. This code allows LAMMPS to find your fix
 when it parses input script. In addition, your fix header must be
 included in the file "style\_fix.h". In case if you use LAMMPS make,
 this file is generated automatically - all files starting with prefix
-fix\_ are included, so call your header the same way. Otherwise, don<EFBFBD>t
+fix\_ are included, so call your header the same way. Otherwise, don't
 forget to add your include into "style\_fix.h".

 Let's write a simple fix which will print average velocity at the end
--- 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="29 Jun 2018 version">
+<META NAME="docnumber" CONTENT="16 Jul 2018 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>
@ -19,7 +19,7 @@
 :line

 LAMMPS Documentation :c,h1
-29 Jun 2018 version :c,h2
+16 Jul 2018 version :c,h2

 Version info: :h3

--- a/doc/src/Section_commands.txt
+++ b/doc/src/Section_commands.txt
@ -582,7 +582,7 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.
 "dt/reset"_fix_dt_reset.html,
 "efield"_fix_efield.html,
 "ehex"_fix_ehex.html,
-"enforce2d"_fix_enforce2d.html,
+"enforce2d (k)"_fix_enforce2d.html,
 "evaporate"_fix_evaporate.html,
 "external"_fix_external.html,
 "freeze"_fix_freeze.html,
--- a/doc/src/angle_dipole.txt
+++ b/doc/src/angle_dipole.txt
@ -96,16 +96,17 @@ USER-MISC package.  See the "Making LAMMPS"_Section_start.html#start_2_3
 section for more info on packages.

 NOTE: In the "Angles" section of the data file, the atom ID 'j'
-corresponding to the dipole to restrain must come before the atom ID
-of the reference atom 'i'. A third atom ID 'k' must also be provided,
-although 'k' is just a 'dummy' atom which can be any atom; it may be
-useful to choose a convention (e.g., 'k'='i') and adhere to it.  For
-example, if ID=1 for the dipolar atom to restrain, and ID=2 for the
-reference atom, the corresponding line in the "Angles" section of the
-data file would read: X X 1 2 2
+defining the direction of the dipole vector to restrain must come
+before the atom ID of the reference atom 'i'. A third atom ID 'k' must
+also be provided to comply with the requirement of a valid angle
+definition. This atom ID k should be chosen to be that of an atom
+bonded to atom 'i' to avoid errors with "lost angle atoms" when running
+in parallel. Since the LAMMPS code checks for valid angle definitions,
+cannot use the same atom ID of either 'i' or 'j' (this was allowed
+and recommended with older LAMMPS versions).

 The "newton" command for intramolecular interactions must be "on"
-(which is the default).
+(which is the default except when using some accelerator packages).

 This angle style should not be used with SHAKE.

--- a/doc/src/fix_enforce2d.txt
+++ b/doc/src/fix_enforce2d.txt
@ -7,6 +7,7 @@
 :line

 fix enforce2d command :h3
+fix enforce2d/kk command :h3

 [Syntax:]

@ -27,12 +28,13 @@ not move from their initial z coordinate.

 :line

-Styles with a suffix are functionally the same as the corresponding
-style without the suffix.  They have been optimized to run faster,
-depending on your available hardware, as discussed in
-"Section 5"_Section_accelerate.html of the manual.  The
-accelerated styles take the same arguments and should produce the same
-results, except for round-off and precision issues.
+Styles with a {gpu}, {intel}, {kk}, {omp}, or {opt} suffix are
+functionally the same as the corresponding style without the suffix.
+They have been optimized to run faster, depending on your available
+hardware, as discussed in "Section 5"_Section_accelerate.html
+of the manual.  The accelerated styles take the same arguments and
+should produce the same results, except for round-off and precision
+issues.

 These accelerated styles are part of the GPU, USER-INTEL, KOKKOS,
 USER-OMP and OPT packages, respectively.  They are only enabled if
--- a/doc/src/fix_langevin_spin.txt
+++ b/doc/src/fix_langevin_spin.txt
@ -98,5 +98,5 @@ integration fix (e.g. {fix nve/spin}).
 [(Mayergoyz)] I.D. Mayergoyz, G. Bertotti, C. Serpico (2009). Elsevier (2009)

 :link(Tranchida2)
-[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson, 
-arXiv preprint arXiv:1801.10233, (2018).
+[(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
+Journal of Computational Physics, (2018).
--- a/doc/src/fix_nve_spin.txt
+++ b/doc/src/fix_nve_spin.txt
@ -73,4 +73,4 @@ instead of "array" is also valid.

 :link(Tranchida1)
 [(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
-arXiv preprint arXiv:1801.10233, (2018).
+Journal of Computational Physics, (2018).
--- a/doc/src/pair_spin_dmi.txt
+++ b/doc/src/pair_spin_dmi.txt
@ -63,4 +63,4 @@ See the "Making LAMMPS"_Section_start.html#start_3 section for more info.

 :link(Tranchida5)
 [(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
-arXiv preprint arXiv:1801.10233, (2018).
+Journal of Computational Physics, (2018).
--- a/doc/src/pair_spin_exchange.txt
+++ b/doc/src/pair_spin_exchange.txt
@ -79,4 +79,4 @@ See the "Making LAMMPS"_Section_start.html#start_3 section for more info.

 :link(Tranchida3)
 [(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
-arXiv preprint arXiv:1801.10233, (2018).
+Journal of Computational Physics, (2018).
--- a/doc/src/pair_spin_magelec.txt
+++ b/doc/src/pair_spin_magelec.txt
@ -70,4 +70,4 @@ See the "Making LAMMPS"_Section_start.html#start_3 section for more info.

 :link(Tranchida4)
 [(Tranchida)] Tranchida, Plimpton, Thibaudeau, and Thompson, 
-arXiv preprint arXiv:1801.10233, (2018).
+Journal of Computational Physics, (2018).
--- a/doc/src/pair_spin_neel.txt
+++ b/doc/src/pair_spin_neel.txt
@ -78,4 +78,4 @@ See the "Making LAMMPS"_Section_start.html#start_3 section for more info.

 :link(Tranchida6)
 [(Tranchida)] Tranchida, Plimpton, Thibaudeau and Thompson,
-arXiv preprint arXiv:1801.10233, (2018).
+Journal of Computational Physics, (2018).
--- a/doc/src/run_style.txt
+++ b/doc/src/run_style.txt
@ -138,13 +138,19 @@ iterations of level 1 for a single iteration of level 2, N2 is the
 iterations of level 2 per iteration of level 3, etc.  N-1 looping
 parameters must be specified.

-The "timestep"_timestep.html command sets the timestep for the
-outermost rRESPA level.  Thus if the example command above for a
-4-level rRESPA had an outer timestep of 4.0 fmsec, the inner timestep
-would be 8x smaller or 0.5 fmsec.  All other LAMMPS commands that
-specify number of timesteps (e.g. "neigh_modify"_neigh_modify.html
-parameters, "dump"_dump.html every N timesteps, etc) refer to the
-outermost timesteps.
+Thus with a 4-level respa setting of "2 2 2" for the 3 loop factors,
+you could choose to have bond interactions computed 8x per large
+timestep, angle interactions computed 4x, pair interactions computed
+2x, and long-range interactions once per large timestep.
+
+The "timestep"_timestep.html command sets the large timestep for the
+outermost rRESPA level.  Thus if the 3 loop factors are "2 2 2" for
+4-level rRESPA, and the outer timestep is set to 4.0 fmsec, then the
+inner timestep would be 8x smaller or 0.5 fmsec.  All other LAMMPS
+commands that specify number of timesteps (e.g. "thermo"_thermo.html
+for thermo output every N steps, "neigh_modify
+delay/every"_neigh_modify.html parameters, "dump"_dump.html every N
+steps, etc) refer to the outermost timesteps.

 The rRESPA keywords enable you to specify at what level of the
 hierarchy various forces will be computed.  If not specified, the
@ -167,11 +173,17 @@ have their force go ramped to 0.0 so the overlap with the next regime
 compute forces for all pairs from 5.0 outward, with those from 5.0 to
 6.0 having their value ramped in an inverse manner.

-Only some pair potentials support the use of the {inner} and {middle}
-and {outer} keywords.  If not, only the {pair} keyword can be used
-with that pair style, meaning all pairwise forces are computed at the
-same rRESPA level.  See the doc pages for individual pair styles for
-details.i
+Note that you can use {inner} and {outer} without using {middle} to
+split the pairwise computations into two portions instead of three.
+Unless you are using a very long pairwise cutoff, a 2-way split is
+often faster than a 3-way split, since it avoids too much duplicate
+computation of pairwise interactions near the intermediate cutoffs.
+
+Also note that only a few pair potentials support the use of the
+{inner} and {middle} and {outer} keywords.  If not, only the {pair}
+keyword can be used with that pair style, meaning all pairwise forces
+are computed at the same rRESPA level.  See the doc pages for
+individual pair styles for details.

 Another option for using pair potentials with rRESPA is with the
 {hybrid} keyword, which requires the use of the "pair_style hybrid or
@ -238,12 +250,24 @@ roughly a 1.5 fold speedup over the {verlet} style with SHAKE and a

 For non-biomolecular simulations, the {respa} style can be
 advantageous if there is a clear separation of time scales - fast and
-slow modes in the simulation.  Even a LJ system can benefit from
-rRESPA if the interactions are divided by the inner, middle and outer
-keywords.  A 2-fold or more speedup can be obtained while maintaining
-good energy conservation.  In real units, for a pure LJ fluid at
-liquid density, with a sigma of 3.0 angstroms, and epsilon of 0.1
-Kcal/mol, the following settings seem to work well:
+slow modes in the simulation.  For example, a system of slowly-moving
+charged polymer chains could be setup as follows:
+
+timestep 4.0
+run_style respa 2 8 :pre
+
+This is two-level rRESPA with an 8x difference between the short and
+long timesteps.  The bonds, angles, dihedrals will be computed every
+0.5 fs (assuming real units), while the pair and kspace interactions
+will be computed once every 4 fs.  These are the default settings for
+each kind of interaction, so no additional keywords are necessary.
+
+Even a LJ system can benefit from rRESPA if the interactions are
+divided by the inner, middle and outer keywords.  A 2-fold or more
+speedup can be obtained while maintaining good energy conservation.
+In real units, for a pure LJ fluid at liquid density, with a sigma of
+3.0 angstroms, and epsilon of 0.1 Kcal/mol, the following settings
+seem to work well:

 timestep  36.0
 run_style respa 3 3 4 inner 1 3.0 4.0 middle 2 6.0 7.0 outer 3 :pre
@ -271,9 +295,9 @@ more instructions on how to use the accelerated styles effectively.
 [Restrictions:]

 The {verlet/split} style can only be used if LAMMPS was built with the
-REPLICA package. Correspondingly the {respa/omp} style is available only
-if the USER-OMP package was included. See the "Making LAMMPS"_Section_start.html#start_3
-section for more info on packages.
+REPLICA package. Correspondingly the {respa/omp} style is available
+only if the USER-OMP package was included. See the "Making
+LAMMPS"_Section_start.html#start_3 section for more info on packages.

 Whenever using rRESPA, the user should experiment with trade-offs in
 speed and accuracy for their system, and verify that they are
@ -287,6 +311,17 @@ conserving energy to adequate precision.

 run_style verlet :pre

+For run_style respa, the default assignment of interactions
+to rRESPA levels is as follows:
+
+bond forces = level 1 (innermost loop)
+angle forces = same level as bond forces
+dihedral forces = same level as angle forces
+improper forces = same level as dihedral forces
+pair forces = leven N (outermost level)
+kspace forces = same level as pair forces
+inner, middle, outer forces = no default :ul
+
 :line

 :link(Tuckerman3)
--- a/doc/src/set.txt
+++ b/doc/src/set.txt
@ -17,6 +17,7 @@ ID = atom ID range or type range or mol ID range or group ID or region ID :l
 one or more keyword/value pairs may be appended :l
 keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \
          {charge} or {dipole} or {dipole/random} or {quat} or \
+          {spin} or {spin/random} or {quat} or \
          {quat/random} or {diameter} or {shape} or \
          {length} or {tri} or {theta} or {theta/random} or \
          {angmom} or {omega} or \
@ -35,6 +36,8 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \
    value can be an atom-style variable (see below)
  {x},{y},{z} value = atom coordinate (distance units)
    value can be an atom-style variable (see below)
+  {vx},{vy},{vz} value = atom velocity (velocity units)
+    value can be an atom-style variable (see below)
  {charge} value = atomic charge (charge units)
    value can be an atom-style variable (see below)
  {dipole} values = x y z
@ -43,6 +46,13 @@ keyword = {type} or {type/fraction} or {mol} or {x} or {y} or {z} or \
  {dipole/random} value = seed Dlen
    seed = random # seed (positive integer) for dipole moment orientations
    Dlen = magnitude of dipole moment (dipole units)
+  {spin} values = g x y z
+    g = magnitude of magnetic spin vector (in Bohr magneton's unit)
+    x,y,z = orientation of magnetic spin vector
+    any of x,y,z can be an atom-style variable (see below)
+  {spin/random} value = seed Dlen
+    seed = random # seed (positive integer) for magnetic spin orientations
+    Dlen = magnitude of magnetic spin vector (in Bohr magneton's unit)
  {quat} values = a b c theta
    a,b,c = unit vector to rotate particle around via right-hand rule
    theta = rotation angle (degrees)
@ -119,6 +129,7 @@ set type 3 charge 0.5
 set type 1*3 charge 0.5
 set atom * charge v_atomfile
 set atom 100*200 x 0.5 y 1.0
+set atom 100 vx 0.0 vy 0.0 vz -1.0
 set atom 1492 type 3 :pre

 [Description:]
@ -217,7 +228,8 @@ IDs.

 Keywords {x}, {y}, {z}, and {charge} set the coordinates or charge of
 all selected atoms.  For {charge}, the "atom style"_atom_style.html
-being used must support the use of atomic charge.
+being used must support the use of atomic charge. Keywords {vx}, {vy},
+and {vz} set the velocities of all selected atoms.

 Keyword {dipole} uses the specified x,y,z values as components of a
 vector to set as the orientation of the dipole moment vectors of the
@ -232,6 +244,15 @@ the orientation of a particular atom is the same, regardless of how
 many processors are being used.  This keyword does not allow use of an
 atom-style variable.

+Keyword {spin} uses the specified g value to set the magnitude of the
+magnetic spin vectors, and the x,y,z values as components of a vector 
+to set as the orientation of the magnetic spin vectors of the selected 
+atoms.  
+
+Keyword {spin/random} randomizes the orientation of the magnetic spin
+vectors for the selected atoms and sets the magnitude of each to the 
+specified {Dlen} value.  
+
 Keyword {quat} uses the specified values to create a quaternion
 (4-vector) that represents the orientation of the selected atoms.  The
 particles must define a quaternion for their orientation
--- a/examples/SPIN/README
+++ b/examples/SPIN/README
@ -0,0 +1,20 @@
+This directory contains examples and applications of the SPIN package
+=====================================================================
+
+- the iron, cobalt_hcp, cobalt_fcc and nickel directories provide 
+examples of spin-lattice calculations.
+
+- the bfo repository provides an example of spin dynamics calculation
+performed on a fixed lattice, and applied to the multiferroic 
+material bismuth-oxide. 
+
+- the read_restart directory provides examples allowing to write or 
+read data files, and restart magneto-mechanical simulations.  
+
+- vizualization of the dump files can be achieved using Ovito or 
+VMD. See the vmd repository for help vizualizing results with VMD. 
+
+** Note, the aim of this repository is mainly to provide users with
+examples. Better values and tuning of the magnetic and mechanical 
+interactions can be achieved for more accurate materials 
+simulations. **
--- a/lib/gpu/Nvidia.makefile_multi
+++ b/lib/gpu/Nvidia.makefile_multi
@ -79,7 +79,10 @@ OBJS = $(OBJ_DIR)/lal_atom.o $(OBJ_DIR)/lal_ans.o \
       $(OBJ_DIR)/lal_lj_cubic.o $(OBJ_DIR)/lal_lj_cubic_ext.o \
       $(OBJ_DIR)/lal_ufm.o $(OBJ_DIR)/lal_ufm_ext.o \
       $(OBJ_DIR)/lal_dipole_long_lj.o $(OBJ_DIR)/lal_dipole_long_lj_ext.o \
-       $(OBJ_DIR)/lal_lj_expand_coul_long.o $(OBJ_DIR)/lal_lj_expand_coul_long_ext.o
+       $(OBJ_DIR)/lal_lj_expand_coul_long.o $(OBJ_DIR)/lal_lj_expand_coul_long_ext.o \
+       $(OBJ_DIR)/lal_coul_long_cs.o $(OBJ_DIR)/lal_coul_long_cs_ext.o \
+       $(OBJ_DIR)/lal_born_coul_long_cs.o $(OBJ_DIR)/lal_born_coul_long_cs_ext.o \
+       $(OBJ_DIR)/lal_born_coul_wolf_cs.o $(OBJ_DIR)/lal_born_coul_wolf_cs_ext.o

 CBNS = $(OBJ_DIR)/device.cubin $(OBJ_DIR)/device_cubin.h \
       $(OBJ_DIR)/atom.cubin $(OBJ_DIR)/atom_cubin.h \
@ -137,7 +140,10 @@ CBNS = $(OBJ_DIR)/device.cubin $(OBJ_DIR)/device_cubin.h \
       $(OBJ_DIR)/lj_cubic.cubin $(OBJ_DIR)/lj_cubic_cubin.h \
       $(OBJ_DIR)/ufm.cubin $(OBJ_DIR)/ufm_cubin.h \
       $(OBJ_DIR)/dipole_long_lj.cubin $(OBJ_DIR)/dipole_long_lj_cubin.h \
-       $(OBJ_DIR)/lj_expand_coul_long.cubin $(OBJ_DIR)/lj_expand_coul_long_cubin.h
+       $(OBJ_DIR)/lj_expand_coul_long.cubin $(OBJ_DIR)/lj_expand_coul_long_cubin.h \
+       $(OBJ_DIR)/coul_long_cs.cubin $(OBJ_DIR)/coul_long_cs_cubin.h \
+       $(OBJ_DIR)/born_coul_long_cs.cubin $(OBJ_DIR)/born_coul_long_cs_cubin.h \
+       $(OBJ_DIR)/born_coul_wolf_cs.cubin $(OBJ_DIR)/born_coul_wolf_cs_cubin.h

 all: $(OBJ_DIR) $(GPU_LIB) $(EXECS)

@ -837,6 +843,42 @@ $(OBJ_DIR)/lal_lj_expand_coul_long.o: $(ALL_H) lal_lj_expand_coul_long.h lal_lj_
 $(OBJ_DIR)/lal_lj_expand_coul_long_ext.o: $(ALL_H) lal_lj_expand_coul_long.h lal_lj_expand_coul_long_ext.cpp lal_base_charge.h
 	$(CUDR) -o $@ -c lal_lj_expand_coul_long_ext.cpp -I$(OBJ_DIR)

+$(OBJ_DIR)/coul_long_cs.cubin: lal_coul_long_cs.cu lal_precision.h lal_preprocessor.h
+	$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_coul_long_cs.cu
+
+$(OBJ_DIR)/coul_long_cs_cubin.h: $(OBJ_DIR)/coul_long_cs.cubin $(OBJ_DIR)/coul_long_cs.cubin
+	$(BIN2C) -c -n coul_long_cs $(OBJ_DIR)/coul_long_cs.cubin > $(OBJ_DIR)/coul_long_cs_cubin.h
+
+$(OBJ_DIR)/lal_coul_long_cs.o: $(ALL_H) lal_coul_long_cs.h lal_coul_long_cs.cpp $(OBJ_DIR)/coul_long_cs_cubin.h $(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_coul_long.o
+	$(CUDR) -o $@ -c lal_coul_long_cs.cpp -I$(OBJ_DIR)
+
+$(OBJ_DIR)/lal_coul_long_cs_ext.o: $(ALL_H) lal_coul_long_cs.h lal_coul_long_cs_ext.cpp lal_coul_long.h
+	$(CUDR) -o $@ -c lal_coul_long_cs_ext.cpp -I$(OBJ_DIR)
+
+$(OBJ_DIR)/born_coul_long_cs.cubin: lal_born_coul_long_cs.cu lal_precision.h lal_preprocessor.h
+	$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_born_coul_long_cs.cu
+
+$(OBJ_DIR)/born_coul_long_cs_cubin.h: $(OBJ_DIR)/born_coul_long_cs.cubin $(OBJ_DIR)/born_coul_long_cs.cubin
+	$(BIN2C) -c -n born_coul_long_cs $(OBJ_DIR)/born_coul_long_cs.cubin > $(OBJ_DIR)/born_coul_long_cs_cubin.h
+
+$(OBJ_DIR)/lal_born_coul_long_cs.o: $(ALL_H) lal_born_coul_long_cs.h lal_born_coul_long_cs.cpp $(OBJ_DIR)/born_coul_long_cs_cubin.h $(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_born_coul_long.o
+	$(CUDR) -o $@ -c lal_born_coul_long_cs.cpp -I$(OBJ_DIR)
+
+$(OBJ_DIR)/lal_born_coul_long_cs_ext.o: $(ALL_H) lal_born_coul_long_cs.h lal_born_coul_long_cs_ext.cpp lal_born_coul_long.h
+	$(CUDR) -o $@ -c lal_born_coul_long_cs_ext.cpp -I$(OBJ_DIR)
+
+$(OBJ_DIR)/born_coul_wolf_cs.cubin: lal_born_coul_wolf_cs.cu lal_precision.h lal_preprocessor.h
+	$(CUDA) --fatbin -DNV_KERNEL -o $@ lal_born_coul_wolf_cs.cu
+
+$(OBJ_DIR)/born_coul_wolf_cs_cubin.h: $(OBJ_DIR)/born_coul_wolf_cs.cubin $(OBJ_DIR)/born_coul_wolf_cs.cubin
+	$(BIN2C) -c -n born_coul_wolf_cs $(OBJ_DIR)/born_coul_wolf_cs.cubin > $(OBJ_DIR)/born_coul_wolf_cs_cubin.h
+
+$(OBJ_DIR)/lal_born_coul_wolf_cs.o: $(ALL_H) lal_born_coul_wolf_cs.h lal_born_coul_wolf_cs.cpp $(OBJ_DIR)/born_coul_wolf_cs_cubin.h $(OBJ_DIR)/lal_base_charge.o $(OBJ_DIR)/lal_born_coul_wolf.o
+	$(CUDR) -o $@ -c lal_born_coul_wolf_cs.cpp -I$(OBJ_DIR)
+
+$(OBJ_DIR)/lal_born_coul_wolf_cs_ext.o: $(ALL_H) lal_born_coul_wolf_cs.h lal_born_coul_wolf_cs_ext.cpp lal_born_coul_wolf.h
+	$(CUDR) -o $@ -c lal_born_coul_wolf_cs_ext.cpp -I$(OBJ_DIR)
+
 $(BIN_DIR)/nvc_get_devices: ./geryon/ucl_get_devices.cpp $(NVD_H)
 	$(CUDR) -o $@ ./geryon/ucl_get_devices.cpp -DUCL_CUDADR $(CUDA_LIB) -lcuda 

--- a/python/lammps.py
+++ b/python/lammps.py
@ -708,6 +708,12 @@ class Atom(object):
            self.lmp.eval("vy[%d]" % self.index),
            self.lmp.eval("vz[%d]" % self.index))

+  @velocity.setter
+  def velocity(self, value):
+     self.lmp.set("atom", self.index, "vx", value[0])
+     self.lmp.set("atom", self.index, "vy", value[1])
+     self.lmp.set("atom", self.index, "vz", value[2])
+
  @property
  def force(self):
    return (self.lmp.eval("fx[%d]" % self.index),
@ -738,6 +744,11 @@ class Atom2D(Atom):
    return (self.lmp.eval("vx[%d]" % self.index),
            self.lmp.eval("vy[%d]" % self.index))

+  @velocity.setter
+  def velocity(self, value):
+     self.lmp.set("atom", self.index, "vx", value[0])
+     self.lmp.set("atom", self.index, "vy", value[1])
+
  @property
  def force(self):
    return (self.lmp.eval("fx[%d]" % self.index),
--- a/src/KOKKOS/Install.sh
+++ b/src/KOKKOS/Install.sh
@ -93,6 +93,8 @@ action domain_kokkos.cpp
 action domain_kokkos.h
 action fix_deform_kokkos.cpp
 action fix_deform_kokkos.h
+action fix_enforce2d_kokkos.cpp
+action fix_enforce2d_kokkos.h
 action fix_eos_table_rx_kokkos.cpp fix_eos_table_rx.cpp
 action fix_eos_table_rx_kokkos.h fix_eos_table_rx.h  
 action fix_langevin_kokkos.cpp
--- a/src/KOKKOS/fix_enforce2d_kokkos.cpp
+++ b/src/KOKKOS/fix_enforce2d_kokkos.cpp
@ -0,0 +1,168 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+/* ----------------------------------------------------------------------
+   Contributing authors: Stefan Paquay & Matthew Peterson (Brandeis University)
+------------------------------------------------------------------------- */
+
+#include "atom_masks.h"
+#include "atom_kokkos.h"
+#include "comm.h"
+#include "error.h"
+#include "fix_enforce2d_kokkos.h"
+
+
+using namespace LAMMPS_NS;
+
+
+template <class DeviceType>
+FixEnforce2DKokkos<DeviceType>::FixEnforce2DKokkos(LAMMPS *lmp, int narg, char **arg) :
+  FixEnforce2D(lmp, narg, arg)
+{
+  kokkosable = 1;
+  atomKK = (AtomKokkos *) atom;
+  execution_space = ExecutionSpaceFromDevice<DeviceType>::space;
+
+  datamask_read   = V_MASK | F_MASK | OMEGA_MASK | MASK_MASK
+	  | TORQUE_MASK | ANGMOM_MASK;
+
+  datamask_modify = V_MASK | F_MASK | OMEGA_MASK
+	  | TORQUE_MASK | ANGMOM_MASK;
+}
+
+
+template <class DeviceType>
+void FixEnforce2DKokkos<DeviceType>::setup(int vflag)
+{
+  post_force(vflag);
+}
+
+
+template <class DeviceType>
+void FixEnforce2DKokkos<DeviceType>::post_force(int vflag)
+{
+  atomKK->sync(execution_space,datamask_read);
+
+  v = atomKK->k_v.view<DeviceType>();
+  f = atomKK->k_f.view<DeviceType>();
+
+  if( atomKK->omega_flag )
+    omega  = atomKK->k_omega.view<DeviceType>();
+
+  if( atomKK->angmom_flag )
+    angmom = atomKK->k_angmom.view<DeviceType>();
+
+  if( atomKK->torque_flag )
+    torque = atomKK->k_torque.view<DeviceType>();
+
+
+  mask = atomKK->k_mask.view<DeviceType>();
+
+  int nlocal = atomKK->nlocal;
+  if (igroup == atomKK->firstgroup) nlocal = atomKK->nfirst;
+
+  int flag_mask = 0;
+  if( atomKK->omega_flag ) flag_mask  |= 1;
+  if( atomKK->angmom_flag ) flag_mask |= 2;
+  if( atomKK->torque_flag ) flag_mask |= 4;
+
+  copymode = 1;
+  switch( flag_mask ){
+    case 0:{
+      FixEnforce2DKokkosPostForceFunctor<DeviceType,0,0,0> functor(this);
+      Kokkos::parallel_for(nlocal,functor);
+      break;
+    }
+    case 1:{
+      FixEnforce2DKokkosPostForceFunctor<DeviceType,1,0,0> functor(this);
+      Kokkos::parallel_for(nlocal,functor);
+      break;
+    }
+    case 2:{
+      FixEnforce2DKokkosPostForceFunctor<DeviceType,0,1,0> functor(this);
+      Kokkos::parallel_for(nlocal,functor);
+      break;
+    }
+    case 3:{
+      FixEnforce2DKokkosPostForceFunctor<DeviceType,1,1,0> functor(this);
+      Kokkos::parallel_for(nlocal,functor);
+      break;
+    }
+    case 4:{
+      FixEnforce2DKokkosPostForceFunctor<DeviceType,0,0,1> functor(this);
+      Kokkos::parallel_for(nlocal,functor);
+      break;
+    }
+    case 5:{
+      FixEnforce2DKokkosPostForceFunctor<DeviceType,1,0,1> functor(this);
+      Kokkos::parallel_for(nlocal,functor);
+      break;
+    }
+    case 6:{
+      FixEnforce2DKokkosPostForceFunctor<DeviceType,0,1,1> functor(this);
+      Kokkos::parallel_for(nlocal,functor);
+      break;
+    }
+    case 7:{
+      FixEnforce2DKokkosPostForceFunctor<DeviceType,1,1,1> functor(this);
+      Kokkos::parallel_for(nlocal,functor);
+      break;
+    }
+    default:
+      error->all(FLERR, "Flag in fix_enforce2d_kokkos outside of what it should be");
+  }
+  copymode = 0;
+
+  atomKK->modified(execution_space,datamask_modify);
+
+  for (int m = 0; m < nfixlist; m++) {
+    atomKK->sync(flist[m]->execution_space,flist[m]->datamask_read);
+    flist[m]->enforce2d();
+    atomKK->modified(flist[m]->execution_space,flist[m]->datamask_modify);
+  }
+
+}
+
+
+template <class DeviceType>
+template <int omega_flag, int angmom_flag, int torque_flag>
+void FixEnforce2DKokkos<DeviceType>::post_force_item( int i ) const
+{
+  if (mask[i] & groupbit){
+    v(i,2) = 0.0;
+    f(i,2) = 0.0;
+
+    if(omega_flag){
+      omega(i,0) = 0.0;
+      omega(i,1) = 0.0;
+    }
+
+    if(angmom_flag){
+      angmom(i,0) = 0.0;
+      angmom(i,1) = 0.0;
+    }
+
+    if(torque_flag){
+      torque(i,0) = 0.0;
+      torque(i,1) = 0.0;
+    }
+  }
+}
+
+
+namespace LAMMPS_NS {
+template class FixEnforce2DKokkos<LMPDeviceType>;
+#ifdef KOKKOS_HAVE_CUDA
+template class FixEnforce2DKokkos<LMPHostType>;
+#endif
+}
--- a/src/KOKKOS/fix_enforce2d_kokkos.h
+++ b/src/KOKKOS/fix_enforce2d_kokkos.h
@ -0,0 +1,84 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   http://lammps.sandia.gov, Sandia National Laboratories
+   Steve Plimpton, sjplimp@sandia.gov
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef FIX_CLASS
+
+FixStyle(enforce2d/kk,FixEnforce2DKokkos<LMPDeviceType>)
+FixStyle(enforce2d/kk/device,FixEnforce2DKokkos<LMPDeviceType>)
+FixStyle(enforce2d/kk/host,FixEnforce2DKokkos<LMPHostType>)
+
+#else
+
+#ifndef LMP_FIX_ENFORCE2D_KOKKOS_H
+#define LMP_FIX_ENFORCE2D_KOKKOS_H
+
+#include "fix_enforce2d.h"
+#include "kokkos_type.h"
+
+namespace LAMMPS_NS {
+
+template<class DeviceType>
+class FixEnforce2DKokkos : public FixEnforce2D {
+ public:
+  FixEnforce2DKokkos(class LAMMPS *, int, char **);
+  // ~FixEnforce2DKokkos() {}
+  void setup(int);
+  void post_force(int);
+
+  template <int omega_flag, int angmom_flag, int torque_flag>
+  KOKKOS_INLINE_FUNCTION
+  void post_force_item(const int i) const;
+
+  // void min_setup(int);       Kokkos does not support minimization (yet)
+  // void min_post_force(int);  Kokkos does not support minimization (yet)
+  // void post_force_respa(int, int, int);  No RRESPA support yet.
+
+ private:
+  typename ArrayTypes<DeviceType>::t_v_array v;
+  typename ArrayTypes<DeviceType>::t_f_array f;
+
+  typename ArrayTypes<DeviceType>::t_v_array omega;
+  typename ArrayTypes<DeviceType>::t_v_array angmom;
+  typename ArrayTypes<DeviceType>::t_f_array torque;
+
+  typename ArrayTypes<DeviceType>::t_int_1d mask;
+};
+
+
+template <class DeviceType, int omega_flag, int angmom_flag, int torque_flag>
+struct FixEnforce2DKokkosPostForceFunctor {
+  typedef DeviceType device_type;
+  FixEnforce2DKokkos<DeviceType> c;
+
+  FixEnforce2DKokkosPostForceFunctor(FixEnforce2DKokkos<DeviceType>* c_ptr):
+    c(*c_ptr) {};
+
+  KOKKOS_INLINE_FUNCTION
+  void operator()(const int i) const {
+    c.template post_force_item <omega_flag, angmom_flag, torque_flag>(i);
+  }
+};
+
+
+}
+
+#endif
+#endif
+
+/* ERROR/WARNING messages:
+
+E: Flag in fix_enforce2d_kokkos outside of what it should be
+
+LAMMPS developer-only error.
+
+*/
--- a/src/KOKKOS/pair_reaxc_kokkos.cpp
+++ b/src/KOKKOS/pair_reaxc_kokkos.cpp
@ -343,6 +343,7 @@ void PairReaxCKokkos<DeviceType>::init_md()

  swa = control->nonb_low;
  swb = control->nonb_cut;
+  enobondsflag = control->enobondsflag;

  if (fabs(swa) > 0.01 )
    error->warning(FLERR,"Warning: non-zero lower Taper-radius cutoff");
@ -2272,12 +2273,12 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeMulti2<NEIGHFLAG,EVF
  int numbonds = d_bo_num[i];

  e_lp = 0.0;
-  if (numbonds > 0 || control->enobondsflag)
+  if (numbonds > 0 || enobondsflag)
    e_lp = p_lp2 * d_Delta_lp[i] * inv_expvd2;
  const F_FLOAT dElp = p_lp2 * inv_expvd2 + 75.0 * p_lp2 * d_Delta_lp[i] * expvd2 * inv_expvd2*inv_expvd2;
  const F_FLOAT CElp = dElp * d_dDelta_lp[i];

-  if (numbonds > 0 || control->enobondsflag)
+  if (numbonds > 0 || enobondsflag)
    a_CdDelta[i] += CElp;

  if (eflag) ev.ereax[0] += e_lp;
@ -2314,7 +2315,7 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeMulti2<NEIGHFLAG,EVF
  const F_FLOAT inv_exp_ovun8 = 1.0 / (1.0 + exp_ovun8);

  e_un = 0;
-  if (numbonds > 0 || control->enobondsflag)
+  if (numbonds > 0 || enobondsflag)
    e_un = -p_ovun5 * (1.0 - exp_ovun6) * inv_exp_ovun2n * inv_exp_ovun8;

  if (eflag) ev.ereax[2] += e_un;
@ -2334,7 +2335,7 @@ void PairReaxCKokkos<DeviceType>::operator()(PairReaxComputeMulti2<NEIGHFLAG,EVF
  // multibody forces

  a_CdDelta[i] += CEover3;
-  if (numbonds > 0 || control->enobondsflag)
+  if (numbonds > 0 || enobondsflag)
    a_CdDelta[i] += CEunder3;

  const int j_start = d_bo_first[i];
--- a/src/KOKKOS/pair_reaxc_kokkos.h
+++ b/src/KOKKOS/pair_reaxc_kokkos.h
@ -427,7 +427,7 @@ class PairReaxCKokkos : public PairReaxC {

  friend void pair_virial_fdotr_compute<PairReaxCKokkos>(PairReaxCKokkos*);

-  int bocnt,hbcnt;
+  int bocnt,hbcnt,enobondsflag;

  typedef LR_lookup_table_kk<DeviceType> LR_lookup_table_kk_DT;

--- a/src/MAKE/MACHINES/Makefile.theta
+++ b/src/MAKE/MACHINES/Makefile.theta
@ -0,0 +1,133 @@
+# knl = Flags for Knights Landing Xeon Phi Processor,Intel Compiler/MPI,MKL FFT
+# module load perftools-base perftools
+# make theta -j 8
+# pat_build -g mpi -u ./lmp_theta
+
+SHELL = /bin/sh
+
+# ---------------------------------------------------------------------
+# compiler/linker settings
+# specify flags and libraries needed for your compiler
+
+CC =        CC -mkl
+#OPTFLAGS =       -O0
+OPTFLAGS =      -xMIC-AVX512 -O3 -fp-model fast=2 -no-prec-div -qoverride-limits
+CCFLAGS =   -g -qopenmp -DLAMMPS_MEMALIGN=64 -qno-offload \
+                -fno-alias -ansi-alias -restrict $(OPTFLAGS)
+#CCFLAGS +=      -DLMP_INTEL_NO_TBB
+#CCFLAGS +=      -DLAMMPS_BIGBIG
+#CCFLAGS +=      -D_USE_PAPI
+#CCFLAGS +=      -D_USE_CRAYPAT_API
+SHFLAGS =   -fPIC
+DEPFLAGS =  -M
+
+LINK =      $(CC)
+LINKFLAGS = -g -qopenmp $(OPTFLAGS)
+LINKFLAGS += -dynamic
+LIB =
+#LIB +=           -L${TBBROOT}/lib/intel64/gcc4.7 -ltbbmalloc
+LIB +=           -ltbbmalloc
+#LIB +=          /soft/debuggers/forge-7.0-2017-02-16/lib/64/libdmallocthcxx.a -zmuldefs
+SIZE =      size
+
+ARCHIVE =   ar
+ARFLAGS =   -rc
+SHLIBFLAGS =    -shared
+
+# ---------------------------------------------------------------------
+# LAMMPS-specific settings, all OPTIONAL
+# specify settings for LAMMPS features you will use
+# if you change any -D setting, do full re-compile after "make clean"
+
+# LAMMPS ifdef settings
+# see possible settings in Section 2.2 (step 4) of manual
+
+LMP_INC =   -DLAMMPS_GZIP #-DLAMMPS_JPEG
+
+# MPI library
+# see discussion in Section 2.2 (step 5) of manual
+# MPI wrapper compiler/linker can provide this info
+# can point to dummy MPI library in src/STUBS as in Makefile.serial
+# use -D MPICH and OMPI settings in INC to avoid C++ lib conflicts
+# INC = path for mpi.h, MPI compiler settings
+# PATH = path for MPI library
+# LIB = name of MPI library
+
+MPI_INC =       -DMPICH_SKIP_MPICXX -DOMPI_SKIP_MPICXX=1
+MPI_PATH =
+MPI_LIB =
+
+# FFT library
+# see discussion in Section 2.2 (step 6) of manaul
+# can be left blank to use provided KISS FFT library
+# INC = -DFFT setting, e.g. -DFFT_FFTW, FFT compiler settings
+# PATH = path for FFT library
+# LIB = name of FFT library
+
+FFT_INC =       -DFFT_MKL -DFFT_SINGLE
+FFT_PATH =
+FFT_LIB =       -L$(MKLROOT)/lib/intel64/ -Wl,--start-group -lmkl_intel_ilp64 \
+                -lmkl_intel_thread -lmkl_core -Wl,--end-group
+
+# JPEG and/or PNG library
+# see discussion in Section 2.2 (step 7) of manual
+# only needed if -DLAMMPS_JPEG or -DLAMMPS_PNG listed with LMP_INC
+# INC = path(s) for jpeglib.h and/or png.h
+# PATH = path(s) for JPEG library and/or PNG library
+# LIB = name(s) of JPEG library and/or PNG library
+
+JPG_INC =
+JPG_PATH =
+JPG_LIB =
+
+# ---------------------------------------------------------------------
+# build rules and dependencies
+# do not edit this section
+
+include Makefile.package.settings
+include Makefile.package
+
+EXTRA_INC = $(LMP_INC) $(PKG_INC) $(MPI_INC) $(FFT_INC) $(JPG_INC) $(PKG_SYSINC)
+EXTRA_PATH = $(PKG_PATH) $(MPI_PATH) $(FFT_PATH) $(JPG_PATH) $(PKG_SYSPATH)
+EXTRA_LIB = $(PKG_LIB) $(MPI_LIB) $(FFT_LIB) $(JPG_LIB) $(PKG_SYSLIB)
+
+# Path to src files
+
+vpath %.cpp ..
+vpath %.h ..
+
+# Link target
+
+$(EXE): $(OBJ)
+    $(LINK) $(LINKFLAGS) $(EXTRA_PATH) $(OBJ) $(EXTRA_LIB) $(LIB) -o $(EXE)
+    $(SIZE) $(EXE)
+
+# Library targets
+
+lib:    $(OBJ)
+    $(ARCHIVE) $(ARFLAGS) $(EXE) $(OBJ)
+
+shlib:  $(OBJ)
+    $(CC) $(CCFLAGS) $(SHFLAGS) $(SHLIBFLAGS) $(EXTRA_PATH) -o $(EXE) \
+        $(OBJ) $(EXTRA_LIB) $(LIB)
+
+# Compilation rules
+
+%.o:%.cpp
+    $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
+
+%.d:%.cpp
+    $(CC) $(CCFLAGS) $(EXTRA_INC) $(DEPFLAGS) $< > $@
+
+%.o:%.cu
+    $(CC) $(CCFLAGS) $(SHFLAGS) $(EXTRA_INC) -c $<
+
+# Individual dependencies
+
+depend : fastdep.exe $(SRC)
+    @./fastdep.exe $(EXTRA_INC) -- $^ > .depend || exit 1
+
+fastdep.exe: ../DEPEND/fastdep.c
+    icc -O -o $@ $<
+
+sinclude .depend
--- a/src/SPIN/atom_vec_spin.cpp
+++ b/src/SPIN/atom_vec_spin.cpp
@ -20,12 +20,12 @@
   Please cite the related publication:
   Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018).
   Massively parallel symplectic algorithm for coupled magnetic spin dynamics
-   and molecular dynamics. arXiv preprint arXiv:1801.10233.
+   and molecular dynamics. Journal of Computational Physics.
 ------------------------------------------------------------------------- */

-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>
 #include "atom.h"
 #include "atom_vec_spin.h"
 #include "comm.h"
@ -54,7 +54,7 @@ AtomVecSpin::AtomVecSpin(LAMMPS *lmp) : AtomVec(lmp)
  size_data_atom = 9;
  size_data_vel = 4;
  xcol_data = 4;
-  
+
  atom->sp_flag = 1;
 }

--- a/src/SPIN/compute_spin.cpp
+++ b/src/SPIN/compute_spin.cpp
@ -18,11 +18,11 @@
   Please cite the related publication:
   Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018).
   Massively parallel symplectic algorithm for coupled magnetic spin dynamics
-   and molecular dynamics. arXiv preprint arXiv:1801.10233.
+   and molecular dynamics. Journal of Computational Physics.
 ------------------------------------------------------------------------- */

 #include <mpi.h>
-#include <string.h>
+#include <cstring>
 #include "atom.h"
 #include "compute_spin.h"
 #include "domain.h"
--- a/src/SPIN/fix_langevin_spin.cpp
+++ b/src/SPIN/fix_langevin_spin.cpp
@ -18,13 +18,13 @@
   Please cite the related publication:
   Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018).
   Massively parallel symplectic algorithm for coupled magnetic spin dynamics
-   and molecular dynamics. arXiv preprint arXiv:1801.10233.
+   and molecular dynamics. Journal of Computational Physics.
 ------------------------------------------------------------------------- */

 #include <mpi.h>
-#include <math.h>
-#include <string.h>
-#include <stdlib.h>
+#include <cmath>
+#include <cstring>
+#include <cstdlib>

 #include "atom.h"
 #include "atom_vec_ellipsoid.h"
--- a/src/SPIN/fix_nve_spin.cpp
+++ b/src/SPIN/fix_nve_spin.cpp
@ -18,12 +18,12 @@
   Please cite the related publication:
   Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018).
   Massively parallel symplectic algorithm for coupled magnetic spin dynamics
-   and molecular dynamics. arXiv preprint arXiv:1801.10233.
+   and molecular dynamics. Journal of Computational Physics.
 ------------------------------------------------------------------------- */

-#include <math.h>
-#include <stdio.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstring>

 #include "atom.h"
 #include "atom_vec.h"
@ -59,8 +59,9 @@ static const char cite_fix_nve_spin[] =
  "title={Massively parallel symplectic algorithm for coupled magnetic spin "
  "dynamics and molecular dynamics},\n"
  "author={Tranchida, J and Plimpton, SJ and Thibaudeau, P and Thompson, AP},\n"
-  "journal={arXiv preprint arXiv:1801.10233},\n"
-  "year={2018}\n"
+  "journal={Journal of Computational Physics},\n"
+  "year={2018},\n"
+  "publisher={Elsevier}\n"
  "}\n\n";

 enum{NONE};
--- a/src/SPIN/fix_precession_spin.cpp
+++ b/src/SPIN/fix_precession_spin.cpp
@ -18,13 +18,13 @@
   Please cite the related publication:
   Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018).
   Massively parallel symplectic algorithm for coupled magnetic spin dynamics
-   and molecular dynamics. arXiv preprint arXiv:1801.10233.
+   and molecular dynamics. Journal of Computational Physics.
 ------------------------------------------------------------------------- */

-#include <math.h>
-#include <stdio.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdio>
+#include <cstdlib>
+#include <cstring>

 #include "atom.h"
 #include "domain.h"
--- a/src/SPIN/pair_spin.cpp
+++ b/src/SPIN/pair_spin.cpp
@ -18,12 +18,12 @@
   Please cite the related publication:
   Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018).
   Massively parallel symplectic algorithm for coupled magnetic spin dynamics
-   and molecular dynamics. arXiv preprint arXiv:1801.10233.
+   and molecular dynamics. Journal of Computational Physics.
 ------------------------------------------------------------------------- */

-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>

 #include "atom.h"
 #include "comm.h"
--- a/src/SPIN/pair_spin_dmi.cpp
+++ b/src/SPIN/pair_spin_dmi.cpp
@ -18,12 +18,12 @@
   Please cite the related publication:
   Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018).
   Massively parallel symplectic algorithm for coupled magnetic spin dynamics
-   and molecular dynamics. arXiv preprint arXiv:1801.10233.
+   and molecular dynamics. Journal of Computational Physics.
 ------------------------------------------------------------------------- */

-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>

 #include "atom.h"
 #include "comm.h"
--- a/src/SPIN/pair_spin_exchange.cpp
+++ b/src/SPIN/pair_spin_exchange.cpp
@ -18,12 +18,12 @@
   Please cite the related publication:
   Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018).
   Massively parallel symplectic algorithm for coupled magnetic spin dynamics
-   and molecular dynamics. arXiv preprint arXiv:1801.10233.
+   and molecular dynamics. Journal of Computational Physics.
 ------------------------------------------------------------------------- */

-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>

 #include "atom.h"
 #include "comm.h"
--- a/src/SPIN/pair_spin_magelec.cpp
+++ b/src/SPIN/pair_spin_magelec.cpp
@ -18,12 +18,12 @@
   Please cite the related publication:
   Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018).
   Massively parallel symplectic algorithm for coupled magnetic spin dynamics
-   and molecular dynamics. arXiv preprint arXiv:1801.10233.
+   and molecular dynamics. Journal of Computational Physics.
 ------------------------------------------------------------------------- */

-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>

 #include "atom.h"
 #include "comm.h"
@ -436,9 +436,9 @@ void PairSpinMagelec::compute_magelec_mech(int i, int j, double fi[3], double sp
  meiy *= ME_mech[itype][jtype];
  meiz *= ME_mech[itype][jtype];

-  fi[0] = meiy*vz - meiz*vy;
-  fi[1] = meiz*vx - meix*vz;
-  fi[2] = meix*vy - meiy*vx;
+  fi[0] += meiy*vz - meiz*vy;
+  fi[1] += meiz*vx - meix*vz;
+  fi[2] += meix*vy - meiy*vx;

 }

--- a/src/SPIN/pair_spin_neel.cpp
+++ b/src/SPIN/pair_spin_neel.cpp
@ -18,12 +18,12 @@
   Please cite the related publication:
   Tranchida, J., Plimpton, S. J., Thibaudeau, P., & Thompson, A. P. (2018).
   Massively parallel symplectic algorithm for coupled magnetic spin dynamics
-   and molecular dynamics. arXiv preprint arXiv:1801.10233.
+   and molecular dynamics. Journal of Computational Physics.
 ------------------------------------------------------------------------- */

-#include <math.h>
-#include <stdlib.h>
-#include <string.h>
+#include <cmath>
+#include <cstdlib>
+#include <cstring>

 #include "atom.h"
 #include "comm.h"
--- a/src/balance.cpp
+++ b/src/balance.cpp
@ -350,13 +350,13 @@ void Balance::command(int narg, char **arg)
  domain->set_local_box();

  // move particles to new processors via irregular()
+  // set disable = 0, so weights migrate with atoms for imbfinal calculation

  if (domain->triclinic) domain->x2lamda(atom->nlocal);
  Irregular *irregular = new Irregular(lmp);
  if (wtflag) fixstore->disable = 0;
  if (style == BISECTION) irregular->migrate_atoms(1,1,rcb->sendproc);
  else irregular->migrate_atoms(1);
-  if (wtflag) fixstore->disable = 1;
  delete irregular;
  if (domain->triclinic) domain->lamda2x(atom->nlocal);

@ -377,9 +377,11 @@ void Balance::command(int narg, char **arg)
  }

  // imbfinal = final imbalance
+  // set disable = 1, so weights no longer migrate with atoms

  double maxfinal;
  double imbfinal = imbalance_factor(maxfinal);
+  if (wtflag) fixstore->disable = 1;

  // stats output

@ -540,6 +542,8 @@ void Balance::weight_storage(char *prefix)
    fixstore = (FixStore *) modify->fix[modify->nfix-1];
  } else fixstore = (FixStore *) modify->fix[ifix];

+  // do not carry weights with atoms during normal atom migration
+
  fixstore->disable = 1;

  if (prefix) delete [] fixargs[0];
--- a/src/fix_balance.cpp
+++ b/src/fix_balance.cpp
@ -114,6 +114,7 @@ FixBalance::FixBalance(LAMMPS *lmp, int narg, char **arg) :

  if (nevery) force_reneighbor = 1;
  lastbalance = -1;
+  next_reneighbor = -1;

  // compute initial outputs

@ -248,6 +249,10 @@ void FixBalance::pre_neighbor()
  if (!pending) return;
  imbfinal = balance->imbalance_factor(maxloadperproc);
  pending = 0;
+
+  // set disable = 1, so weights no longer migrate with atoms
+
+  if (wtflag) balance->fixstore->disable = 1;
 }

 /* ----------------------------------------------------------------------
@ -275,21 +280,23 @@ void FixBalance::rebalance()

  // reset proc sub-domains
  // check and warn if any proc's subbox is smaller than neigh skin
-  //   since may lead to lost atoms in exchange()
+  //   since may lead to lost atoms in comm->exchange()

  if (domain->triclinic) domain->set_lamda_box();
  domain->set_local_box();
  domain->subbox_too_small_check(neighbor->skin);

  // move atoms to new processors via irregular()
-  // only needed if migrate_check() says an atom moves to far
+  // for non-RCB only needed if migrate_check() says an atom moves too far
  // else allow caller's comm->exchange() to do it
+  // set disable = 0, so weights migrate with atoms
+  //   important to delay disable = 1 until after pre_neighbor imbfinal calc
+  //   b/c atoms may migrate again in comm->exchange()

  if (domain->triclinic) domain->x2lamda(atom->nlocal);
  if (wtflag) balance->fixstore->disable = 0;
  if (lbstyle == BISECTION) irregular->migrate_atoms(0,1,sendproc);
  else if (irregular->migrate_check()) irregular->migrate_atoms();
-  if (wtflag) balance->fixstore->disable = 1;
  if (domain->triclinic) domain->lamda2x(atom->nlocal);

  // invoke KSpace setup_grid() to adjust to new proc sub-domains
--- a/src/fix_enforce2d.cpp
+++ b/src/fix_enforce2d.cpp
@ -38,6 +38,8 @@ FixEnforce2D::FixEnforce2D(LAMMPS *lmp, int narg, char **arg) :

 FixEnforce2D::~FixEnforce2D()
 {
+  if (copymode) return;
+
  delete [] flist;
 }

--- a/src/fix_enforce2d.h
+++ b/src/fix_enforce2d.h
@ -36,7 +36,7 @@ class FixEnforce2D : public Fix {
  void post_force_respa(int, int, int);
  void min_post_force(int);

- private:
+ protected:
  int nfixlist;
  class Fix **flist;
 };
--- a/src/fix_store.cpp
+++ b/src/fix_store.cpp
@ -154,8 +154,6 @@ void FixStore::reset_global(int nrow_caller, int ncol_caller)
  if (vecflag) memory->create(vstore,nrow,"fix/store:vstore");
  else memory->create(astore,nrow,ncol,"fix/store:astore");
  memory->create(rbuf,nrow*ncol+2,"fix/store:rbuf");
-
- // printf("AAA HOW GET HERE\n");
 }

 /* ----------------------------------------------------------------------
--- a/src/read_restart.cpp
+++ b/src/read_restart.cpp
@ -62,7 +62,9 @@ enum{VERSION,SMALLINT,TAGINT,BIGINT,
     MULTIPROC,MPIIO,PROCSPERFILE,PERPROC,
     IMAGEINT,BOUNDMIN,TIMESTEP,
     ATOM_ID,ATOM_MAP_STYLE,ATOM_MAP_USER,ATOM_SORTFREQ,ATOM_SORTBIN,
-     COMM_MODE,COMM_CUTOFF,COMM_VEL,NO_PAIR};
+     COMM_MODE,COMM_CUTOFF,COMM_VEL,NO_PAIR,
+     EXTRA_BOND_PER_ATOM,EXTRA_ANGLE_PER_ATOM,EXTRA_DIHEDRAL_PER_ATOM,
+     EXTRA_IMPROPER_PER_ATOM,EXTRA_SPECIAL_PER_ATOM};

 #define LB_FACTOR 1.1

@ -914,6 +916,17 @@ void ReadRestart::header(int incompatible)
    } else if (flag == COMM_VEL) {
      comm->ghost_velocity = read_int();

+    } else if (flag == EXTRA_BOND_PER_ATOM) {
+      atom->extra_bond_per_atom = read_int();
+    } else if (flag == EXTRA_ANGLE_PER_ATOM) {
+      atom->extra_angle_per_atom = read_int();
+    } else if (flag == EXTRA_DIHEDRAL_PER_ATOM) {
+      atom->extra_dihedral_per_atom = read_int();
+    } else if (flag == EXTRA_IMPROPER_PER_ATOM) {
+      atom->extra_improper_per_atom = read_int();
+    } else if (flag == EXTRA_SPECIAL_PER_ATOM) {
+      force->special_extra = read_int();
+
    } else error->all(FLERR,"Invalid flag in header section of restart file");

    flag = read_int();
--- a/src/reset_ids.cpp
+++ b/src/reset_ids.cpp
@ -16,6 +16,7 @@
 #include "atom_vec.h"
 #include "domain.h"
 #include "comm.h"
+#include "special.h"
 #include "memory.h"
 #include "error.h"

@ -44,7 +45,7 @@ void ResetIDs::command(int narg, char **arg)
  }

  // create an atom map if one doesn't exist already
-  
+
  int mapflag = 0;
  if (atom->map_style == 0) {
    mapflag = 1;
@ -93,7 +94,7 @@ void ResetIDs::command(int narg, char **arg)
  // forward_comm_array acquires new IDs for ghost atoms

  double **newIDs;
-  memory->create(newIDs,nall,1,"reset_ids:newIDs");  
+  memory->create(newIDs,nall,1,"reset_ids:newIDs");

  for (int i = 0; i < nlocal; i++) {
    newIDs[i][0] = tag[i];
@ -105,7 +106,7 @@ void ResetIDs::command(int narg, char **arg)
  // loop over bonds, angles, etc and reset IDs in stored topology arrays
  // only necessary for molecular = 1, not molecular = 2
  // badcount = atom IDs that could not be found
-  
+
  int badcount = 0;

  if (atom->molecular == 1) {
@ -232,8 +233,15 @@ void ResetIDs::command(int narg, char **arg)
  atom->map_init();
  atom->map_set();

+  // need to update exclusions with new atom IDs
+
+  if (atom->molecular == 1) {
+    Special special(lmp);
+    special.build();
+  }
+
  // delete temporary atom map
-  
+
  if (mapflag) {
    atom->map_delete();
    atom->map_style = 0;
--- a/src/set.cpp
+++ b/src/set.cpp
@ -48,7 +48,7 @@ enum{TYPE,TYPE_FRACTION,MOLECULE,X,Y,Z,CHARGE,MASS,SHAPE,LENGTH,TRI,
     THETA,THETA_RANDOM,ANGMOM,OMEGA,
     DIAMETER,DENSITY,VOLUME,IMAGE,BOND,ANGLE,DIHEDRAL,IMPROPER,
     MESO_E,MESO_CV,MESO_RHO,EDPD_TEMP,EDPD_CV,CC,SMD_MASS_DENSITY,
-     SMD_CONTACT_RADIUS,DPDTHETA,INAME,DNAME};
+     SMD_CONTACT_RADIUS,DPDTHETA,INAME,DNAME,VX,VY,VZ};

 #define BIG INT_MAX

@ -141,6 +141,27 @@ void Set::command(int narg, char **arg)
      set(Z);
      iarg += 2;

+    } else if (strcmp(arg[iarg],"vx") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
+      if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1);
+      else dvalue = force->numeric(FLERR,arg[iarg+1]);
+      set(VX);
+      iarg += 2;
+
+    } else if (strcmp(arg[iarg],"vy") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
+      if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1);
+      else dvalue = force->numeric(FLERR,arg[iarg+1]);
+      set(VY);
+      iarg += 2;
+
+    } else if (strcmp(arg[iarg],"vz") == 0) {
+      if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
+      if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1);
+      else dvalue = force->numeric(FLERR,arg[iarg+1]);
+      set(VZ);
+      iarg += 2;
+
    } else if (strcmp(arg[iarg],"charge") == 0) {
      if (iarg+2 > narg) error->all(FLERR,"Illegal set command");
      if (strstr(arg[iarg+1],"v_") == arg[iarg+1]) varparse(arg[iarg+1],1);
@ -732,6 +753,9 @@ void Set::set(int keyword)
    else if (keyword == X) atom->x[i][0] = dvalue;
    else if (keyword == Y) atom->x[i][1] = dvalue;
    else if (keyword == Z) atom->x[i][2] = dvalue;
+    else if (keyword == VX) atom->v[i][0] = dvalue;
+    else if (keyword == VY) atom->v[i][1] = dvalue;
+    else if (keyword == VZ) atom->v[i][2] = dvalue;
    else if (keyword == CHARGE) atom->q[i] = dvalue;
    else if (keyword == MASS) {
      if (dvalue <= 0.0) error->one(FLERR,"Invalid mass in set command");
--- a/src/version.h
+++ b/src/version.h
@ -1 +1 @@
-#define LAMMPS_VERSION "29 Jun 2018"
+#define LAMMPS_VERSION "16 Jul 2018"
--- a/src/write_restart.cpp
+++ b/src/write_restart.cpp
@ -61,7 +61,9 @@ enum{VERSION,SMALLINT,TAGINT,BIGINT,
     MULTIPROC,MPIIO,PROCSPERFILE,PERPROC,
     IMAGEINT,BOUNDMIN,TIMESTEP,
     ATOM_ID,ATOM_MAP_STYLE,ATOM_MAP_USER,ATOM_SORTFREQ,ATOM_SORTBIN,
-     COMM_MODE,COMM_CUTOFF,COMM_VEL,NO_PAIR};
+     COMM_MODE,COMM_CUTOFF,COMM_VEL,NO_PAIR,
+     EXTRA_BOND_PER_ATOM,EXTRA_ANGLE_PER_ATOM,EXTRA_DIHEDRAL_PER_ATOM,
+     EXTRA_IMPROPER_PER_ATOM,EXTRA_SPECIAL_PER_ATOM};

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

@ -527,6 +529,12 @@ void WriteRestart::header()
  write_double(COMM_CUTOFF,comm->cutghostuser);
  write_int(COMM_VEL,comm->ghost_velocity);

+  write_int(EXTRA_BOND_PER_ATOM,atom->extra_bond_per_atom);
+  write_int(EXTRA_ANGLE_PER_ATOM,atom->extra_angle_per_atom);
+  write_int(EXTRA_DIHEDRAL_PER_ATOM,atom->extra_dihedral_per_atom);
+  write_int(EXTRA_IMPROPER_PER_ATOM,atom->extra_improper_per_atom);
+  write_int(EXTRA_SPECIAL_PER_ATOM,force->special_extra);
+
  // -1 flag signals end of header

  int flag = -1;
Author	SHA1	Message	Date
Steven J. Plimpton	fa73fab5df	patch 16Jul18	2018-07-16 18:12:15 -06:00
Steve Plimpton	a3b6f38a42	Merge pull request #1003 from akohlmey/restart_extra_flags include support for 'extra/XXX/per/atom' info in restart files	2018-07-16 15:07:43 -06:00
Axel Kohlmeyer	783839e985	add support for restarting extra/XXX/per/atom settings in binary restarts	2018-07-16 15:21:52 -04:00
Steve Plimpton	c589029219	Merge pull request #1002 from rbberger/set_velocity_command Allow 'set' command to change atom velocities	2018-07-16 08:50:15 -06:00
Steve Plimpton	140767be16	Merge pull request #1001 from stanmoore1/kk_bugfix Fix rare crash in Kokkos ReaxFF on GPUs	2018-07-16 08:49:30 -06:00
Steve Plimpton	1c007ce7a1	Merge pull request #1000 from HaoZeke/fixDocs docs: Fix sneaky unicode character	2018-07-16 08:49:13 -06:00
Steve Plimpton	6f1b6e7abd	Merge pull request #999 from junghans/cmake_doc cmake/README.md: fix GPU_ARCH options	2018-07-16 08:48:48 -06:00
Steve Plimpton	5fc4aaef06	Merge pull request #940 from Pakketeretet2/port-enforce2d-kokkos Port enforce2d kokkos	2018-07-16 08:48:21 -06:00
Richard Berger	aa3d3213c9	Update set command documentation	2018-07-13 23:06:42 -04:00
Richard Berger	d00eaef070	Allow 'set' command to change atom velocities	2018-07-13 23:05:44 -04:00
Stan Moore	d4f8940ff2	Update command doc page for Kokkos enforce2d	2018-07-13 07:40:06 -06:00
Stan Moore	16381a52b1	Fix crash in ReaxFF on GPUs	2018-07-12 20:22:38 -06:00
HaoZeke	85511a4db8	docs: Fix sneaky unicode character Fixes the `pdf` target of the `Makefile`.	2018-07-13 00:44:04 +05:30
Christoph Junghans	4ac47ba037	cmake/README.md: fix GPU_ARCH options	2018-07-12 07:27:11 -06:00
Steve Plimpton	6dfb74f23e	Merge pull request #997 from lammps/balance-bug-fix 2 small bug fixes to load balancing	2018-07-11 16:13:22 -06:00
Steven J. Plimpton	b31f0245d0	2 small bug fixes to load balancing	2018-07-11 15:55:16 -06:00
Steve Plimpton	f288331874	Merge pull request #993 from lammps/doc-plus-makefile better rRESPA doc page, also a new Makefile.theta	2018-07-11 12:53:31 -06:00
Stan Moore	71f6991233	Small tweaks to fix_enforce2d_kokkos	2018-07-11 12:39:04 -06:00
Stan Moore	5d13321425	Standardize suffix paragraph in fix_enforce2d.txt	2018-07-11 12:15:50 -06:00
Steven J. Plimpton	acdc240cdd	better rRESPA doc page, also a new Makefile.theta	2018-07-11 08:42:28 -06:00
Steve Plimpton	69baaaec16	Merge pull request #991 from akohlmey/collected-small-updates Collected small updates for the next patch release	2018-07-11 07:50:31 -06:00
Axel Kohlmeyer	1f1447c3ac	need to update exclusions with the new atom IDs in case of molecular systems	2018-07-11 07:22:47 -04:00
Axel Kohlmeyer	1ed25d195b	convert c-style includes for c-library calls to c++-style	2018-07-10 09:48:49 -04:00
Axel Kohlmeyer	792b182cb0	whitespace cleanup	2018-07-10 09:46:08 -04:00
julient31	ade9b7bfc3	Commit2 JT 070918 - modified the citeme reference (replaced by the JCP one) - same modification in doc and src/SPIN	2018-07-10 09:44:14 -04:00
julient31	9d5dc561ca	Commit1 JT 070918 - created README in examples/SPIN - modified doc/src/set.txt to define 'spin' and 'spin/random' keywords	2018-07-10 09:44:14 -04:00
Axel Kohlmeyer	199c96f985	update and clarify the choice of atom ids for angle style dipole (which is not really an angle potential)	2018-07-10 09:22:41 -04:00
Axel Kohlmeyer	ad4f61a5ce	update fatbin makefile for libgpu.a to latest additions	2018-07-10 09:07:54 -04:00
Stan Moore	0c1dcfb617	Favor copymode instead of cleanup_copy	2018-07-06 17:06:37 -06:00
Stefan Paquay	db75232957	Removed debug print and comment.	2018-07-06 11:31:48 -04:00
Stefan Paquay	24405217d0	Updated Install.sh in KOKKOS.	2018-07-05 11:20:27 -04:00
Stefan Paquay	e08ccd0a7c	Forgot to include change in fix_enforce2d to access fixlist in kokkos port.	2018-06-29 11:58:27 -04:00
Stefan Paquay	14c4aea32d	Merge branch 'master' into port-enforce2d-kokkos	2018-06-13 14:59:07 -04:00
Stefan Paquay	666a13ea8a	Merge branch 'master' of https://www.github.com/lammps/lammps	2018-06-13 14:58:58 -04:00
Stefan Paquay	4bf9a93c11	Removed x dependency from enforce2d_kokkos.	2018-06-06 10:47:07 -04:00
Stefan Paquay	824a21a661	Removed debug printing from setup.	2018-06-04 12:28:06 -04:00
Stefan Paquay	0e96918313	Made enforce2d_kokkos actually set data masks.	2018-06-01 17:22:25 -04:00
Stefan Paquay	031077b4fa	Made enforce2d also set rotations to in-plane.	2018-06-01 17:19:53 -04:00
Stefan Paquay	962946ee45	Ported fix enforce2d to Kokkos.	2018-06-01 14:52:34 -04:00
Stefan Paquay	1ee85e59c3	Removed obsolete changes to fix_nve-manifold_rattle	2018-06-01 14:50:41 -04:00