Merge pull request #991 from akohlmey/collected-small-updates

Collected small updates for the next patch release

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.
 

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).

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).

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).

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).

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).

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).

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 \
@@ -43,6 +44,13 @@ 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)
@@ -232,6 +240,15 @@ 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

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. **

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 
 

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;
 }
 

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"

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"

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};

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"

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"

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"

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"

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;
 
 }
 

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"

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;