Collected small changes and bugfixes

cmake/Modules/Documentation.cmake

@@ -55,8 +55,8 @@ if(BUILD_DOC)
     COMMAND ${DOCENV_BINARY_DIR}/pip $ENV{PIP_OPTIONS} install -r ${DOC_BUILD_DIR}/requirements.txt --upgrade
   )
 
-  set(MATHJAX_URL "https://github.com/mathjax/MathJax/archive/3.1.2.tar.gz" CACHE STRING "URL for MathJax tarball")
-  set(MATHJAX_MD5 "a4a6a093a89bc2ccab1452d766b98e53" CACHE STRING "MD5 checksum of MathJax tarball")
+  set(MATHJAX_URL "https://github.com/mathjax/MathJax/archive/3.1.3.tar.gz" CACHE STRING "URL for MathJax tarball")
+  set(MATHJAX_MD5 "d1c98c746888bfd52ca8ebc10704f92f" CACHE STRING "MD5 checksum of MathJax tarball")
   mark_as_advanced(MATHJAX_URL)
 
   # download mathjax distribution and unpack to folder "mathjax"

cmake/Modules/Packages/USER-PACE.cmake

@@ -20,7 +20,7 @@ file(GLOB PACE_EVALUATOR_SOURCES ${CMAKE_BINARY_DIR}/lammps-user-pace-*/USER-PAC
 list(FILTER PACE_EVALUATOR_SOURCES EXCLUDE REGEX pair_pace.cpp)
 
 add_library(pace STATIC ${PACE_EVALUATOR_SOURCES})
-set_target_properties(pace PROPERTIES OUTPUT_NAME pace${LAMMPS_MACHINE})
+set_target_properties(pace PROPERTIES OUTPUT_NAME lammps_pace${LAMMPS_MACHINE})
 target_include_directories(pace PUBLIC ${PACE_EVALUATOR_INCLUDE_DIR})
 target_link_libraries(lammps PRIVATE pace)
 

cmake/presets/all_off.cmake

@@ -2,16 +2,16 @@
 # an existing package selection without losing any other settings
 
 set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
-        GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MESSAGE MLIAP
-        MOLECULE MPIIO MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK
-        SNAP SPIN SRD VORONOI
-        USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
-        USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
-        USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD
-        USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
-        USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
-        USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ
-        USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF)
+  GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE
+  MPIIO MSCG OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN
+  SRD VORONOI
+  USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
+  USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-INTEL
+  USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD USER-MESONT USER-MGPT
+  USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PACE USER-PHONON
+  USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-REACTION USER-REAXC
+  USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF
+  USER-VTK USER-YAFF)
 
 foreach(PKG ${ALL_PACKAGES})
   set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

cmake/presets/all_on.cmake

@@ -4,16 +4,16 @@
 # with just a working C++ compiler and an MPI library.
 
 set(ALL_PACKAGES ASPHERE BODY CLASS2 COLLOID COMPRESS CORESHELL DIPOLE GPU
-        GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MISC MESSAGE MLIAP
-        MOLECULE MPIIO MSCG OPT PERI POEMS PYTHON QEQ REPLICA RIGID SHOCK
-        SNAP SPIN SRD VORONOI
-        USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK
-        USER-COLVARS USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP
-        USER-H5MD USER-INTEL USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD
-        USER-MESONT USER-MGPT USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP
-        USER-PHONON USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP
-        USER-REACTION USER-REAXC USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ
-        USER-SPH USER-TALLY USER-UEF USER-VTK USER-YAFF)
+  GRANULAR KIM KOKKOS KSPACE LATTE MANYBODY MC MESSAGE MISC MLIAP MOLECULE
+  MPIIO MSCG OPT PERI PLUGIN POEMS PYTHON QEQ REPLICA RIGID SHOCK SNAP SPIN
+  SRD VORONOI
+  USER-ADIOS USER-ATC USER-AWPMD USER-BOCS USER-CGDNA USER-CGSDK USER-COLVARS
+  USER-DIFFRACTION USER-DPD USER-DRUDE USER-EFF USER-FEP USER-H5MD USER-INTEL
+  USER-LB USER-MANIFOLD USER-MEAMC USER-MESODPD USER-MESONT USER-MGPT
+  USER-MISC USER-MOFFF USER-MOLFILE USER-NETCDF USER-OMP USER-PACE USER-PHONON
+  USER-PLUMED USER-PTM USER-QMMM USER-QTB USER-QUIP USER-REACTION USER-REAXC
+  USER-SCAFACOS USER-SDPD USER-SMD USER-SMTBQ USER-SPH USER-TALLY USER-UEF
+  USER-VTK USER-YAFF)
 
 foreach(PKG ${ALL_PACKAGES})
   set(PKG_${PKG} ON CACHE BOOL "" FORCE)

cmake/presets/nolib.cmake

@@ -1,10 +1,11 @@
 # preset that turns off all packages that require some form of external
 # library or special compiler (fortran or cuda) or equivalent.
 
-set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MPIIO MSCG PYTHON
-        VORONOI USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-LB
-        USER-MOLFILE USER-MESONT USER-NETCDF USER-PLUMED USER-QMMM USER-QUIP
-        USER-SCAFACOS USER-SMD USER-VTK)
+set(PACKAGES_WITH_LIB COMPRESS GPU KIM KOKKOS LATTE MESSAGE MPIIO MSCG
+  PYTHON VORONOI
+  USER-ADIOS USER-ATC USER-AWPMD USER-H5MD USER-LB USER-MOLFILE USER-MESONT
+  USER-NETCDF USER-PACE USER-PLUMED USER-QMMM USER-QUIP USER-SCAFACOS
+  USER-SMD USER-VTK)
 
 foreach(PKG ${PACKAGES_WITH_LIB})
   set(PKG_${PKG} OFF CACHE BOOL "" FORCE)

doc/Makefile

@@ -236,7 +236,7 @@ $(VENV):
 	)
 
 $(MATHJAX):
-	@git clone --depth 1 git://github.com/mathjax/MathJax.git $@
+	@git clone -b 3.1.4 -c advice.detachedHead=0 --depth 1 git://github.com/mathjax/MathJax.git $@
 
 $(TXT2RST) $(ANCHORCHECK): $(VENV)
 	@( \

doc/src/fix_precession_spin.rst

@@ -125,10 +125,10 @@ axis along the :math:`(1 1 1)`-type cube diagonals).  :math:`K_2^c >
 diagonals.  See chapter 2 of :ref:`(Skomski) <Skomski1>` for more
 details on cubic anisotropies.
 
-Style *stt* is used to simulate the interaction between the spins and 
+Style *stt* is used to simulate the interaction between the spins and
 a spin-transfer torque.
-See equation (7) of :ref:`(Chirac) <Chirac1>` for more details about the 
-implemented spin-transfer torque term. 
+See equation (7) of :ref:`(Chirac) <Chirac1>` for more details about the
+implemented spin-transfer torque term.
 
 In all cases, the choice of :math:`(x y z)` only imposes the vector
 directions for the forces. Only the direction of the vector is
@@ -139,12 +139,12 @@ Those styles can be combined within one single command line.
 
 .. note::
 
-   The norm of all vectors defined with the precession/spin command 
+   The norm of all vectors defined with the precession/spin command
    have to be non-zero. For example, defining
    "fix 1 all precession/spin zeeman 0.1 0.0 0.0 0.0" would result
-   in an error message. 
+   in an error message.
    Since those vector components are used to compute the inverse of the
-   field (or anisotropy) vector norm, setting a zero-vector would result 
+   field (or anisotropy) vector norm, setting a zero-vector would result
    in a division by zero.
 
 ----------
@@ -197,6 +197,6 @@ Oxford University Press.
 
 .. _Chirac1:
 
-**(Chirac)** Chirac, Théophile, et al.  Ultrafast antiferromagnetic 
-switching in NiO induced by spin transfer torques. 
+**(Chirac)** Chirac, Theophile, et al.  Ultrafast antiferromagnetic
+switching in NiO induced by spin transfer torques.
 Physical Review B 102.13 (2020): 134415.

doc/utils/sphinx-config/false_positives.txt

@@ -101,6 +101,7 @@ anisotropic
 anisotropies
 anisotropy
 ansi
+antiferromagnetic
 antiquewhite
 Antisymmetrized
 antisymmetry
@@ -2177,6 +2178,7 @@ nimpropers
 nimpropertypes
 Nimpropertype
 Ninteger
+NiO
 Nissila
 nist
 nitride
@@ -3163,6 +3165,7 @@ th
 thb
 thei
 Theodorou
+Theophile
 Theor
 thermalization
 thermalize
@@ -3315,6 +3318,7 @@ Uleft
 uloop
 Ulomek
 ulsph
+Ultrafast
 uMech
 umin
 Umin
@@ -3595,6 +3599,7 @@ ZBL
 Zc
 zcm
 Zeeman
+zeeman
 Zemer
 Zepeda
 zflag

src/KOKKOS/atom_vec_spin_kokkos.cpp

@@ -637,11 +637,12 @@ int AtomVecSpinKokkos::unpack_border_hybrid(int n, int first, double *buf)
 
   m = 0;
   last = first + n;
-  for (i = first; i < last; i++)
+  for (i = first; i < last; i++) {
     h_sp(i,0) = buf[m++];
     h_sp(i,1) = buf[m++];
     h_sp(i,2) = buf[m++];
     h_sp(i,3) = buf[m++];
+  }
   return m;
 }
 

src/KOKKOS/fix_eos_table_rx_kokkos.cpp

@@ -531,11 +531,11 @@ void FixEOStableRXKokkos<DeviceType>::create_kokkos_tables()
     h_table->hi[i] = tb->hi;
     h_table->invdelta[i] = tb->invdelta;
 
-    for (int j = 0; j<h_table->r.extent(1); j++)
+    for (int j = 0; j < (int)h_table->r.extent(1); j++)
       h_table->r(i,j) = tb->r[j];
-    for (int j = 0; j<h_table->e.extent(1); j++)
+    for (int j = 0; j < (int)h_table->e.extent(1); j++)
       h_table->e(i,j) = tb->e[j];
-    for (int j = 0; j<h_table->de.extent(1); j++)
+    for (int j = 0; j < (int)h_table->de.extent(1); j++)
       h_table->de(i,j) = tb->de[j];
   }
 

src/KOKKOS/fix_rx_kokkos.cpp

@@ -1451,7 +1451,7 @@ void FixRxKokkos<DeviceType>::solve_reactions(const int /*vflag*/, const bool is
   {
     const int count = nlocal + (newton_pair ? nghost : 0);
 
-    if (count > k_dpdThetaLocal.template view<DeviceType>().extent(0)) {
+    if (count > (int) k_dpdThetaLocal.template view<DeviceType>().extent(0)) {
       memoryKK->destroy_kokkos (k_dpdThetaLocal, dpdThetaLocal);
       memoryKK->create_kokkos (k_dpdThetaLocal, dpdThetaLocal, count, "FixRxKokkos::dpdThetaLocal");
       this->d_dpdThetaLocal = k_dpdThetaLocal.template view<DeviceType>();

src/KSPACE/ewald_dipole.cpp

@@ -806,7 +806,6 @@ void EwaldDipole::slabcorr()
 
   if (atom->torque) {
     double ffact = qscale * (-4.0*MY_PI/volume);
-    double **mu = atom->mu;
     double **torque = atom->torque;
     for (int i = 0; i < nlocal; i++) {
       torque[i][0] += ffact * dipole_all * mu[i][1];

src/KSPACE/msm_cg.cpp

@@ -166,7 +166,7 @@ void MSMCG::compute(int eflag, int vflag)
   // forward communicate charge density values to fill ghost grid points
   // compute direct sum interaction and then restrict to coarser grid
 
-  for (int n=0; n<=levels-2; n++) {
+  for (n=0; n<=levels-2; n++) {
     if (!active_flag[n]) continue;
     current_level = n;
     gc[n]->forward_comm_kspace(this,1,sizeof(double),FORWARD_RHO,
@@ -209,7 +209,7 @@ void MSMCG::compute(int eflag, int vflag)
   // prolongate energy/virial from coarser grid to finer grid
   // reverse communicate from ghost grid points to get full sum
 
-  for (int n=levels-2; n>=0; n--) {
+  for (n=levels-2; n>=0; n--) {
     if (!active_flag[n]) continue;
     prolongation(n);
 

src/KSPACE/pair_born_coul_msm.cpp

@@ -195,7 +195,7 @@ void PairBornCoulMSM::compute(int eflag, int vflag)
 
   if (force->kspace->scalar_pressure_flag && vflag) {
     for (i = 0; i < 3; i++) virial[i] += force->pair->eng_coul/3.0;
-    for (int i = 0; i < nmax; i++) {
+    for (i = 0; i < nmax; i++) {
       f[i][0] += ftmp[i][0];
       f[i][1] += ftmp[i][1];
       f[i][2] += ftmp[i][2];

src/KSPACE/pair_buck_coul_msm.cpp

@@ -191,7 +191,7 @@ void PairBuckCoulMSM::compute(int eflag, int vflag)
 
   if (force->kspace->scalar_pressure_flag && vflag) {
     for (i = 0; i < 3; i++) virial[i] += force->pair->eng_coul/3.0;
-    for (int i = 0; i < nmax; i++) {
+    for (i = 0; i < nmax; i++) {
       f[i][0] += ftmp[i][0];
       f[i][1] += ftmp[i][1];
       f[i][2] += ftmp[i][2];

src/KSPACE/pair_buck_long_coul_long.cpp

@@ -506,40 +506,39 @@ void PairBuckLongCoulLong::compute(int eflag, int vflag)
 
       if (order1 && (rsq < cut_coulsq)) {                // coulombic
         if (!ncoultablebits || rsq <= tabinnersq) {        // series real space
-          double x = g_ewald*r;
-          double s = qri*q[j], t = 1.0/(1.0+EWALD_P*x);
+          double x1 = g_ewald*r;
+          double s = qri*q[j], t = 1.0/(1.0+EWALD_P*x1);
           if (ni == 0) {
-            s *= g_ewald*exp(-x*x);
-            force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s;
+            s *= g_ewald*exp(-x1*x1);
+            force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x1)+EWALD_F*s;
             if (eflag) ecoul = t;
-          }
-          else {                                        // special case
-            double f = s*(1.0-special_coul[ni])/r;
-            s *= g_ewald*exp(-x*x);
-            force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x)+EWALD_F*s-f;
-            if (eflag) ecoul = t-f;
+          } else {                                        // special case
+            double fc = s*(1.0-special_coul[ni])/r;
+            s *= g_ewald*exp(-x1*x1);
+            force_coul = (t *= ((((t*A5+A4)*t+A3)*t+A2)*t+A1)*s/x1)+EWALD_F*s-fc;
+            if (eflag) ecoul = t-fc;
           }
         }                                                // table real space
         else {
           union_int_float_t t;
           t.f = rsq;
           const int k = (t.i & ncoulmask) >> ncoulshiftbits;
-          double f = (rsq-rtable[k])*drtable[k], qiqj = qi*q[j];
+          double fc = (rsq-rtable[k])*drtable[k], qiqj = qi*q[j];
           if (ni == 0) {
-            force_coul = qiqj*(ftable[k]+f*dftable[k]);
-            if (eflag) ecoul = qiqj*(etable[k]+f*detable[k]);
+            force_coul = qiqj*(ftable[k]+fc*dftable[k]);
+            if (eflag) ecoul = qiqj*(etable[k]+fc*detable[k]);
           }
           else {                                        // special case
-            t.f = (1.0-special_coul[ni])*(ctable[k]+f*dctable[k]);
-            force_coul = qiqj*(ftable[k]+f*dftable[k]-t.f);
-            if (eflag) ecoul = qiqj*(etable[k]+f*detable[k]-t.f);
+            t.f = (1.0-special_coul[ni])*(ctable[k]+fc*dctable[k]);
+            force_coul = qiqj*(ftable[k]+fc*dftable[k]-t.f);
+            if (eflag) ecoul = qiqj*(etable[k]+fc*detable[k]-t.f);
           }
         }
       } else force_coul = ecoul = 0.0;
 
       if (rsq < cut_bucksqi[typej]) {                        // buckingham
-        double rn = r2inv*r2inv*r2inv,
-                        expr = exp(-r*rhoinvi[typej]);
+        double rn = r2inv*r2inv*r2inv;
+        double expr = exp(-r*rhoinvi[typej]);
         if (order6) {                                        // long-range
           if (!ndisptablebits || rsq <= tabinnerdispsq) {
             double x2 = g2*rsq, a2 = 1.0/x2;
@@ -549,10 +548,10 @@ void PairBuckLongCoulLong::compute(int eflag, int vflag)
                 r*expr*buck1i[typej]-g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq;
               if (eflag) evdwl = expr*buckai[typej]-g6*((a2+1.0)*a2+0.5)*x2;
             } else {                                        // special case
-              double f = special_lj[ni], t = rn*(1.0-f);
-              force_buck = f*r*expr*buck1i[typej]-
+              double fc = special_lj[ni], t = rn*(1.0-fc);
+              force_buck = fc*r*expr*buck1i[typej]-
                 g8*(((6.0*a2+6.0)*a2+3.0)*a2+1.0)*x2*rsq+t*buck2i[typej];
-              if (eflag) evdwl = f*expr*buckai[typej] -
+              if (eflag) evdwl = fc*expr*buckai[typej] -
                            g6*((a2+1.0)*a2+0.5)*x2+t*buckci[typej];
             }
           } else {                                              //table real space
@@ -564,9 +563,9 @@ void PairBuckLongCoulLong::compute(int eflag, int vflag)
               force_buck = r*expr*buck1i[typej]-(fdisptable[disp_k]+f_disp*dfdisptable[disp_k])*buckci[typej];
               if (eflag) evdwl = expr*buckai[typej]-(edisptable[disp_k]+f_disp*dedisptable[disp_k])*buckci[typej];
             } else {                                             //special case
-              double f = special_lj[ni], t = rn*(1.0-f);
-              force_buck = f*r*expr*buck1i[typej] -(fdisptable[disp_k]+f_disp*dfdisptable[disp_k])*buckci[typej] +t*buck2i[typej];
-              if (eflag) evdwl = f*expr*buckai[typej] -(edisptable[disp_k]+f_disp*dedisptable[disp_k])*buckci[typej]+t*buckci[typej];
+              double fc = special_lj[ni], t = rn*(1.0-fc);
+              force_buck = fc*r*expr*buck1i[typej] -(fdisptable[disp_k]+f_disp*dfdisptable[disp_k])*buckci[typej] +t*buck2i[typej];
+              if (eflag) evdwl = fc*expr*buckai[typej] -(edisptable[disp_k]+f_disp*dedisptable[disp_k])*buckci[typej]+t*buckci[typej];
             }
           }
         } else {                                                // cut
@@ -575,10 +574,10 @@ void PairBuckLongCoulLong::compute(int eflag, int vflag)
             if (eflag) evdwl = expr*buckai[typej] -
                          rn*buckci[typej]-offseti[typej];
           } else {                                        // special case
-            double f = special_lj[ni];
-            force_buck = f*(r*expr*buck1i[typej]-rn*buck2i[typej]);
+            double fc = special_lj[ni];
+            force_buck = fc*(r*expr*buck1i[typej]-rn*buck2i[typej]);
             if (eflag)
-              evdwl = f*(expr*buckai[typej]-rn*buckci[typej]-offseti[typej]);
+              evdwl = fc*(expr*buckai[typej]-rn*buckci[typej]-offseti[typej]);
           }
         }
       }
@@ -587,10 +586,10 @@ void PairBuckLongCoulLong::compute(int eflag, int vflag)
       fpair = (force_coul+force_buck)*r2inv;
 
       if (newton_pair || j < nlocal) {
-        double *fj = f0+(j+(j<<1)), f;
-        fi[0] += f = d[0]*fpair; fj[0] -= f;
-        fi[1] += f = d[1]*fpair; fj[1] -= f;
-        fi[2] += f = d[2]*fpair; fj[2] -= f;
+        double *fj = f0+(j+(j<<1)), fp;
+        fi[0] += fp = d[0]*fpair; fj[0] -= fp;
+        fi[1] += fp = d[1]*fpair; fj[1] -= fp;
+        fi[2] += fp = d[2]*fpair; fj[2] -= fp;
       }
       else {
         fi[0] += d[0]*fpair;