Commit JT 020618

- Documentation
- Memory leaks solved

doc/src/Eqs/force_spin_aniso.tex

@@ -0,0 +1,11 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath,amssymb,amsthm,bm}
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \bm{H}_{aniso}  = -\sum_{{ i}=1}^{N} K_{an}(\bm{r}_{i})\, \left( \vec{s}_{i} \cdot \vec{n}_{i} \right)^2, \nonumber
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/Eqs/force_spin_zeeman.tex

@@ -0,0 +1,11 @@
+\documentclass[preview]{standalone}
+\usepackage{varwidth}
+\usepackage[utf8x]{inputenc}
+\usepackage{amsmath,amssymb,amsthm,bm}
+\begin{document}
+\begin{varwidth}{50in}
+  \begin{equation}
+    \bm{H}_{zeeman} = -\mu_{B}\mu_0\sum_{i=0}^{N}g_{i} \vec{s}_{i} \cdot \vec{H}_{ext} \nonumber 
+  \end{equation}
+\end{varwidth}
+\end{document}

doc/src/fix_force_spin.txt

@@ -20,14 +20,13 @@ style = {zeeman} or {aniso} :l
     x y z = vector direction of the field
   {aniso} args = K x y z
     K = intensity of the magnetic anisotropy (in eV)
-    x y z = vector direction of the anisotropy
+    x y z = vector direction of the anisotropy :pre
 :ule
 
 [Examples:]
 
 fix 1 all force/spin zeeman 0.1 0.0 0.0 1.0
-fix 1 all force/spin aniso 0.001 0.0 0.0 1.0
+fix 1 all force/spin aniso 0.001 0.0 0.0 1.0 :pre
-
 
 [Description:]
 
@@ -35,48 +34,40 @@ Impose a force torque to each magnetic spin in the group.
 
 Style {zeeman} is used for the simulation of the interaction 
 between the magnetic spins in the defined group and an external 
-magnetic field.
+magnetic field:
+
+:c,image(Eqs/force_spin_zeeman.pdf)
+
+with mu0 the vacuum permeability, muB the Bohr magneton (muB = 5.788 eV/T 
+in metal units), 
 
 Style {aniso} is used to simulate an easy axis or an easy plane 
-for the magnetic spins in the defined group. 
+for the magnetic spins in the defined group: 
-If K>0, an easy axis is defined, and if K<0, an easy plane is
-defined.
 
-In both cases, x y z impose is the vector direction for the force. 
+:c,image(Eqs/force_spin_aniso.pdf)
+
+with n defining the direction of the anisotropy, and K (in eV) its intensity. 
+If K>0, an easy axis is defined, and if K<0, an easy plane is defined.
+
+In both cases, the choice of (x y z) imposes the vector direction for the force. 
 Only the direction of the vector is important; it's length is ignored.  
 
 :line
 
-
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
 No information about this fix is written to "binary restart
 files"_restart.html.
 
-The "fix_modify"_fix_modify.html {energy} option is supported by this
+[Restrictions:]
-fix to add the gravitational potential energy of the system to the
-system's potential energy as part of "thermodynamic
-output"_thermo_style.html.
 
-The "fix_modify"_fix_modify.html {respa} option is supported by this
+The {force/spin} style is part of the SPIN package. 
-fix. This allows to set at which level of the "r-RESPA"_run_style.html
+This style is only enabled if LAMMPS was built with this package, and
-integrator the fix is adding its forces. Default is the outermost level.
+if the atom_style "spin" was declared. 
-
+See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
-This fix computes a global scalar which can be accessed by various
-"output commands"_Section_howto.html#howto_15.  This scalar is the
-gravitational potential energy of the particles in the defined field,
-namely mass * (g dot x) for each particles, where x and mass are the
-particles position and mass, and g is the gravitational field.  The
-scalar value calculated by this fix is "extensive".
-
-No parameter of this fix can be used with the {start/stop} keywords of
-the "run"_run.html command.  This fix is not invoked during "energy
-minimization"_minimize.html.
-
-[Restrictions:] none
 
 [Related commands:]
 
-"atom_style sphere"_atom_style.html, "fix addforce"_fix_addforce.html
+"atom_style spin"_atom_style.html
 
 [Default:] none

doc/src/pair_spin_exchange.txt

@@ -1,11 +1,3 @@
-<script type="text/javascript"
-  src="https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML">
-</script>
-<script type="text/x-mathjax-config">
-  MathJax.Hub.Config({ TeX: { equationNumbers: {autoNumber: "AMS"} } });
-</script>
-
-
 "LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c
 
 :link(lws,http://lammps.sandia.gov)
@@ -33,7 +25,7 @@ pair_coeff 1 2 exchange 6.0 -0.01575 0.0 1.965 :pre
 [Description:]
 
 Style {pair/spin/exchange} computes the exchange interaction between 
-pairs of magnetic spins. 
+pairs of magnetic spins: 
 
 :c,image(Eqs/pair_spin_exchange_interaction.pdf)
 
@@ -46,18 +38,15 @@ This function is defined as:
 
 :c,image(Eqs/pair_spin_exchange_function.pdf)
 
-where a, b and d are the three constants defined in the associated "pair_coeff"
+where a, b and d are the three constant coefficients defined in the associated 
-command.   
+"pair_coeff" command.   
 
-More explanations the {pair/spin/exchange} and its parametrization are reported 
+The coefficients a, b, and c need to be fitted so that the function above matches with 
+the value of the exchange interaction for the N neighbor shells taken into account.
+
+Examles and more explanations about this function and its parametrization are reported 
 in "(Tranchida)"_#Tranchida1.
 
-
-
-The {lj/cut} and {lj/cut/coul/long} pair styles support the use of the
-{inner}, {middle}, and {outer} keywords of the "run_style
-respa"_run_style.html command, meaning the pairwise forces can be
-
 :line
 
 [Restrictions:]
@@ -69,9 +58,8 @@ See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
 
 [Related commands:]
 
-"eam"
+"atom_style spin"_atom_style.html, "pair_coeff"_pair_coeff.html, 
-
+"pair_eam"_pair_eam.html,
-"pair_coeff"_pair_coeff.html
 
 [Default:] none
 

examples/SPIN/in.spin.cobalt

@@ -87,8 +87,8 @@ neigh_modify every 10 check yes delay 20
 #fix 2 all langevin/spin 0.0 0.0 0.0 21
 
 #Magnetic integration fix
-#fix 3 all integration/spin mpi
+fix 3 all integration/spin lattice yes
-fix 3 all integration/spin serial lattice yes
+#fix 3 all integration/spin lattice no
 
 #compute real time, total magnetization, magnetic energy, and spin temperature
 #Iteration | Time | Mx | My | Mz | |M| | Em | Tm
@@ -120,5 +120,6 @@ thermo_modify   format float %20.15g
 dump 1 all custom 50 dump_cobalt.lammpstrj type x y z spx spy spz
 
 #Running the simulations for N timesteps
-run 1000
+run 10
+#run 1000
 

src/SPIN/compute_spin.cpp

@@ -54,6 +54,7 @@ ComputeSpin::ComputeSpin(LAMMPS *lmp, int narg, char **arg) :
 
 ComputeSpin::~ComputeSpin()
 {
+  memory->destroy(vector);
 }
 
 /* ---------------------------------------------------------------------- */

src/SPIN/fix_integration_spin.cpp

@@ -73,16 +73,20 @@ FixIntegrationSpin::FixIntegrationSpin(LAMMPS *lmp, int narg, char **arg) :
     extra = SPIN;
   } else error->all(FLERR,"Illegal fix integration/spin command");
   
-  int iarg = 3;
+  // defining mpi_flag 
 
-  while (iarg < narg) { 
+  int nprocs_tmp = comm->nprocs;
-    if (strcmp(arg[iarg],"serial") == 0){
+  if (nprocs_tmp == 1) {
     mpi_flag = 0;
-      iarg += 1;
+  } else if (nprocs_tmp >= 1) {
-    } else if (strcmp(arg[iarg],"mpi") == 0) {
     mpi_flag = 1;
-      iarg += 1;
+  } else error->all(FLERR,"Illegal fix/integration/spin command");
-    } else if (strcmp(arg[iarg],"lattice") == 0) {
+
+  // defining mech_flag 
+
+  int iarg = 3;
+  while (iarg < narg) { 
+    if (strcmp(arg[iarg],"lattice") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal fix/integration/spin command");
       if (strcmp(arg[iarg+1],"no") == 0) mech_flag = 0;
       else if (strcmp(arg[iarg+1],"yes") == 0) mech_flag = 1;
@@ -94,8 +98,8 @@ FixIntegrationSpin::FixIntegrationSpin(LAMMPS *lmp, int narg, char **arg) :
   if (extra == SPIN && !atom->mumag_flag)
     error->all(FLERR,"Fix integration/spin requires spin attribute mumag");
 
-  //if (mpi_flag == NONE)
+  if (mpi_flag == 0 && nprocs_tmp == 1)
-  //  error->all(FLERR,"Illegal fix/integration/spin command");
+    error->all(FLERR,"Illegal fix/integration/spin command");
 
   magpair_flag = 0;
   exch_flag = 0;
@@ -134,6 +138,7 @@ int FixIntegrationSpin::setmask()
 
 void FixIntegrationSpin::init()
 {
+
   // set timesteps
 
   dtv = update->dt;
@@ -202,29 +207,20 @@ void FixIntegrationSpin::init()
    if (locklangevinspin->temp_flag == 1) temp_flag = 1;
   }
   
-
+  nsectors = 0;
   memory->create(rsec,3,"integration/spin:rsec");
   
   // perform the sectoring if mpi integration
 
-  if (mpi_flag) {
+  if (mpi_flag) sectoring();
-    sectoring();
 
-    // grow tables of stacking variables
+  // grow tables of stacking variables (mpi)
   
   stack_head = memory->grow(stack_head,nsectors,"integration/spin:stack_head");
   stack_foot = memory->grow(stack_foot,nsectors,"integration/spin:stack_foot");
   forward_stacks = memory->grow(forward_stacks,atom->nmax,"integration/spin:forward_stacks");
   backward_stacks = memory->grow(backward_stacks,atom->nmax,"integration/spin:backward_stacks");
-  }
 
-  // grow tables of stacking variables
- /* 
-  stack_head = memory->grow(stack_head,nsectors,"integration/spin:stack_head");
-  stack_foot = memory->grow(stack_foot,nsectors,"integration/spin:stack_foot");
-  forward_stacks = memory->grow(forward_stacks,atom->nmax,"integration/spin:forward_stacks");
-  backward_stacks = memory->grow(backward_stacks,atom->nmax,"integration/spin:backward_stacks");
-*/
 }
 
 /* ---------------------------------------------------------------------- */
@@ -358,7 +354,7 @@ void FixIntegrationSpin::setup_pre_neighbor()
 }
 
 /* ---------------------------------------------------------------------- 
-   store in two linked lists the advance order of the spins
+   store in two linked lists the advance order of the spins (mpi)
 ---------------------------------------------------------------------- */
 
 void FixIntegrationSpin::pre_neighbor()
@@ -591,23 +587,9 @@ int FixIntegrationSpin::coords2sector(double *x)
     sublo[dim]=sublotmp[dim];
   }
 
-//#define M1
-#if defined M1
-  double rix = (x[0] - sublo[0])/rsec[0];
-  double riy = (x[1] - sublo[1])/rsec[1];
-  double riz = (x[2] - sublo[2])/rsec[2];
-
-  seci[0] = static_cast<int>(rix);
-  seci[1] = static_cast<int>(riy);
-  seci[2] = static_cast<int>(riz);
-#endif
-
-#define M2
-#if defined M2
   seci[0] = x[0] > (sublo[0] + rsec[0]);
   seci[1] = x[1] > (sublo[1] + rsec[1]);
   seci[2] = x[2] > (sublo[2] + rsec[2]);
-#endif
 
   nseci = (seci[0] + 2*seci[1] + 4*seci[2]); 
 

src/SPIN/fix_integration_spin.h

@@ -45,7 +45,8 @@ class FixIntegrationSpin : public Fix {
 
  protected:
   int extra;
-  int mpi_flag;			//mpi_flag =  if parallel algorithm
+  int mpi_flag;			// mpi_flag = 0  if serial algorithm
+  				// mpi_flag = 1  if parallel algorithm
   int mech_flag; 		// mech_flag = 0 if spins only
   				// mech_flag = 1 if spin-lattice calc. 
 

src/atom.cpp

@@ -278,6 +278,10 @@ Atom::~Atom()
   memory->destroy(tri);
   memory->destroy(body);
 
+  memory->destroy(mumag);
+  memory->destroy(sp);
+  memory->destroy(fm);
+
   memory->destroy(vfrac);
   memory->destroy(s0);
   memory->destroy(x0);