git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@13831 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Manual.txt

@@ -85,7 +85,7 @@ it gives quick access to documentation for all LAMMPS commands.
 
 .. toctree::
    :maxdepth: 2
-   :numbered:
+   :numbered: // comment
    
    Section_intro
    Section_start
@@ -105,8 +105,8 @@ it gives quick access to documentation for all LAMMPS commands.
 Indices and tables
 ==================
 
-* :ref:`genindex`
-* :ref:`search`
+* :ref:`genindex` // comment
+* :ref:`search` // comment
    
 END_RST -->
 

doc/prd.txt

@@ -31,8 +31,8 @@ keyword = {min} or {temp} or {vel} :l
   {vel} values = loop dist
     loop = {all} or {local} or {geom}, used in dephasing
     dist = {uniform} or {gaussian}, used in dephasing
-  {time} value = {step} or {clock}
-    {step} = simulation runs for N timesteps on each replica (default)
+  {time} value = {steps} or {clock}
+    {steps} = simulation runs for N timesteps on each replica (default)
     {clock} = simulation runs for N timesteps across all replicas :pre
 :ule
 
@@ -158,7 +158,7 @@ dynamics have been performed.  Note that {N} only includes the
 dynamics of stages 2 and 3, not the steps taken during dephasing or
 the minimization iterations of quenching.  The specified {N} is
 interpreted in one of two ways, depending on the {time} keyword.  If
-the {time} value is {step}, which is the default, then each replica
+the {time} value is {steps}, which is the default, then each replica
 runs for {N} timesteps.  If the {time} value is {clock}, then the
 simulation runs until {N} aggregate timesteps across all replicas have
 elapsed.  This aggregate time is the "clock" time defined below, which
@@ -310,7 +310,7 @@ dt/reset"_fix_dt_reset.html and "fix deposit"_fix_deposit.html.
 [Default:] 
 
 The option defaults are min = 0.1 0.1 40 50, no temp setting, vel =
-geom gaussian, and time = step.
+geom gaussian, and time = steps.
 
 :line
 

lib/README

@@ -45,7 +45,7 @@ quip          interface to QUIP/libAtoms framework, USER-QUIP package
                 from Albert Bartok-Partay and Gabor Csanyi (U Cambridge)
 reax          ReaxFF potential, REAX package
 	        from Adri van Duin (Penn State) and Aidan Thompson (Sandia)
-quip          interface to QUIP/libAtoms framework, USER-QUIP package
-                from Albert Bartok-Partay and Gabor Csanyi (U Cambridge)
+smd           hooks to Eigen library, used by USER-SMD package
+                from Georg Ganzenmueller (Ernst Mach Institute, Germany)
 voronoi       hooks to the Voro++ library, used by compute voronoi/atom command
 	        from Daniel Schwen (LANL)

src/Makefile

@@ -48,7 +48,7 @@ PACKAGE = asphere body class2 colloid coreshell dipole fld gpu granular kim \
 PACKUSER = user-atc user-awpmd user-cg-cmm user-colvars user-cuda \
 	   user-diffraction user-drude user-eff user-fep user-intel user-lb \
 	   user-misc user-molfile user-omp user-phonon user-qmmm user-qtb \
-	   user-quip user-reaxc user-sph
+	   user-quip user-reaxc user-smd user-sph
 
 PACKLIB = gpu kim kokkos meam poems python reax voronoi \
 	  user-atc user-awpmd user-colvars user-cuda user-molfile \

src/atom.cpp

@@ -94,6 +94,17 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
   rho = drho = e = de = cv = NULL;
   vest = NULL;
 
+  // USER-SMD
+
+  contact_radius = NULL;
+  smd_data_9 = NULL;
+  smd_stress = NULL;
+  eff_plastic_strain = NULL;
+  eff_plastic_strain_rate = NULL;
+  damage = NULL;
+
+  // molecular info
+
   bond_per_atom =  extra_bond_per_atom = 0;
   num_bond = NULL;
   bond_type = NULL;
@@ -148,6 +159,17 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
 
   rho_flag = e_flag = cv_flag = vest_flag = 0;
 
+  // USER-SMD
+
+  smd_flag = 0;
+  contact_radius_flag = 0;
+  smd_data_9_flag = 0;
+  smd_stress_flag = 0;
+  x0_flag = 0;
+  eff_plastic_strain_flag = 0;
+  eff_plastic_strain_rate_flag = 0;
+  damage_flag = 0;
+
   // Peridynamic scale factor
 
   pdscale = 1.0;
@@ -245,6 +267,13 @@ Atom::~Atom()
   memory->destroy(cv);
   memory->destroy(vest);
 
+  memory->destroy(contact_radius);
+  memory->destroy(smd_data_9);
+  memory->destroy(smd_stress);
+  memory->destroy(eff_plastic_strain);
+  memory->destroy(eff_plastic_strain_rate);
+  memory->destroy(damage);
+
   memory->destroy(nspecial);
   memory->destroy(special);
 
@@ -2010,6 +2039,15 @@ void *Atom::extract(char *name)
   if (strcmp(name,"cv") == 0) return (void *) cv;
   if (strcmp(name,"vest") == 0) return (void *) vest;
 
+  if (strcmp(name, "contact_radius") == 0) return (void *) contact_radius;
+  if (strcmp(name, "smd_data_9") == 0) return (void *) smd_data_9;
+  if (strcmp(name, "smd_stress") == 0) return (void *) smd_stress;
+  if (strcmp(name, "eff_plastic_strain") == 0) 
+    return (void *) eff_plastic_strain;
+  if (strcmp(name, "eff_plastic_strain_rate") == 0) 
+    return (void *) eff_plastic_strain_rate;
+  if (strcmp(name, "damage") == 0) return (void *) damage;
+
   return NULL;
 }
 

src/atom.h

@@ -76,6 +76,17 @@ class Atom : protected Pointers {
   double *rho,*drho,*e,*de,*cv;
   double **vest;
 
+  // USER-SMD package
+
+  double *contact_radius;
+  double **smd_data_9;
+  double **smd_stress;
+  double *eff_plastic_strain;
+  double *eff_plastic_strain_rate;
+  double *damage;
+
+  // molecular info
+
   int **nspecial;               // 0,1,2 = cummulative # of 1-2,1-3,1-4 neighs
   tagint **special;             // IDs of 1-2,1-3,1-4 neighs of each atom
   int maxspecial;               // special[nlocal][maxspecial]
@@ -123,6 +134,17 @@ class Atom : protected Pointers {
   int cs_flag,csforce_flag,vforce_flag,ervelforce_flag,etag_flag;
   int rho_flag,e_flag,cv_flag,vest_flag;
 
+  // USER-SMD package
+
+  int smd_flag;
+  int contact_radius_flag;
+  int smd_data_9_flag;
+  int smd_stress_flag;
+  int x0_flag;
+  int eff_plastic_strain_flag;
+  int eff_plastic_strain_rate_flag;
+  int damage_flag;
+
   // Peridynamics scale factor, used by dump cfg
 
   double pdscale;