additional fix external hooks for calling programs

doc/src/fix_msst.txt

@@ -17,19 +17,22 @@ msst = style name of this fix :l
 dir = {x} or {y} or {z} :l
 shockvel = shock velocity (strictly positive, distance/time units) :l
 zero or more keyword value pairs may be appended :l
-keyword = {q} or {mu} or {p0} or {v0} or {e0} or {tscale} :l
+keyword = {q} or {mu} or {p0} or {v0} or {e0} or {tscale} or {beta} or {dftb} :l
   {q} value = cell mass-like parameter (mass^2/distance^4 units)
   {mu} value = artificial viscosity (mass/length/time units)
   {p0} value = initial pressure in the shock equations (pressure units)
   {v0} value = initial simulation cell volume in the shock equations (distance^3 units)
   {e0} value = initial total energy (energy units)
-  {tscale} value = reduction in initial temperature (unitless fraction between 0.0 and 1.0) :pre
+  {tscale} value = reduction in initial temperature (unitless fraction between 0.0 and 1.0) 
+  {dftb} value = {yes} or {no} for whether using MSST in conjunction with DFTB+
+  {beta} value = scale factor on energy contribution of DFTB+ :pre
 :ule
 
 [Examples:]
 
 fix 1 all msst y 100.0 q 1.0e5 mu 1.0e5
-fix 2 all msst z 50.0 q 1.0e4 mu 1.0e4  v0 4.3419e+03 p0 3.7797e+03 e0 -9.72360e+02 tscale 0.01 :pre
+fix 2 all msst z 50.0 q 1.0e4 mu 1.0e4  v0 4.3419e+03 p0 3.7797e+03 e0 -9.72360e+02 tscale 0.01
+fix 1 all msst y 100.0 q 1.0e5 mu 1.0e5 dftb yes beta 0.5 :pre
 
 [Description:]
 
@@ -58,11 +61,11 @@ oscillations have physical significance in some cases.  The optional
 symmetry to equilibrate to the shock Hugoniot and Rayleigh line more
 rapidly in such cases.
 
-{tscale} is a factor between 0 and 1 that determines what fraction of
-thermal kinetic energy is converted to compressive strain kinetic
-energy at the start of the simulation.  Setting this parameter to a
-non-zero value may assist in compression at the start of simulations
-where it is slow to occur.
+The keyword {tscale} is a factor between 0 and 1 that determines what
+fraction of thermal kinetic energy is converted to compressive strain
+kinetic energy at the start of the simulation.  Setting this parameter
+to a non-zero value may assist in compression at the start of
+simulations where it is slow to occur.
 
 If keywords {e0}, {p0},or {v0} are not supplied, these quantities will
 be calculated on the first step, after the energy specified by
@@ -77,17 +80,40 @@ For all pressure styles, the simulation box stays orthogonal in shape.
 Parrinello-Rahman boundary conditions (tilted box) are supported by
 LAMMPS, but are not implemented for MSST.
 
-This fix computes a temperature and pressure each timestep. To do
-this, the fix creates its own computes of style "temp" and "pressure",
-as if these commands had been issued:
+This fix computes a temperature and pressure and potential energy each
+timestep. To do this, the fix creates its own computes of style "temp"
+"pressure", and "pe", as if these commands had been issued:
 
-compute fix-ID_temp group-ID temp
-compute fix-ID_press group-ID pressure fix-ID_temp :pre
+compute fix-ID_MSST_temp all temp
+compute fix-ID_MSST_press all pressure fix-ID_MSST_temp :pre
+compute fix-ID_MSST_pe all pe :pre
 
 See the "compute temp"_compute_temp.html and "compute
 pressure"_compute_pressure.html commands for details.  Note that the
-IDs of the new computes are the fix-ID + underscore + "temp" or fix_ID
-+ underscore + "press".  The group for the new computes is "all".
+IDs of the new computes are the fix-ID + "_MSST_temp" or "_MSST_press"
+or "_MSST_pe".  The group for the new computes is "all".
+
+:line
+
+The {dftb} and {beta} keywords are to allow this fix to be used when
+LAMMPS is being driven by DFTB+, a density-functional tight-binding
+code.
+
+If the keyword {dftb} is used with a value of {yes}, then the MSST
+equations are altered to account for an energy contribution compute by
+DFTB+.  In this case, you must define a "fix
+external"_fix_external.html command in your input script, which is
+used to callback to DFTB+ during the LAMMPS timestepping.  DFTB+ will
+communicate its info to LAMMPS via that fix.
+
+The keyword {beta} is a scale factor on the DFTB+ energy contribution.
+The value of {beta} must be between 0.0 and 1.0 inclusive.  A value of
+0.0 means no contribution, a value of 1.0 means a full contribution.
+
+(July 2017) More information about these keywords and the use of
+LAMMPS with DFTB+ will be added to the LAMMMPS documention soon.
+
+:line
 
 [Restart, fix_modify, output, run start/stop, minimize info:]
 
@@ -149,8 +175,9 @@ all.
 
 [Default:]
 
-The keyword defaults are q = 10, mu = 0, tscale = 0.01. p0, v0, and e0
-are calculated on the first step.
+The keyword defaults are q = 10, mu = 0, tscale = 0.01, dftb = no,
+beta = 0.0.  Note that p0, v0, and e0 are calculated on the first
+timestep.
 
 :line
 

src/SHOCK/fix_msst.h

@@ -10,10 +10,6 @@
 
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
-/* Implementation of the Multi-Scale Shock Method.
-   See Reed, Fried, Joannopoulos, Phys. Rev. Lett., 90, 235503(2003).
-   Implementation by Laurence Fried, LLNL, 4/2007.
-*/
 
 #ifdef FIX_CLASS
 
@@ -42,55 +38,68 @@ class FixMSST : public Fix {
   void write_restart(FILE *);
   void restart(char *);
   int modify_param(int, char **);
+  double memory_usage();
 
  private:
-  double dtv,dtf,dthalf;           // Full and half step sizes.
-  double boltz,nktv2p, mvv2e;      // Boltzmann factor and unit conversions.
-  double total_mass;               // Mass of the computational cell.
+  double dtv,dtf,dthalf;           // Full and half step sizes
+  double boltz,nktv2p, mvv2e;      // Boltzmann factor and unit conversions
+  double total_mass;               // Mass of the computational cell
 
-  double omega[3];                 // Time derivative of the volume.
+  double omega[3];                 // Time derivative of the volume
   double p_current[3],dilation[3];
-  double qmass;                    // Effective cell mass.
-  double mu;                       // Effective cell viscosity.
+  double qmass;                    // Effective cell mass
+  double mu;                       // Effective cell viscosity
   double tscale;                   // Converts thermal energy to compressive
                                    // strain ke at simulation start
+  int dftb;                        // flag for use with DFTB+
 
-  double velocity_sum;             // Sum of the velocities squared.
+  double velocity_sum;             // Sum of the velocities squared
+  double damping;		   // Damping function for TS force term at 
+                                   //   small volume difference (v0 - vol)
+  double T0S0;			   // Initial TS term for DFTB+ simulations
+  double S_elec,S_elec_1,S_elec_2; // time history of electron entropy 
+                                   //   for DFTB+ simulaitons 
+  double TS_dot;                   // time derivative of TS term for 
+                                   //   DFTB+ simulations
 
-  double **old_velocity;           // Saved velocities.
+  double **old_velocity;           // Saved velocities
 
   int kspace_flag;                 // 1 if KSpace invoked, 0 if not
   int nrigid;                      // number of rigid fixes
   int *rfix;                       // indices of rigid fixes
 
   char *id_temp,*id_press;         // Strings with identifiers of
-  char *id_pe;                     // created computes.
+  char *id_pe;                     // created computes
 
   class Compute *temperature;      // Computes created to evaluate
-  class Compute *pressure;         // thermodynamic quantities.
+  class Compute *pressure;         // thermodynamic quantities
   class Compute *pe;
   int tflag,pflag,vsflag,peflag;   // Flags to keep track of computes that
-                                   // were created.
+                                   // were created
 
-  // shock initial conditions.
+  // shock initial conditions
 
   double e0;                       // Initial energy
   double v0;                       // Initial volume
   double p0;                       // Initial pressure
-  double velocity;                 // Velocity of the shock.
+  double velocity;                 // Velocity of the shock
   double lagrangian_position;      // Lagrangian location of computational cell
   int direction;                   // Direction of shock
-  int p0_set;                      // Is pressure set.
-  int v0_set;                      // Is volume set.
-  int e0_set;                      // Is energy set.
+  int p0_set;                      // Is pressure set
+  int v0_set;                      // Is volume set
+  int e0_set;                      // Is energy set
+  double TS_int;                   // Needed for conserved quantity 
+                                   //   with thermal electronic excitations
+  double beta;                     // Energy conservation scaling factor
 
-  int atoms_allocated;             // The number of allocated atoms in old_velocity.
+  int maxold;                      // allocated size of old_velocity
+  double TS_dftb;                  // value needed from DFTB+ via fix external
+  class FixExternal *fix_external; // ptr to fix external
 
   // functions
 
   void couple();
   void remap(int);
-  void check_alloc(int n);
   double compute_etotal();
   double compute_vol();
   double compute_hugoniot();

src/fix_external.cpp

@@ -30,7 +30,7 @@ enum{PF_CALLBACK,PF_ARRAY};
 
 FixExternal::FixExternal(LAMMPS *lmp, int narg, char **arg) :
   Fix(lmp, narg, arg),
-  fexternal(NULL)
+  fexternal(NULL), caller_vector(NULL)
 {
   if (narg < 4) error->all(FLERR,"Illegal fix external command");
 
@@ -62,6 +62,11 @@ FixExternal::FixExternal(LAMMPS *lmp, int narg, char **arg) :
   atom->add_callback(0);
 
   user_energy = 0.0;
+
+  // optional vector of values provided by caller
+  // vector_flag and size_vector are setup via set_vector_length()
+
+  caller_vector = NULL;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -73,6 +78,7 @@ FixExternal::~FixExternal()
   atom->delete_callback(id,0);
 
   memory->destroy(fexternal);
+  delete [] caller_vector;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -167,10 +173,15 @@ void FixExternal::min_post_force(int vflag)
   post_force(vflag);
 }
 
+// ----------------------------------------------------------------------
+// "set" methods caller can invoke directly
+// ----------------------------------------------------------------------
+
 /* ----------------------------------------------------------------------
    caller invokes this method to set its contribution to global energy
-   do not just return if eflag_global is not set
-     input script could access this quantity via compute_scalar()
+   unlike other energy/virial set methods:
+     do not just return if eflag_global is not set
+     b/c input script could access this quantity via compute_scalar()
      even if eflag is not set on a particular timestep
 ------------------------------------------------------------------------- */
 
@@ -220,6 +231,34 @@ void FixExternal::set_virial_peratom(double **caller_virial)
       vatom[i][j] = caller_virial[i][j];
 }
 
+/* ----------------------------------------------------------------------
+   caller invokes this method to set length of vector of values
+   assume all vector values are extensive, could make this an option
+------------------------------------------------------------------------- */
+
+void FixExternal::set_vector_length(int n)
+{
+  delete [] caller_vector;
+
+  vector_flag = 1;
+  size_vector = n;
+  extvector = 1;
+
+  caller_vector = new double[n];
+}
+
+/* ----------------------------------------------------------------------
+   caller invokes this method to set Index value in vector
+   index ranges from 1 to N inclusive
+------------------------------------------------------------------------- */
+
+void FixExternal::set_vector(int index, double value)
+{
+  if (index >= size_vector)
+    error->all(FLERR,"Invalid set_vector index in fix external");
+  caller_vector[index-1] = value;
+}
+
 /* ----------------------------------------------------------------------
    potential energy of added force
    up to user to set it via set_energy()
@@ -230,6 +269,16 @@ double FixExternal::compute_scalar()
   return user_energy;
 }
 
+/* ----------------------------------------------------------------------
+   arbitrary value computed by caller
+   up to user to set it via set_vector()
+------------------------------------------------------------------------- */
+
+double FixExternal::compute_vector(int n)
+{
+  return caller_vector[n];
+}
+
 /* ----------------------------------------------------------------------
    memory usage of local atom-based array
 ------------------------------------------------------------------------- */

src/fix_external.h

@@ -39,11 +39,14 @@ class FixExternal : public Fix {
   void post_force(int);
   void min_post_force(int);
   double compute_scalar();
+  double compute_vector(int);
 
   void set_energy_global(double);
   void set_virial_global(double *);
   void set_energy_peratom(double *);
   void set_virial_peratom(double **);
+  void set_vector_length(int);
+  void set_vector(int,double);
 
   double memory_usage();
   void grow_arrays(int);
@@ -59,6 +62,7 @@ class FixExternal : public Fix {
   FnPtr callback;
   void *ptr_caller;
   double user_energy;
+  double *caller_vector;
 };
 
 }