Simplified GJF formalism

src/fix_langevin.h

@@ -2,12 +2,10 @@
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    http://lammps.sandia.gov, Sandia National Laboratories
    Steve Plimpton, sjplimp@sandia.gov
-
    Copyright (2003) Sandia Corporation.  Under the terms of Contract
    DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
    certain rights in this software.  This software is distributed under
    the GNU General Public License.
-
    See the README file in the top-level LAMMPS directory.
 ------------------------------------------------------------------------- */
 
@@ -24,68 +22,64 @@ FixStyle(langevin,FixLangevin)
 
 namespace LAMMPS_NS {
 
-class FixLangevin : public Fix {
- public:
-  FixLangevin(class LAMMPS *, int, char **);
-  virtual ~FixLangevin();
-  int setmask();
-  void init();
-  void setup(int);
-  //virtual void initial_integrate(int);
-  virtual void post_integrate();
-  virtual void post_force(int);
-  void post_force_respa(int, int, int);
-  virtual void end_of_step();
-  void reset_target(double);
-  void reset_dt();
-  int modify_param(int, char **);
-  virtual double compute_scalar();
-  double memory_usage();
-  virtual void *extract(const char *, int &);
-  void grow_arrays(int);
-  void copy_arrays(int, int, int);
-  int pack_exchange(int, double *);
-  int unpack_exchange(int, double *);
+  class FixLangevin : public Fix {
+  public:
+    FixLangevin(class LAMMPS *, int, char **);
+    virtual ~FixLangevin();
+    int setmask();
+    void init();
+    void setup(int);
+    void initial_integrate_respa(int, int, int);
+    virtual void initial_integrate(int);
+    virtual void post_force(int);
+    void post_force_respa(int, int, int);
+    virtual void end_of_step();
+    void reset_target(double);
+    void reset_dt();
+    int modify_param(int, char **);
+    virtual double compute_scalar();
+    double memory_usage();
+    virtual void *extract(const char *, int &);
+    void grow_arrays(int);
+    void copy_arrays(int, int, int);
+    int pack_exchange(int, double *);
+    int unpack_exchange(int, double *);
 
- protected:
-  int gjfflag,oflag,tallyflag,zeroflag,tbiasflag,hsflag;
-  int flangevin_allocated;
-  double ascale;
-  double t_start,t_stop,t_period,t_target;
-  double *gfactor1,*gfactor2,*ratio;
-  double energy,energy_onestep;
-  double tsqrt;
-  int tstyle,tvar;
-  double gjffac;
-  char *tstr;
+  protected:
+    int gjfflag,oflag,tallyflag,zeroflag,tbiasflag;
+    int flangevin_allocated;
+    double ascale;
+    double t_start,t_stop,t_period,t_target;
+    double *gfactor1,*gfactor2,*ratio;
+    double energy,energy_onestep;
+    double tsqrt;
+    int tstyle,tvar;
+    double gjfa, gjfsib; //gjf a and gjf sqrt inverse b
+    char *tstr;
 
-  class AtomVecEllipsoid *avec;
+    class AtomVecEllipsoid *avec;
 
-  int maxatom1,maxatom2;
-  double **flangevin;
-  double *tforce;
-  double **franprev;
-  double **lv;  //2GJ velocity or half-step velocity
-  double **wildcard;
-  double **bias; //Bias velocity
+    int maxatom1,maxatom2;
+    double **flangevin;
+    double *tforce;
+    double **franprev;
+    double **lv; //half step velocity
 
-  int nvalues;
+    char *id_temp;
+    class Compute *temperature;
 
-  char *id_temp;
-  class Compute *temperature;
+    int nlevels_respa;
+    class RanMars *random;
+    int seed;
 
-  int nlevels_respa;
-  class RanMars *random;
-  int seed;
+    template < int Tp_TSTYLEATOM, int Tp_GJF, int Tp_TALLY,
+        int Tp_BIAS, int Tp_RMASS, int Tp_ZERO >
+    void post_force_templated();
 
-  template < int Tp_TSTYLEATOM, int Tp_GJF, int Tp_TALLY,
-             int Tp_BIAS, int Tp_RMASS, int Tp_ZERO >
-  void post_force_templated();
-
-  void omega_thermostat();
-  void angmom_thermostat();
-  void compute_target();
-};
+    void omega_thermostat();
+    void angmom_thermostat();
+    void compute_target();
+  };
 
 }
 
@@ -93,62 +87,35 @@ class FixLangevin : public Fix {
 #endif
 
 /* ERROR/WARNING messages:
-
 E: Illegal ... command
-
 Self-explanatory.  Check the input script syntax and compare to the
 documentation for the command.  You can use -echo screen as a
 command-line option when running LAMMPS to see the offending line.
-
 E: Fix langevin period must be > 0.0
-
 The time window for temperature relaxation must be > 0
-
 E: Fix langevin omega requires atom style sphere
-
 Self-explanatory.
-
 E: Fix langevin angmom requires atom style ellipsoid
-
 Self-explanatory.
-
 E: Variable name for fix langevin does not exist
-
 Self-explanatory.
-
 E: Variable for fix langevin is invalid style
-
 It must be an equal-style variable.
-
 E: Fix langevin omega requires extended particles
-
 One of the particles has radius 0.0.
-
 E: Fix langevin angmom requires extended particles
-
 This fix option cannot be used with point particles.
-
 E: Cannot zero Langevin force of 0 atoms
-
 The group has zero atoms, so you cannot request its force
 be zeroed.
-
 E: Fix langevin variable returned negative temperature
-
 Self-explanatory.
-
 E: Could not find fix_modify temperature ID
-
 The compute ID for computing temperature does not exist.
-
 E: Fix_modify temperature ID does not compute temperature
-
 The compute ID assigned to the fix must compute temperature.
-
 W: Group for fix_modify temp != fix group
-
 The fix_modify command is specifying a temperature computation that
 computes a temperature on a different group of atoms than the fix
 itself operates on.  This is probably not what you want to do.
-
 */