git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@8164 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/Make.py

@@ -71,8 +71,9 @@ support = ["Makefile","Make.sh","Makefile.package.empty",
 
 # packages that have external libs with their external lib dir
 
-extlibs = {"USER-ATC": "atc", "USER-AWPMD": "awpmd", "USER-CUDA": "cuda",
+extlibs = {"USER-ATC": "atc", "USER-AWPMD": "awpmd", "USER-COLVARS": "colvars",
-           "GPU": "gpu","MEAM": "meam", "POEMS": "poems", "REAX": "reax"}
+           "USER-CUDA": "cuda","GPU": "gpu","MEAM": "meam", "POEMS": "poems",
+           "REAX": "reax"}
 
 # help messages
 

src/Makefile

@@ -17,10 +17,10 @@ PACKAGE = asphere class2 colloid dipole fld gpu granular kim \
 	  kspace manybody mc meam molecule opt peri poems reax replica \
 	  shock srd xtc
 
-PACKUSER = user-misc user-atc user-awpmd user-cg-cmm \
+PACKUSER = user-misc user-atc user-awpmd user-cg-cmm user-colvars \
 	   user-cuda user-eff user-ewaldn user-omp user-reaxc user-sph
 
-PACKLIB = gpu kim meam poems reax user-atc user-awpmd user-cuda
+PACKLIB = gpu kim meam poems reax user-atc user-awpmd user-colvars user-cuda
 
 PACKALL = $(PACKAGE) $(PACKUSER)
 

src/fix.h

@@ -151,6 +151,7 @@ class Fix : protected Pointers {
   virtual bigint read_data_skip_lines(char *) {return 0;}
 
   virtual int modify_param(int, char **) {return 0;}
+  virtual void *extract(const char *, int &) {return NULL;}
 
   virtual double memory_usage() {return 0.0;}
 

src/fix_langevin.cpp

@@ -66,6 +66,7 @@ FixLangevin::FixLangevin(LAMMPS *lmp, int narg, char **arg) :
     strcpy(tstr,&arg[3][2]);
   } else {
     t_start = atof(arg[3]);
+    t_target = t_start;
     tstyle = CONSTANT;
   }
 
@@ -274,7 +275,7 @@ void FixLangevin::post_force_respa(int vflag, int ilevel, int iloop)
 
 void FixLangevin::post_force_no_tally()
 {
-  double gamma1,gamma2,t_target;
+  double gamma1,gamma2;
 
   double **v = atom->v;
   double **f = atom->f;
@@ -461,7 +462,7 @@ void FixLangevin::post_force_no_tally()
 
 void FixLangevin::post_force_tally()
 {
-  double gamma1,gamma2,t_target;
+  double gamma1,gamma2;
 
   // reallocate flangevin if necessary
 
@@ -727,7 +728,7 @@ void FixLangevin::end_of_step()
 
 void FixLangevin::reset_target(double t_new)
 {
-  t_start = t_stop = t_new;
+  t_target = t_start = t_stop = t_new;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -798,6 +799,19 @@ double FixLangevin::compute_scalar()
   return -energy_all;
 }
 
+/* ----------------------------------------------------------------------
+   extract thermostat properties
+------------------------------------------------------------------------- */
+
+void *FixLangevin::extract(const char *str, int &dim)
+{
+  dim=0;
+  if (strcmp(str,"t_target") == 0) {
+    return &t_target;
+  } 
+  return NULL;
+}
+
 /* ----------------------------------------------------------------------
    memory usage of tally array
 ------------------------------------------------------------------------- */

src/fix_langevin.h

@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    http://lammps.sandia.gov, Sandia National Laboratories
    Steve Plimpton, sjplimp@sandia.gov
@@ -39,10 +39,11 @@ class FixLangevin : public Fix {
   int modify_param(int, char **);
   virtual double compute_scalar();
   double memory_usage();
+  virtual void *extract(const char *, int &);
 
  protected:
   int which,tally,zeroflag,oflag,aflag;
-  double t_start,t_stop,t_period;
+  double t_start,t_stop,t_period,t_target;
   double *gfactor1,*gfactor2,*ratio;
   double energy,energy_onestep;
   double tsqrt;

src/fix_nh.cpp

@@ -115,6 +115,7 @@ FixNH::FixNH(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
       if (iarg+4 > narg) error->all(FLERR,"Illegal fix nvt/npt/nph command");
       tstat_flag = 1;
       t_start = atof(arg[iarg+1]);
+      t_target = t_start;
       t_stop = atof(arg[iarg+2]);
       t_period = atof(arg[iarg+3]);
       if (t_start < 0.0 || t_stop <= 0.0)
@@ -1597,7 +1598,7 @@ double FixNH::compute_vector(int n)
 
 void FixNH::reset_target(double t_new)
 {
-  t_start = t_stop = t_new;
+  t_target = t_start = t_stop = t_new;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -1623,6 +1624,19 @@ void FixNH::reset_dt()
     tdrag_factor = 1.0 - (update->dt * t_freq * drag / nc_tchain);
 }
 
+/* ----------------------------------------------------------------------
+   extract thermostat properties
+------------------------------------------------------------------------- */
+
+void *FixNH::extract(const char *str, int &dim)
+{
+  dim=0;
+  if (strcmp(str,"t_target") == 0) {
+    return &t_target;
+  } 
+  return NULL;
+}
+
 /* ----------------------------------------------------------------------
    perform half-step update of chain thermostat variables
 ------------------------------------------------------------------------- */

src/fix_nh.h

@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    http://lammps.sandia.gov, Sandia National Laboratories
    Steve Plimpton, sjplimp@sandia.gov
@@ -38,6 +38,7 @@ class FixNH : public Fix {
   int modify_param(int, char **);
   void reset_target(double);
   void reset_dt();
+  virtual void *extract(const char*,int &);
 
  protected:
   int dimension,which;

src/fix_rigid.cpp

@@ -352,6 +352,7 @@ FixRigid::FixRigid(LAMMPS *lmp, int narg, char **arg) :
 
     } else error->all(FLERR,"Illegal fix rigid command");
   }
+  t_target = t_start;
 
   // initialize Marsaglia RNG with processor-unique seed
 
@@ -1231,7 +1232,7 @@ void FixRigid::post_force(int vflag)
 
     double delta = update->ntimestep - update->beginstep;
     delta /= update->endstep - update->beginstep;
-    double t_target = t_start + delta * (t_stop-t_start);
+    t_target = t_start + delta * (t_stop-t_start);
     double tsqrt = sqrt(t_target);
 
     double boltz = force->boltz;
@@ -2084,6 +2085,19 @@ double FixRigid::compute_scalar()
   return t;
 }
 
+/* ----------------------------------------------------------------------
+   extract thermostat properties
+------------------------------------------------------------------------- */
+
+void *FixRigid::extract(const char *str, int &dim)
+{
+  dim=0;
+  if (strcmp(str,"t_target") == 0) {
+    return &t_target;
+  } 
+  return NULL;
+}
+
 /* ----------------------------------------------------------------------
    return attributes of a rigid body
    15 values per body

src/fix_rigid.h

@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    http://lammps.sandia.gov, Sandia National Laboratories
    Steve Plimpton, sjplimp@sandia.gov
@@ -49,6 +49,7 @@ class FixRigid : public Fix {
   int dof(int);
   void deform(int);
   void reset_dt();
+  virtual void *extract(const char*,int &);
   double compute_array(int, int);
 
  protected:
@@ -94,7 +95,7 @@ class FixRigid : public Fix {
   int langflag;             // 0/1 = no/yes Langevin thermostat
 
   int tempflag;             // NVT settings
-  double t_start,t_stop;
+  double t_start,t_stop,t_target;
   double t_period,t_freq;
   int t_chain,t_iter,t_order;
 

src/fix_temp_berendsen.cpp

@@ -44,6 +44,7 @@ FixTempBerendsen::FixTempBerendsen(LAMMPS *lmp, int narg, char **arg) :
   extscalar = 1;
 
   t_start = atof(arg[3]);
+  t_target = t_start;
   t_stop = atof(arg[4]);
   t_period = atof(arg[5]);
 
@@ -113,7 +114,7 @@ void FixTempBerendsen::end_of_step()
 
   double delta = update->ntimestep - update->beginstep;
   delta /= update->endstep - update->beginstep;
-  double t_target = t_start + delta * (t_stop-t_start);
+  t_target = t_start + delta * (t_stop-t_start);
 
   // rescale velocities by lamda
   // for BIAS:
@@ -181,7 +182,7 @@ int FixTempBerendsen::modify_param(int narg, char **arg)
 
 void FixTempBerendsen::reset_target(double t_new)
 {
-  t_start = t_stop = t_new;
+  t_target = t_start = t_stop = t_new;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -190,3 +191,17 @@ double FixTempBerendsen::compute_scalar()
 {
   return energy;
 }  
+
+/* ----------------------------------------------------------------------
+   extract thermostat properties
+------------------------------------------------------------------------- */
+
+void *FixTempBerendsen::extract(const char *str, int &dim)
+{
+  dim=0;
+  if (strcmp(str,"t_target") == 0) {
+    return &t_target;
+  } 
+  return NULL;
+}
+

src/fix_temp_berendsen.h

@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    http://lammps.sandia.gov, Sandia National Laboratories
    Steve Plimpton, sjplimp@sandia.gov
@@ -34,10 +34,11 @@ class FixTempBerendsen : public Fix {
   int modify_param(int, char **);
   void reset_target(double);
   double compute_scalar();
+  virtual void *extract(const char *, int &);
 
  private:
   int which;
-  double t_start,t_stop,t_period;
+  double t_start,t_stop,t_period,t_target;
   double energy;
 
   char *id_temp;

src/fix_temp_rescale.cpp

@@ -46,6 +46,7 @@ FixTempRescale::FixTempRescale(LAMMPS *lmp, int narg, char **arg) :
   extscalar = 1;
 
   t_start = atof(arg[4]);
+  t_target = t_start;
   t_stop = atof(arg[5]);
   t_window = atof(arg[6]);
   fraction = atof(arg[7]);
@@ -112,7 +113,7 @@ void FixTempRescale::end_of_step()
 
   double delta = update->ntimestep - update->beginstep;
   delta /= update->endstep - update->beginstep;
-  double t_target = t_start + delta * (t_stop-t_start);
+  t_target = t_start + delta * (t_stop-t_start);
 
   // rescale velocity of appropriate atoms if outside window
   // for BIAS:
@@ -186,7 +187,7 @@ int FixTempRescale::modify_param(int narg, char **arg)
 
 void FixTempRescale::reset_target(double t_new)
 {
-  t_start = t_stop = t_new;
+  t_target = t_start = t_stop = t_new;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -195,3 +196,17 @@ double FixTempRescale::compute_scalar()
 {
   return energy;
 }
+
+/* ----------------------------------------------------------------------
+   extract thermostat properties
+------------------------------------------------------------------------- */
+
+void *FixTempRescale::extract(const char *str, int &dim)
+{
+  dim=0;
+  if (strcmp(str,"t_target") == 0) {
+    return &t_target;
+  } 
+  return NULL;
+}
+

src/fix_temp_rescale.h

@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    http://lammps.sandia.gov, Sandia National Laboratories
    Steve Plimpton, sjplimp@sandia.gov
@@ -34,10 +34,11 @@ class FixTempRescale : public Fix {
   int modify_param(int, char **);
   void reset_target(double);
   double compute_scalar();
+  virtual void *extract(const char *, int &);
 
  protected:
   int which;
-  double t_start,t_stop,t_window;
+  double t_start,t_stop,t_window,t_target;
   double fraction,energy,efactor;
 
   char *id_temp;

src/force.h

@@ -1,4 +1,4 @@
-/* ----------------------------------------------------------------------
+/* -*- c++ -*- ----------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    http://lammps.sandia.gov, Sandia National Laboratories
    Steve Plimpton, sjplimp@sandia.gov
@@ -37,6 +37,7 @@ class Force : protected Pointers {
   double mvh2r;                      // conversion of mv/hbar to distance 
                                      // hbar = h/(2*pi)
   double angstrom;                   // 1 angstrom in native units
+  double femtosecond;                // 1 femtosecond in native units
   double qelectron;                  // 1 electron charge abs() in native units
 
   int newton,newton_pair,newton_bond;   // Newton's 3rd law settings

src/update.cpp

@@ -132,6 +132,7 @@ void Update::set_units(const char *style)
     force->hhmrr2e = 0.0;
     force->mvh2r = 0.0;
     force->angstrom = 1.0;
+    force->femtosecond = 1.0;
     force->qelectron = 1.0;
 
     dt = 0.005;
@@ -152,6 +153,7 @@ void Update::set_units(const char *style)
     force->hhmrr2e = 0.0957018663603261;
     force->mvh2r = 1.5339009481951;
     force->angstrom = 1.0;
+    force->femtosecond = 1.0;
     force->qelectron = 1.0;
 
     dt = 1.0;
@@ -172,6 +174,7 @@ void Update::set_units(const char *style)
     force->hhmrr2e = 0.0;
     force->mvh2r = 0.0;
     force->angstrom = 1.0;
+    force->femtosecond = 1.0e-3;
     force->qelectron = 1.0;
 
     dt = 0.001;
@@ -192,6 +195,7 @@ void Update::set_units(const char *style)
     force->hhmrr2e = 0.0;
     force->mvh2r = 0.0;
     force->angstrom = 1.0e-10;
+    force->femtosecond = 1.0e-15;
     force->qelectron = 1.6021765e-19;
 
     dt = 1.0e-8;
@@ -212,6 +216,7 @@ void Update::set_units(const char *style)
     force->hhmrr2e = 0.0;
     force->mvh2r = 0.0;
     force->angstrom = 1.0e-8;
+    force->femtosecond = 1.0e-15;
     force->qelectron = 4.8032044e-10;
 
     dt = 1.0e-8;
@@ -232,6 +237,7 @@ void Update::set_units(const char *style)
     force->hhmrr2e = 0.0;
     force->mvh2r = 0.0;
     force->angstrom = 1.88972612;
+    force->femtosecond = 0.0241888428;
     force->qelectron = 1.0;
 
     dt = 0.001;