ATC version 2.0, date: Aug7

git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@10560 f3b2605a-c512-4ea7-a41b-209d697bcdaa

src/USER-ATC/fix_atc.h

@@ -1,72 +1,109 @@
-/* -*- c++ -*- ----------------------------------------------------------
-   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.
-------------------------------------------------------------------------- */
-
 #ifdef FIX_CLASS
 
 FixStyle(atc,FixATC)
 
 #else
 
-#ifndef LMP_FIX_ATC_H
-#define LMP_FIX_ATC_H
+#ifndef FIX_ATC_H
+#define FIX_ATC_H
 
 #include "fix.h"
-
 #include "pointers.h" // access to lammps pointers
 
-namespace ATC {
-  class ATC_Transfer;
-}
+#include <string>
+using std::string;
 
+namespace ATC {
+  class ATC_Method;
+}
 namespace LAMMPS_NS {
-  // fwd decl
   class  NeighList;
 
+  /**
+   *  @class FixATC 
+   *  @brief Class for an atom-to-continuum (ATC) Lammps fix. 
+   */
+
   class FixATC : public Fix {
-  public:
+  public: 
     /** constructor & destructor */
     FixATC(class LAMMPS *, int, char **);
     ~FixATC();
 
-    /** calls ATC_Transfer */
+    /** initialization functions */
     void init();
-    void init_list(int, NeighList *);
+    void init_list(int id, NeighList *ptr) ; 
     void setup(int vflag);
+    void min_setup(int vflag);
 
     /** setmask: tell LAMMPS which fix methods to call */
     int setmask();
 
-    /** initial_integrate: calls ATC_Transfer */
+    /** initial_integrate */
     void initial_integrate(int vflag);
 
-    /** final_integrate: calls ATC_Transfer */
+    /** final_integrate */
     void final_integrate();
 
-    /** calls ATC_Transfer */
+    /** end of step for run or minimize */
+    void end_of_step();
+
+    /** pre_exchange is used to modify fix-specific data
+       and is called before domain->pbc() and comm->exchange().  */
+    void setup_pre_exchange();
     void pre_exchange();
+    void min_setup_pre_exchange();
     void min_pre_exchange();
-    double memory_usage();
+
+    double memory_usage(); 
     void grow_arrays(int);
     void copy_arrays(int, int, int);
+
+    /** pack_exchange called from atom_vec->pack_exchange()
+       and packs fix-specific data for a given real (local) 
+       atom being sent to another processor.  */
     int pack_exchange(int, double *);
+
+    /** unpack_exchange called from atom_vec->unpack_exchange()
+       and unpacks fix-specific data for a given real (local) 
+       atom received from another processor. */
     int unpack_exchange(int, double *);
-    int pack_comm(int , int *, double *, int, int *);
+
+    /** pack_comm called from comm->forward_comm_fix and
+       packs fix-specific data for a given ghost atom
+       from exchange with another proc */
+    int pack_comm(int , int *, double *, int, int *);  
+ 
+    /** unpack_comm called from comm->forward_comm_fix and
+       unpacks fix-specific data for a given ghost atom
+       from exchange with another proc */
     void unpack_comm(int, int, double *);
 
+    /** pre_neighbor is used to modify fix-specific data
+       and is called before neighbor list is built in 
+       neighbor->build().  */
+    void pre_neighbor();
+    void setup_pre_neighbor();
+    void min_setup_pre_neighbor();
+
+    /** pre/post_force is used to modify fix-specific data
+        and is before/after the various force computations. */
+    void pre_force(int vflag);
+    void post_force(int vflag);
+
+    /** post_run is called after a run completes */
+    void post_run();
+
+    /** min_pre_force is called before forces are calculated in minimize */
+    void min_pre_force(int vflag);
+
+    /** min_post_force is called after forces are calculated in minimize */
+    void min_post_force(int vflag);
+
     /** modify atc parameters (parser) */
     int modify_param(int narg, char** arg);
 
-    /** calls ATC_Transfer to handle restarting/checkpointing */
+    /** calls ATC_Method to handle restarting/checkpointing */
     /** these four methods are for writing per-atom quantities */
     int pack_restart(int, double *);
     void unpack_restart(int, int);
@@ -76,15 +113,19 @@ namespace LAMMPS_NS {
     void write_restart(FILE *);
     void restart(char *);
 
+    /** accessor function for ATC_Method class pointer */
+    const ATC::ATC_Method* atc() { return atc_; }
+
   protected:
+    LAMMPS * lammps_;
+
     /** functions for "thermo" output */
-    virtual double compute_scalar();
-    virtual double compute_vector(int n);
-
+    virtual double compute_scalar() ;
+    virtual double compute_vector(int n) ;
+    virtual double compute_array(int irow, int icol) ;
     double dtv,dtf;
-    ATC::ATC_Transfer *atcTransfer_;
+    ATC::ATC_Method *atc_;
   };
-
 }
 
 #endif

src/USER-ATC/svn.stdout

@@ -1,4 +1,5 @@
 Sending        USER-ATC/Install.sh
 Sending        USER-ATC/fix_atc.cpp
 Adding         USER-ATC/svn.stdout
-Transmitting file data ..
+Transmitting file data ...
+Committed revision 10556.