Merge branch 'master' into last-minute-fixes

doc/src/Howto.rst

@@ -54,6 +54,7 @@ Analysis howto
    Howto_kappa
    Howto_viscosity
    Howto_diffusion
+   Howto_structured_data
 
 Force fields howto
 ==================

doc/src/Howto_structured_data.rst

@@ -0,0 +1,154 @@
+Output structured data from LAMMPS
+##################################
+
+LAMMPS can output structured data with the :doc:`print <print>` and :doc:`fix
+print <fix_print>` command.  This gives you flexibility since you can build
+custom data formats that contain system properties, thermo data, and variables
+values. This output can be directed to the screen and/or to a file for post
+processing.
+
+Writing the current system state, thermo data, variable values
+==============================================================
+
+Use the :doc:`print <print>` command to output the current system state, which
+can include system properties, thermo data and variable values.
+
+YAML
+----
+
+.. code-block:: LAMMPS
+
+   print """---
+   timestep: $(step)
+   pe: $(pe)
+   ke: $(ke)""" file current_state.yaml screen no
+
+.. code-block:: yaml
+   :caption: current_state.yaml
+
+   ---
+   timestep: 250
+   pe: -4.7774327356321810711
+   ke: 2.4962152903997174569
+
+JSON
+----
+
+.. code-block:: LAMMPS
+
+   print """{
+     "timestep": $(step),
+     "pe": $(pe),
+     "ke": $(ke)
+   }""" file current_state.json screen no
+
+.. code-block:: JSON
+   :caption: current_state.json
+  
+   {
+     "timestep": 250,
+     "pe": -4.7774327356321810711,
+     "ke": 2.4962152903997174569
+   }
+
+
+Writing continuous data during a simulation
+===========================================
+
+The :doc:`fix print <fix_print>` command allows you to output an arbitrary string at defined times during a simulation run.
+
+YAML
+----
+
+.. code-block:: LAMMPS
+
+   fix extra all print 50 """
+   - timestep: $(step)
+     pe: $(pe)
+     ke: $(ke)""" file output.yaml screen no
+
+.. code-block:: yaml
+   :caption: output.yaml
+
+   # Fix print output for fix extra
+   - timestep: 0
+     pe: -6.77336805325924729
+     ke: 4.4988750000000026219
+   
+   - timestep: 50
+     pe: -4.8082494418323200591
+     ke: 2.5257981827119797558
+   
+   - timestep: 100
+     pe: -4.7875608875581505686
+     ke: 2.5062598821985102582
+   
+   - timestep: 150
+     pe: -4.7471033686005483787
+     ke: 2.466095925545450207
+   
+   - timestep: 200
+     pe: -4.7509052858544134068
+     ke: 2.4701136792591693592
+   
+   - timestep: 250
+     pe: -4.7774327356321810711
+     ke: 2.4962152903997174569
+
+Post-processing of YAML files can be easily be done with Python and other
+scripting languages. In case of Python the `yaml` package allows you to load the
+data files and obtain a list of dictionaries.
+
+.. code-block:: python
+
+   import yaml
+
+   with open("output.yaml") as f:
+      data = yaml.load(f, Loader=yaml.FullLoader)
+
+   print(data)
+
+.. code-block::
+
+   [{'timestep': 0, 'pe': -6.773368053259247, 'ke': 4.498875000000003}, {'timestep': 50, 'pe': -4.80824944183232, 'ke': 2.5257981827119798}, {'timestep': 100, 'pe': -4.787560887558151, 'ke': 2.5062598821985103}, {'timestep': 150, 'pe': -4.747103368600548, 'ke': 2.46609592554545}, {'timestep': 200, 'pe': -4.750905285854413, 'ke': 2.4701136792591694}, {'timestep': 250, 'pe': -4.777432735632181, 'ke': 2.4962152903997175}]
+
+Line Delimited JSON (LD-JSON)
+-----------------------------
+
+The JSON format itself is very strict when it comes to delimiters. For continous
+output/streaming data it is beneficial use the *line delimited JSON* format.
+Each line represents one JSON object.
+
+.. code-block:: LAMMPS
+
+   fix extra all print 50 """{"timestep": $(step), "pe": $(pe), "ke": $(ke)}""" title "" file output.json screen no
+
+.. code-block:: json
+   :caption: output.json
+
+   {"timestep": 0, "pe": -6.77336805325924729, "ke": 4.4988750000000026219}
+   {"timestep": 50, "pe": -4.8082494418323200591, "ke": 2.5257981827119797558}
+   {"timestep": 100, "pe": -4.7875608875581505686, "ke": 2.5062598821985102582}
+   {"timestep": 150, "pe": -4.7471033686005483787, "ke": 2.466095925545450207}
+   {"timestep": 200, "pe": -4.7509052858544134068, "ke": 2.4701136792591693592}
+   {"timestep": 250, "pe": -4.7774327356321810711, "ke": 2.4962152903997174569}
+
+One simple way to load this data into a Python script is to use the `pandas`
+package. It can directly load these files into a data frame:
+
+.. code-block:: python
+
+   import pandas as pd
+
+   data = pd.read_json('output.json', lines=True)
+   print(data)
+
+.. code-block:: bash
+
+      timestep        pe        ke
+   0         0 -6.773368  4.498875
+   1        50 -4.808249  2.525798
+   2       100 -4.787561  2.506260
+   3       150 -4.747103  2.466096
+   4       200 -4.750905  2.470114
+   5       250 -4.777433  2.496215

doc/src/fix_ttm.rst

@@ -5,7 +5,7 @@ fix ttm command
 ===============
 
 fix ttm/grid command
-===============
+====================
 
 fix ttm/mod command
 ===================
@@ -45,7 +45,7 @@ Syntax
        Nz = number of thermal solve grid points in the z-direction (positive integer)
 
 * zero or more keyword/value(s) pairs may be appended
-* keyword = *set* or *infile" or *outfile"
+* keyword = *set* or *infile* or *outfile*
 
   .. parsed-literal::
 

src/KOKKOS/comm_kokkos.cpp

@@ -1315,3 +1315,13 @@ void CommKokkos::grow_swap(int n)
   memory->grow(maxsendlist,n,"comm:maxsendlist");
   for (int i=0;i<maxswap;i++) maxsendlist[i]=size;
 }
+
+/* ----------------------------------------------------------------------
+   forward communication of N values in per-atom array
+------------------------------------------------------------------------- */
+
+void CommKokkos::forward_comm_array(int nsize, double **array)
+{
+  k_sendlist.sync<LMPHostType>();
+  CommBrick::forward_comm_array(nsize,array);
+}

src/KOKKOS/comm_kokkos.h

@@ -51,6 +51,8 @@ class CommKokkos : public CommBrick {
   void forward_comm_dump(class Dump *);    // forward comm from a Dump
   void reverse_comm_dump(class Dump *);    // reverse comm from a Dump
 
+  void forward_comm_array(int, double **);            // forward comm of array
+
   template<class DeviceType> void forward_comm_device(int dummy);
   template<class DeviceType> void reverse_comm_device();
   template<class DeviceType> void forward_comm_pair_device(Pair *pair);

src/comm_brick.h

@@ -44,7 +44,7 @@ class CommBrick : public Comm {
   virtual void forward_comm_dump(class Dump *);          // forward comm from a Dump
   virtual void reverse_comm_dump(class Dump *);          // reverse comm from a Dump
 
-  void forward_comm_array(int, double **);            // forward comm of array
+  virtual void forward_comm_array(int, double **);    // forward comm of array
   int exchange_variable(int, double *, double *&);    // exchange on neigh stencil
   void *extract(const char *, int &);
   virtual double memory_usage();