From 286112ffbc5e3b48620957abb1508078a8326e6c Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 28 Feb 2019 11:00:55 -0500
Subject: [PATCH] count each force computation as one simulation step. this
 avoids accessing uninitialized data, too.

---
 .../phonon/dynamical_matrix_command/Manual.md | 48 -------------------
 src/USER-PHONON/dynamical_matrix.cpp          |  4 +-
 src/USER-PHONON/third_order.cpp               |  4 +-
 3 files changed, 6 insertions(+), 50 deletions(-)
 delete mode 100755 examples/USER/phonon/dynamical_matrix_command/Manual.md

diff --git a/examples/USER/phonon/dynamical_matrix_command/Manual.md b/examples/USER/phonon/dynamical_matrix_command/Manual.md
deleted file mode 100755
index c361f80325..0000000000
--- a/examples/USER/phonon/dynamical_matrix_command/Manual.md
+++ /dev/null
@@ -1,48 +0,0 @@
-# dynamical_matrix command
-
-## Syntax
-
-```
-dynamical_matrix group-ID style args keyword value ...
-```
-
-* group-ID = ID of group of atoms to displace
-* style = *regular* or *eskm*
-```
-*regular* args = gamma
-  gamma = finite difference displacement length
-*eskm* args = gamma
-  gamma = finite difference displacement length
-```
-* zero or more keyword/value pairs may be appended
-* keyword = *file* or *binary*
-```
-*file* value = output_file
-  output_file = name of file to dump the dynamical matrix into
-*binary* values = *yes* or *no* or *gzip*
-```
-
-## Examples
-
-```
-dynamical_matrix 1 regular 0.000001
-dynamical_matrix 1 eskm 0.000001
-dynamical_matrix 3 regular 0.00004 file dynmat.dat
-dynamical_matrix 5 eskm 0.00000001 file dynamical.dat binary yes
-```
-
-## Description
-
-Calculate the dynamical matrix of the selected group.
-
-## Restrictions
-
-None
-
-## Related commands
-
-None
-
-## Default
-
-The option defaults are file = "dynmat.dyn", binary = no  
diff --git a/src/USER-PHONON/dynamical_matrix.cpp b/src/USER-PHONON/dynamical_matrix.cpp
index da98a23a7d..cef59b3a63 100644
--- a/src/USER-PHONON/dynamical_matrix.cpp
+++ b/src/USER-PHONON/dynamical_matrix.cpp
@@ -258,6 +258,7 @@ void DynamicalMatrix::calculateMatrix()
 
     if (comm->me == 0 && screen) fprintf(screen,"Calculating Dynamical Matrix...\n");
 
+    update->nsteps = 0;
     for (bigint i=1; i<=natoms; i++){
         local_idx = atom->map(i);
         for (bigint alpha=0; alpha<3; alpha++){
@@ -390,6 +391,7 @@ void DynamicalMatrix::update_force()
         comm->reverse_comm();
         timer->stamp(Timer::COMM);
     }
+    ++ update->nsteps;
 }
 
 /* ----------------------------------------------------------------------
@@ -545,4 +547,4 @@ void DynamicalMatrix::create_groupmap()
     delete[] displs;
     delete[] sub_groupmap;
     delete[] temp_groupmap;
-}
\ No newline at end of file
+}
diff --git a/src/USER-PHONON/third_order.cpp b/src/USER-PHONON/third_order.cpp
index 41382e64cb..b4d2032a04 100644
--- a/src/USER-PHONON/third_order.cpp
+++ b/src/USER-PHONON/third_order.cpp
@@ -247,6 +247,7 @@ void ThirdOrder::calculateMatrix()
 
     if (comm->me == 0 && screen) fprintf(screen,"Calculating Anharmonic Dynamical Matrix...\n");
 
+    update->nsteps = 0;
     for (bigint i=1; i<=natoms; i++){
         local_idx = atom->map(i);
         for (bigint alpha=0; alpha<3; alpha++){
@@ -411,6 +412,7 @@ void ThirdOrder::update_force()
         comm->reverse_comm();
         timer->stamp(Timer::COMM);
     }
+    ++ update->nsteps;
 }
 
 /* ----------------------------------------------------------------------
@@ -551,4 +553,4 @@ void ThirdOrder::create_groupmap()
     delete[] displs;
     delete[] sub_groupmap;
     delete[] temp_groupmap;
-}
\ No newline at end of file
+}