From 4c1fbc359a414ae82fa0d40e107a0392df307c1b Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 14 Nov 2018 05:28:19 -0500
Subject: [PATCH 1/9] use tagint when unpacking atom tags from communication
 buffers

---
 src/MOLECULE/atom_vec_molecular.cpp | 48 ++++++++++++++---------------
 1 file changed, 24 insertions(+), 24 deletions(-)

diff --git a/src/MOLECULE/atom_vec_molecular.cpp b/src/MOLECULE/atom_vec_molecular.cpp
index 6e903a936e..cdd3f02505 100644
--- a/src/MOLECULE/atom_vec_molecular.cpp
+++ b/src/MOLECULE/atom_vec_molecular.cpp
@@ -677,33 +677,33 @@ int AtomVecMolecular::unpack_exchange(double *buf)
   num_bond[nlocal] = (int) ubuf(buf[m++]).i;
   for (k = 0; k < num_bond[nlocal]; k++) {
     bond_type[nlocal][k] = (int) ubuf(buf[m++]).i;
-    bond_atom[nlocal][k] = (int) ubuf(buf[m++]).i;
+    bond_atom[nlocal][k] = (tagint) ubuf(buf[m++]).i;
   }
 
   num_angle[nlocal] = (int) ubuf(buf[m++]).i;
   for (k = 0; k < num_angle[nlocal]; k++) {
     angle_type[nlocal][k] = (int) ubuf(buf[m++]).i;
-    angle_atom1[nlocal][k] = (int) ubuf(buf[m++]).i;
-    angle_atom2[nlocal][k] = (int) ubuf(buf[m++]).i;
-    angle_atom3[nlocal][k] = (int) ubuf(buf[m++]).i;
+    angle_atom1[nlocal][k] = (tagint) ubuf(buf[m++]).i;
+    angle_atom2[nlocal][k] = (tagint) ubuf(buf[m++]).i;
+    angle_atom3[nlocal][k] = (tagint) ubuf(buf[m++]).i;
   }
 
   num_dihedral[nlocal] = (int) ubuf(buf[m++]).i;
   for (k = 0; k < num_dihedral[nlocal]; k++) {
     dihedral_type[nlocal][k] = (int) ubuf(buf[m++]).i;
-    dihedral_atom1[nlocal][k] = (int) ubuf(buf[m++]).i;
-    dihedral_atom2[nlocal][k] = (int) ubuf(buf[m++]).i;
-    dihedral_atom3[nlocal][k] = (int) ubuf(buf[m++]).i;
-    dihedral_atom4[nlocal][k] = (int) ubuf(buf[m++]).i;
+    dihedral_atom1[nlocal][k] = (tagint) ubuf(buf[m++]).i;
+    dihedral_atom2[nlocal][k] = (tagint) ubuf(buf[m++]).i;
+    dihedral_atom3[nlocal][k] = (tagint) ubuf(buf[m++]).i;
+    dihedral_atom4[nlocal][k] = (tagint) ubuf(buf[m++]).i;
   }
 
   num_improper[nlocal] = (int) ubuf(buf[m++]).i;
   for (k = 0; k < num_improper[nlocal]; k++) {
     improper_type[nlocal][k] = (int) ubuf(buf[m++]).i;
-    improper_atom1[nlocal][k] = (int) ubuf(buf[m++]).i;
-    improper_atom2[nlocal][k] = (int) ubuf(buf[m++]).i;
-    improper_atom3[nlocal][k] = (int) ubuf(buf[m++]).i;
-    improper_atom4[nlocal][k] = (int) ubuf(buf[m++]).i;
+    improper_atom1[nlocal][k] = (tagint) ubuf(buf[m++]).i;
+    improper_atom2[nlocal][k] = (tagint) ubuf(buf[m++]).i;
+    improper_atom3[nlocal][k] = (tagint) ubuf(buf[m++]).i;
+    improper_atom4[nlocal][k] = (tagint) ubuf(buf[m++]).i;
   }
 
   nspecial[nlocal][0] = (int) ubuf(buf[m++]).i;
@@ -840,33 +840,33 @@ int AtomVecMolecular::unpack_restart(double *buf)
   num_bond[nlocal] = (int) ubuf(buf[m++]).i;
   for (k = 0; k < num_bond[nlocal]; k++) {
     bond_type[nlocal][k] = (int) ubuf(buf[m++]).i;
-    bond_atom[nlocal][k] = (int) ubuf(buf[m++]).i;
+    bond_atom[nlocal][k] = (tagint) ubuf(buf[m++]).i;
   }
 
   num_angle[nlocal] = (int) ubuf(buf[m++]).i;
   for (k = 0; k < num_angle[nlocal]; k++) {
     angle_type[nlocal][k] = (int) ubuf(buf[m++]).i;
-    angle_atom1[nlocal][k] = (int) ubuf(buf[m++]).i;
-    angle_atom2[nlocal][k] = (int) ubuf(buf[m++]).i;
-    angle_atom3[nlocal][k] = (int) ubuf(buf[m++]).i;
+    angle_atom1[nlocal][k] = (tagint) ubuf(buf[m++]).i;
+    angle_atom2[nlocal][k] = (tagint) ubuf(buf[m++]).i;
+    angle_atom3[nlocal][k] = (tagint) ubuf(buf[m++]).i;
   }
 
   num_dihedral[nlocal] = (int) ubuf(buf[m++]).i;
   for (k = 0; k < num_dihedral[nlocal]; k++) {
     dihedral_type[nlocal][k] = (int) ubuf(buf[m++]).i;
-    dihedral_atom1[nlocal][k] = (int) ubuf(buf[m++]).i;
-    dihedral_atom2[nlocal][k] = (int) ubuf(buf[m++]).i;
-    dihedral_atom3[nlocal][k] = (int) ubuf(buf[m++]).i;
-    dihedral_atom4[nlocal][k] = (int) ubuf(buf[m++]).i;
+    dihedral_atom1[nlocal][k] = (tagint) ubuf(buf[m++]).i;
+    dihedral_atom2[nlocal][k] = (tagint) ubuf(buf[m++]).i;
+    dihedral_atom3[nlocal][k] = (tagint) ubuf(buf[m++]).i;
+    dihedral_atom4[nlocal][k] = (tagint) ubuf(buf[m++]).i;
   }
 
   num_improper[nlocal] = (int) ubuf(buf[m++]).i;
   for (k = 0; k < num_improper[nlocal]; k++) {
     improper_type[nlocal][k] = (int) ubuf(buf[m++]).i;
-    improper_atom1[nlocal][k] = (int) ubuf(buf[m++]).i;
-    improper_atom2[nlocal][k] = (int) ubuf(buf[m++]).i;
-    improper_atom3[nlocal][k] = (int) ubuf(buf[m++]).i;
-    improper_atom4[nlocal][k] = (int) ubuf(buf[m++]).i;
+    improper_atom1[nlocal][k] = (tagint) ubuf(buf[m++]).i;
+    improper_atom2[nlocal][k] = (tagint) ubuf(buf[m++]).i;
+    improper_atom3[nlocal][k] = (tagint) ubuf(buf[m++]).i;
+    improper_atom4[nlocal][k] = (tagint) ubuf(buf[m++]).i;
   }
 
   nspecial[nlocal][0] = nspecial[nlocal][1] = nspecial[nlocal][2] = 0;

From 7a22b8aa621528327637ab3bc159b467db9c7478 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 14 Nov 2018 05:29:26 -0500
Subject: [PATCH 2/9] check only in currently added data file atoms for
 dihedral overflow

---
 src/read_data.cpp | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/read_data.cpp b/src/read_data.cpp
index 26c406c1d6..1dbb9506c6 100644
--- a/src/read_data.cpp
+++ b/src/read_data.cpp
@@ -1435,7 +1435,7 @@ void ReadData::dihedrals(int firstpass)
 
   if (firstpass) {
     int max = 0;
-    for (int i = 0; i < nlocal; i++) max = MAX(max,count[i]);
+    for (int i = nlocal_previous; i < nlocal; i++) max = MAX(max,count[i]);
     int maxall;
     MPI_Allreduce(&max,&maxall,1,MPI_INT,MPI_MAX,world);
     if (addflag == NONE) maxall += atom->extra_dihedral_per_atom;

From a942d8b3ba0bfb784bb71e091e7ef5ae1af38c59 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 14 Nov 2018 05:30:23 -0500
Subject: [PATCH 3/9] use memset() for clearing of arrays

---
 src/read_data.cpp | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/src/read_data.cpp b/src/read_data.cpp
index 1dbb9506c6..373ba30151 100644
--- a/src/read_data.cpp
+++ b/src/read_data.cpp
@@ -1248,7 +1248,7 @@ void ReadData::bonds(int firstpass)
   int *count = NULL;
   if (firstpass) {
     memory->create(count,nlocal,"read_data:count");
-    for (int i = 0; i < nlocal; i++) count[i] = 0;
+    memset(count,0,nlocal*sizeof(int));
   }
 
   // read and process bonds
@@ -1331,7 +1331,7 @@ void ReadData::angles(int firstpass)
   int *count = NULL;
   if (firstpass) {
     memory->create(count,nlocal,"read_data:count");
-    for (int i = 0; i < nlocal; i++) count[i] = 0;
+    memset(count,0,nlocal*sizeof(int));
   }
 
   // read and process angles
@@ -1414,7 +1414,7 @@ void ReadData::dihedrals(int firstpass)
   int *count = NULL;
   if (firstpass) {
     memory->create(count,nlocal,"read_data:count");
-    for (int i = 0; i < nlocal; i++) count[i] = 0;
+    memset(count,0,nlocal*sizeof(int));
   }
 
   // read and process dihedrals
@@ -1497,7 +1497,7 @@ void ReadData::impropers(int firstpass)
   int *count = NULL;
   if (firstpass) {
     memory->create(count,nlocal,"read_data:count");
-    for (int i = 0; i < nlocal; i++) count[i] = 0;
+    memset(count,0,nlocal*sizeof(int));
   }
 
   // read and process impropers

From 952e52982e3c66541a4bb07f465863d81ab5f7d1 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Wed, 14 Nov 2018 05:37:59 -0500
Subject: [PATCH 4/9] add comment to indicate code intended for backward
 compatibility only

---
 src/read_restart.cpp | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/read_restart.cpp b/src/read_restart.cpp
index 252c48d251..6b9ea8d773 100644
--- a/src/read_restart.cpp
+++ b/src/read_restart.cpp
@@ -924,11 +924,13 @@ void ReadRestart::header(int incompatible)
       atom->extra_dihedral_per_atom = read_int();
     } else if (flag == EXTRA_IMPROPER_PER_ATOM) {
       atom->extra_improper_per_atom = read_int();
-    } else if (flag == EXTRA_SPECIAL_PER_ATOM) {
-      force->special_extra = read_int();
     } else if (flag == ATOM_MAXSPECIAL) {
       atom->maxspecial = read_int();
 
+      // for backward compatibility
+    } else if (flag == EXTRA_SPECIAL_PER_ATOM) {
+      force->special_extra = read_int();
+
     } else error->all(FLERR,"Invalid flag in header section of restart file");
 
     flag = read_int();

From e1603763657826355ff25ee01a5db215d4da32f9 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 15 Nov 2018 12:45:15 -0500
Subject: [PATCH 5/9] incomplete first draft. committed for checking the markup
 in github.

---
 doc/github-development-workflow.md | 82 ++++++++++++++++++++++++++++++
 1 file changed, 82 insertions(+)
 create mode 100644 doc/github-development-workflow.md

diff --git a/doc/github-development-workflow.md b/doc/github-development-workflow.md
new file mode 100644
index 0000000000..b81dbb417e
--- /dev/null
+++ b/doc/github-development-workflow.md
@@ -0,0 +1,82 @@
+# Outline of the GitHub Development Workflow
+
+This purpose of this document is to provide a point of reference for the
+core LAMMPS developers and other LAMMPS contibutors to understand the
+choices the LAMMPS developers have agreed on. Git and GitHub provide the
+tools, but do not set policies, so it is up to the developers to come to
+an agreement as to how to define and interpret policies. This document
+is likely to change as our experiences and needs change and we try to
+adapt accordingly. Last change 2018-11-15.
+
+## Table of Contents
+
+  * [GitHub Merge Management](#github-merge-management)
+  * [Pull Requests](#pull-requests)
+    * [Pull Request Assignments](#pull-request-assignments)
+    * [Pull Request Reviews](#pull-request-reviews)
+    * [Pull Request Discussions](#pull-request-discussions)
+    * [Checklist for Pull Requests](#checklist-for-pull-requests)
+  * [GitHub Issues](#github-issues)
+    * [Feature Request Issues](#feature-request-issues)
+    * [Bug Report Issues](#bug-report-issues)
+  * [Milestones and Release Planning](#milestones-and-release-planning)
+
+## GitHub Merge Management
+
+In the interest of consistency, ONLY ONE of the core LAMMPS developers
+should doing the merging itself.  This is currently @akohlmey (Axel
+Kohlmeyer).  If this assignment needs to be changed, it shall be done
+right after a stable release.
+
+## Pull Requests
+
+ALL changes to the LAMMPS code and documentation, however trivial, MUST
+be submitted as a pull request to GitHub. All changes to the "master"
+branch must be made exclusively through merging pull requests. The
+"unstable" and "stable" branches are only to be updated upon patch or
+stable releases with fast-forward merges based on the associated
+tags. Pull requests may also be submitted to (long-running) feature
+branches created by LAMMPS developers inside the LAMMPS project, if
+needed. Those are not subject to the merge and review restrictions
+discussed in this document, though.
+
+### Pull Request Assignments
+
+Pull requests can be "chaperoned" by one of the LAMMPS core developers.
+This is indicated by who the pull request is assigned to. LAMMPS core
+developers can self-assign or they can decide to assign a pull request
+to a different LAMMPS developer. Being assigned to a pull request means,
+that this pull request may need some work and the assignee is tasked to
+determine what this might be needed or not, and may either implement the
+required changes or ask the submitter of the pull request to implement
+them.  Even though, all LAMMPS developers may have write access to pull
+requests (if enabled by the submitter, which is the default), only the
+submitter or the assignee of a pull request may do so.  During this
+period the "work_in_progress" label shall be applied to the pull
+request.  The assignee gets to decide what happens to the pull request
+next, e.g. whether it should be assigned to a different developer for
+additional checks and changes, or is recommended to be merged.  Removing
+the "work_in_progress" label and assigning the pull request to the
+developer tasked with merging signals that a pull request is ready to be
+merged.
+
+### Pull Request Reviews
+
+People can be assigned to review a pull request in two ways:
+  * They can be assigned manually to review a pull request
+    by the submitter or a LAMMPS developer
+  * They can be automatically assigned, because 
+developer
+
+### Pull Request Discussions
+
+### Checklist for Pull Requests
+
+## GitHub Issues
+
+### Feature Request Issues
+
+### Bug Report Issues
+
+## Milestones and Release Planning
+

From db29ec7eee14cef6f256fbe7190f7b262fc0a472 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 15 Nov 2018 14:58:02 -0500
Subject: [PATCH 6/9] complete workflow document

---
 doc/github-development-workflow.md | 132 +++++++++++++++++++++++++----
 1 file changed, 117 insertions(+), 15 deletions(-)

diff --git a/doc/github-development-workflow.md b/doc/github-development-workflow.md
index b81dbb417e..31fd3f23f0 100644
--- a/doc/github-development-workflow.md
+++ b/doc/github-development-workflow.md
@@ -17,28 +17,28 @@ adapt accordingly. Last change 2018-11-15.
     * [Pull Request Discussions](#pull-request-discussions)
     * [Checklist for Pull Requests](#checklist-for-pull-requests)
   * [GitHub Issues](#github-issues)
-    * [Feature Request Issues](#feature-request-issues)
-    * [Bug Report Issues](#bug-report-issues)
   * [Milestones and Release Planning](#milestones-and-release-planning)
 
 ## GitHub Merge Management
 
 In the interest of consistency, ONLY ONE of the core LAMMPS developers
-should doing the merging itself.  This is currently @akohlmey (Axel
-Kohlmeyer).  If this assignment needs to be changed, it shall be done
-right after a stable release.
+should doing the merging itself.  This is currently
+[@akohlmey](https://github.com/akohlmey) (Axel Kohlmeyer).
+If this assignment needs to be changed, it shall be done right after a
+stable release.
 
 ## Pull Requests
 
 ALL changes to the LAMMPS code and documentation, however trivial, MUST
 be submitted as a pull request to GitHub. All changes to the "master"
 branch must be made exclusively through merging pull requests. The
-"unstable" and "stable" branches are only to be updated upon patch or
-stable releases with fast-forward merges based on the associated
-tags. Pull requests may also be submitted to (long-running) feature
-branches created by LAMMPS developers inside the LAMMPS project, if
-needed. Those are not subject to the merge and review restrictions
-discussed in this document, though.
+"unstable" and "stable" branches, respectively are only to be updated
+upon patch or stable releases with fast-forward merges based on the
+associated tags. Pull requests may also be submitted to (long-running)
+feature branches created by LAMMPS developers inside the LAMMPS project,
+if needed. Those are not subject to the merge and review restrictions
+discussed in this document, though, but get manages as needed on a
+case-by-case basis.
 
 ### Pull Request Assignments
 
@@ -63,20 +63,122 @@ merged.
 ### Pull Request Reviews
 
 People can be assigned to review a pull request in two ways:
+
   * They can be assigned manually to review a pull request
     by the submitter or a LAMMPS developer
-  * They can be automatically assigned, because 
-developer
+  * They can be automatically assigned, because a developers matches
+    a file pattern in the `.github/CODEOWNERS` file, which associates
+    developers with the code they contributed and maintain.
+
+Reviewers are requested to state their appraisal of the proposed changes
+and either approve or request changes. People may unassign themselves
+from review, if they feel not competent about the changes proposed. At
+least one review from a LAMMPS developer with write access is required
+before merging in addition to the automated compilation tests.  The
+feature, that reviews from code owners are "hard" reviews (i.e. they
+must all be approved before merging is allowed), is currently disabled
+and it is in the discretion of the merge maintainer to assess when
+a sufficient degree of approval has been reached.  Reviews may be
+(automatically) dismissed, when the reviewed code has been changed,
+and then approval is required a second time.
 
 ### Pull Request Discussions
 
+All discussions about a pull request should be kept as much as possible
+on the pull request discussion page on GitHub, so that other developers
+can later review the entire discussion after the fact and understand the
+rationale behind choices made.  Exceptions to this policy are technical
+discussions, that are centered on tools or policies themselves
+(git, github, c++) rather than on the content of the pull request.
+
 ### Checklist for Pull Requests
 
+Here are some items to check:
+  * source and text files should not have CR/LF line endings (use dos2unix to remove)
+  * every new command or style should have documentation. The names of
+  source files (c++ and manual) should follow the name of the style.
+  (example: `src/fix_nve.cpp`, `src/fix_nve.h` for `fix nve` command,
+  implementing the class `FixNVE`, documented in `doc/src/fix_nve.txt`)
+  * all new style names should be lower case, the must be no dashes,
+  blanks, or underscores separating words, only forward slashes.
+  * new style docs should be added to the "overview" files in
+  `doc/src/Commands_*.txt`, `doc/src/{fixes,computes,pairs,bonds,...}.txt`
+  and `doc/src/lammps.book`
+  * new files in packages should be added to `src/.gitignore`
+  * removed or renamed files in packages should be added to `src/Purge.list`
+  * C++ source files should use C++ style include files for accessing
+  C-library APIs, e.g. `#include <cstdlib>` instead of `#include <stdlib.h>`.
+  And they should use angular brackets instead of double quotes. Full list:
+    * assert.h -> cassert
+    * ctype.h -> cctype
+    * errno.h -> cerrno
+    * float.h -> cfloat
+    * limits.h -> climits
+    * math.h -> cmath
+    * omplex.h -> complex
+    * setjmp.h -> csetjmp
+    * signal.h -> csignal
+    * stddef.h -> cstddef
+    * stdint.h -> cstdint
+    * stdio.h -> cstdio
+    * stdlib.h -> cstdlib
+    * string.h -> cstring
+    * time.h -> ctime
+  Do not replace (as they are C++-11): `inttypes.h` and `stdint.h`.
+  * Code should follow the C++-98 standard. C++-11 is only accepted
+  in individual special purpose packages
+  * indentation is two spaces per level
+  * there should be no tabs and no trailing whitespace
+  * header files, especially of new styles, should not include any
+  other headers, except the header with the base class or cstdio.
+  Forward declarations should be used instead when possible.
+  * iostreams should be avoided. LAMMPS uses stdio from the C-library.
+  * use of STL in headers and class definitions should be avoided.
+  * static class members should be avoided at all cost.
+  * anything storing atom IDs should be using `tagint` and not `int`.
+  This can be flagged by the compiler only for pointers and only when
+  compiling LAMMPS with `-DLAMMPS_BIGBIG`.
+  * when including both `lmptype.h` (and using defines or macros from it)
+  and `mpi.h`, `lmptype.h` must be included first.
+
 ## GitHub Issues
 
-### Feature Request Issues
+The GitHub issue tracker is the location where the LAMMPS developers
+and other contributors or LAMMPS users can report issues or bugs with
+the LAMMPS code or request new features to be added. Feature requests
+are usually indicated by a `[Feature Request]` marker in the subject.
+Issues are assigned to a person, if this person is working on this
+feature or working to resolve an issue. Issues that have nobody working
+on them at the moment, have the label `volunteer needed` attached.
 
-### Bug Report Issues
+When an issue, say `#125` is resolved by a specific pull request,
+the comment for the pull request shall contain the text `closes #125`
+or `fixes #125`, so that the issue is automatically deleted when
+the pull request is merged.
 
 ## Milestones and Release Planning
 
+LAMMPS uses a continuous release development model with incremental
+changes, i.e. significant effort is made - including automated pre-merge
+testing - that the code in the branch "master" does not get broken.
+More extensive testing (including regression testing) is performed after
+code is merged to the "master" branch. There are patch releases of
+LAMMPS every 1-3 weeks at a point, when the LAMMPS developers feel, that
+a sufficient amount of changes have happened, and the post-merge testing
+has been successful. These patch releases are marked with a
+`patch_<version date>` tag and the "unstable" branch follows only these
+versions (and thus is always supposed to be of production quality,
+unlike "master", which may be temporary broken, in the case of larger
+change sets or unexpected incompatibilities or side effects.
+
+About 3-4 times each year, there are going to be "stable" releases
+of LAMMPS.  These have seen additional, manual testing and review of
+results from testing with instrumented code and static code analysis.
+Also, in the last 2-3 patch releases before a stable release are
+"release candidate" versions which only contain bugfixes and
+documentation updates.  For release planning and the information of
+code contributors, issues and pull requests being actively worked on
+are assigned a "milestone", which corresponds to the next stable
+release or the stable release after that, with a tentative release
+date.
+

From eae9d27f6d37ec7f935a5e3112fa34b7f78f5fea Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 15 Nov 2018 16:03:33 -0500
Subject: [PATCH 7/9] OpenMP support from the compiler is not a requirement for
 USER-OMP. Without OpenMP, it is like the OPT package but for many more
 styles, so it is still useful and should be supported.

---
 cmake/CMakeLists.txt | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index cc5a3356a6..6d559bebe3 100644
--- a/cmake/CMakeLists.txt
+++ b/cmake/CMakeLists.txt
@@ -304,7 +304,7 @@ pkg_depends(USER-SCAFACOS MPI)
 
 find_package(OpenMP QUIET)
 option(BUILD_OMP "Build with OpenMP support" ${OpenMP_FOUND})
-if(BUILD_OMP OR PKG_USER-OMP OR PKG_KOKKOS OR PKG_USER-INTEL)
+if(BUILD_OMP OR PKG_KOKKOS OR PKG_USER-INTEL)
   find_package(OpenMP REQUIRED)
   set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
   set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${OpenMP_CXX_FLAGS}")

From 1fc3b4618c5d015255ed8d9f1afb76f3fc623950 Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 15 Nov 2018 16:31:04 -0500
Subject: [PATCH 8/9] remove dead code and silence compiler warnings

---
 src/BODY/pair_body_rounded_polygon.cpp       |  2 +-
 src/MISC/pair_nm_cut.cpp                     |  8 -------
 src/MISC/pair_nm_cut_coul_cut.cpp            |  8 -------
 src/MISC/pair_nm_cut_coul_long.cpp           |  8 -------
 src/MOLECULE/fix_cmap.cpp                    |  2 +-
 src/POEMS/fix_poems.cpp                      | 22 ++++++--------------
 src/REPLICA/fix_hyper_local.cpp              |  2 +-
 src/REPLICA/fix_hyper_local.h                |  4 ++--
 src/SPIN/pair_spin_exchange.cpp              |  2 +-
 src/USER-CGDNA/pair_oxdna2_coaxstk.cpp       | 10 ++-------
 src/USER-MISC/compute_stress_mop.cpp         |  9 ++++----
 src/USER-MISC/compute_stress_mop_profile.cpp | 15 +++++++------
 src/USER-MISC/compute_stress_mop_profile.h   |  1 -
 src/USER-MISC/fix_ffl.cpp                    |  8 +++----
 src/USER-MISC/fix_filter_corotate.cpp        | 11 ++++------
 src/USER-OMP/fix_omp.cpp                     |  2 ++
 src/USER-OMP/thr_omp.h                       |  1 +
 src/compute_chunk_atom.cpp                   |  4 ++--
 src/compute_dihedral_local.h                 |  2 +-
 src/create_bonds.cpp                         |  2 +-
 src/displace_atoms.cpp                       |  4 ++--
 src/dump_image.cpp                           |  2 +-
 src/fix_deform.cpp                           |  2 +-
 src/fix_move.cpp                             |  2 +-
 src/input.cpp                                |  2 +-
 src/set.cpp                                  |  2 +-
 src/variable.cpp                             |  4 ++--
 src/velocity.cpp                             |  4 ++--
 src/write_dump.cpp                           |  2 +-
 29 files changed, 51 insertions(+), 96 deletions(-)

diff --git a/src/BODY/pair_body_rounded_polygon.cpp b/src/BODY/pair_body_rounded_polygon.cpp
index 6a176f1083..9040817772 100644
--- a/src/BODY/pair_body_rounded_polygon.cpp
+++ b/src/BODY/pair_body_rounded_polygon.cpp
@@ -107,7 +107,7 @@ void PairBodyRoundedPolygon::compute(int eflag, int vflag)
   int nei,nej,iefirst,jefirst;
   double xtmp,ytmp,ztmp,delx,dely,delz,evdwl;
   double rsq,rsqinv,r,radi,radj,eradi,eradj,rradi,rradj,k_nij,k_naij;
-  double xi[3],xj[3],facc[3];
+  double facc[3];
   int *ilist,*jlist,*numneigh,**firstneigh;
 
   evdwl = 0.0;
diff --git a/src/MISC/pair_nm_cut.cpp b/src/MISC/pair_nm_cut.cpp
index ce077a7a04..4b1611b137 100644
--- a/src/MISC/pair_nm_cut.cpp
+++ b/src/MISC/pair_nm_cut.cpp
@@ -274,14 +274,6 @@ double PairNMCut::init_one(int i, int j)
     }
     MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
 
-    double rr1 = mm[i][j]*(nn[i][j]-1)*pow(r0[i][j],nn[i][j]);
-    double rr2 = nn[i][j]*(mm[i][j]-1)*pow(r0[i][j],mm[i][j]);
-    double p1 = 1-nn[i][j];
-    double p2 = 1-mm[i][j];
-
-    double rrr1 = pow(r0[i][j],nn[i][j])*(1-nn[i][j]);
-    double rrr2 = pow(r0[i][j],mm[i][j])*(1-mm[i][j]);
-
     double cut3 = cut[i][j]*cut[i][j]*cut[i][j];
     ptail_ij = 2.*MY_PI/3.*all[0]*all[1]*e0nm[i][j]*nm[i][j]*cut3 *
       (pow(r0[i][j]/cut[i][j],nn[i][j])/(nn[i][j]-3) - pow(r0[i][j]/cut[i][j],mm[i][j])/(mm[i][j]-3));
diff --git a/src/MISC/pair_nm_cut_coul_cut.cpp b/src/MISC/pair_nm_cut_coul_cut.cpp
index b807bc972b..999fab1d6e 100644
--- a/src/MISC/pair_nm_cut_coul_cut.cpp
+++ b/src/MISC/pair_nm_cut_coul_cut.cpp
@@ -324,14 +324,6 @@ double PairNMCutCoulCut::init_one(int i, int j)
     }
     MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
 
-    double rr1 = mm[i][j]*(nn[i][j]-1)*pow(r0[i][j],nn[i][j]);
-    double rr2 = nn[i][j]*(mm[i][j]-1)*pow(r0[i][j],mm[i][j]);
-    double p1 = 1-nn[i][j];
-    double p2 = 1-mm[i][j];
-
-    double rrr1 = pow(r0[i][j],nn[i][j])*(1-nn[i][j]);
-    double rrr2 = pow(r0[i][j],mm[i][j])*(1-mm[i][j]);
-
     double cut_lj3 = cut_lj[i][j]*cut_lj[i][j]*cut_lj[i][j];
     ptail_ij = 2.*MY_PI/3.*all[0]*all[1]*e0nm[i][j]*nm[i][j]*cut_lj3 *
       (pow(r0[i][j]/cut_lj[i][j],nn[i][j])/(nn[i][j]-3) - pow(r0[i][j]/cut_lj[i][j],mm[i][j])/(mm[i][j]-3));
diff --git a/src/MISC/pair_nm_cut_coul_long.cpp b/src/MISC/pair_nm_cut_coul_long.cpp
index 325f3da003..fb82436dba 100644
--- a/src/MISC/pair_nm_cut_coul_long.cpp
+++ b/src/MISC/pair_nm_cut_coul_long.cpp
@@ -371,14 +371,6 @@ double PairNMCutCoulLong::init_one(int i, int j)
     }
     MPI_Allreduce(count,all,2,MPI_DOUBLE,MPI_SUM,world);
 
-    double rr1 = mm[i][j]*(nn[i][j]-1)*pow(r0[i][j],nn[i][j]);
-    double rr2 = nn[i][j]*(mm[i][j]-1)*pow(r0[i][j],mm[i][j]);
-    double p1 = 1-nn[i][j];
-    double p2 = 1-mm[i][j];
-
-    double rrr1 = pow(r0[i][j],nn[i][j])*(1-nn[i][j]);
-    double rrr2 = pow(r0[i][j],mm[i][j])*(1-mm[i][j]);
-
     double cut_lj3 = cut_lj[i][j]*cut_lj[i][j]*cut_lj[i][j];
     ptail_ij = 2.*MY_PI/3.*all[0]*all[1]*e0nm[i][j]*nm[i][j]*cut_lj3 *
       (pow(r0[i][j]/cut_lj[i][j],nn[i][j])/(nn[i][j]-3) - pow(r0[i][j]/cut_lj[i][j],mm[i][j])/(mm[i][j]-3));
diff --git a/src/MOLECULE/fix_cmap.cpp b/src/MOLECULE/fix_cmap.cpp
index a889a8d0db..ec2588e61b 100644
--- a/src/MOLECULE/fix_cmap.cpp
+++ b/src/MOLECULE/fix_cmap.cpp
@@ -943,7 +943,7 @@ double FixCMAP::dihedral_angle_atan2(double fx, double fy, double fz,
 {
   // calculate the dihedral angle
 
-  double angle, arg1, arg2;
+  double angle = 0.0, arg1, arg2;
 
   arg1 = absg*(fx*bx+fy*by+fz*bz);
   arg2 = ax*bx+ay*by+az*bz;
diff --git a/src/POEMS/fix_poems.cpp b/src/POEMS/fix_poems.cpp
index f345d52aab..a01878bffd 100644
--- a/src/POEMS/fix_poems.cpp
+++ b/src/POEMS/fix_poems.cpp
@@ -748,19 +748,9 @@ void FixPOEMS::initial_integrate(int vflag)
 
 /* ---------------------------------------------------------------------- */
 
-void FixPOEMS::post_force(int vflag)
+void FixPOEMS::post_force(int /* vflag */)
 {
   if (earlyflag) compute_forces_and_torques();
-
-  /*
-  for (int ibody = 0; ibody < nbody; ibody++) {
-    if (ibody == 0) {
-    printf("PFF %d %g %g %g\n",ibody,fcm[ibody][0],fcm[ibody][1],fcm[ibody][2]);
-    printf("PFT %d %g %g %g\n",ibody,
-           torque[ibody][0],torque[ibody][1],torque[ibody][2]);
-    }
-  }
-  */
 }
 
 /* ----------------------------------------------------------------------
@@ -850,7 +840,7 @@ void FixPOEMS::final_integrate()
 
 /* ---------------------------------------------------------------------- */
 
-void FixPOEMS::initial_integrate_respa(int vflag, int ilevel, int iloop)
+void FixPOEMS::initial_integrate_respa(int vflag, int ilevel, int /* iloop */)
 {
   dtv = step_respa[ilevel];
   dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
@@ -862,14 +852,14 @@ void FixPOEMS::initial_integrate_respa(int vflag, int ilevel, int iloop)
 
 /* ---------------------------------------------------------------------- */
 
-void FixPOEMS::post_force_respa(int vflag, int ilevel, int iloop)
+void FixPOEMS::post_force_respa(int vflag, int ilevel, int /* iloop */)
 {
   if (ilevel == nlevels_respa-1) post_force(vflag);
 }
 
 /* ---------------------------------------------------------------------- */
 
-void FixPOEMS::final_integrate_respa(int ilevel, int iloop)
+void FixPOEMS::final_integrate_respa(int ilevel, int /* iloop */)
 {
   dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
   final_integrate();
@@ -949,7 +939,7 @@ int FixPOEMS::dof(int igroup)
          thus this routine does nothing for now
 ------------------------------------------------------------------------- */
 
-void FixPOEMS::deform(int flag) {}
+void FixPOEMS::deform(int /* flag */) {}
 
 /* ---------------------------------------------------------------------- */
 
@@ -1607,7 +1597,7 @@ void FixPOEMS::grow_arrays(int nmax)
    copy values within local atom-based arrays
 ------------------------------------------------------------------------- */
 
-void FixPOEMS::copy_arrays(int i, int j, int delflag)
+void FixPOEMS::copy_arrays(int i, int j, int /* delflag */)
 {
   natom2body[j] = natom2body[i];
   for (int k = 0; k < natom2body[j]; k++) atom2body[j][k] = atom2body[i][k];
diff --git a/src/REPLICA/fix_hyper_local.cpp b/src/REPLICA/fix_hyper_local.cpp
index dac88a8efa..4868cd75de 100644
--- a/src/REPLICA/fix_hyper_local.cpp
+++ b/src/REPLICA/fix_hyper_local.cpp
@@ -716,7 +716,7 @@ void FixHyperLocal::pre_reverse(int /* eflag */, int /* vflag */)
     if (update->ntimestep % histo_print == 0) {
       MPI_Allreduce(histo,allhisto,histo_count+2,MPI_LMP_BIGINT,MPI_SUM,world);
 
-      bigint total;
+      bigint total = 0;
       for (i = 0; i < histo_count+2; i++) total += allhisto[i];
 
       if (me == 0) {
diff --git a/src/REPLICA/fix_hyper_local.h b/src/REPLICA/fix_hyper_local.h
index 9fe4d03fb9..967101837e 100644
--- a/src/REPLICA/fix_hyper_local.h
+++ b/src/REPLICA/fix_hyper_local.h
@@ -87,7 +87,7 @@ class FixHyperLocal : public FixHyper {
   int nevent;                // # of events that trigger bond rebuild
   int nevent_atom;           // # of atoms that experienced an event
   double cutbondsq,dcutsq;
-  double beta,t_hyper,invqfactorsq;
+  double beta,invqfactorsq;
   double mybias;
   double maxbondlen;         // cummulative max length of any bond
   double maxdriftsq;         // max distance any atom drifts from original pos
@@ -147,7 +147,7 @@ class FixHyperLocal : public FixHyper {
 
   // histogramming of bond boost cooeficients
 
-  int histo_flag,histo_every,histo_count,histo_print,histo_steps;
+  int histo_every,histo_count,histo_print,histo_steps;
   double histo_delta,invhisto_delta,histo_lo;
   bigint *histo,*allhisto;
 };
diff --git a/src/SPIN/pair_spin_exchange.cpp b/src/SPIN/pair_spin_exchange.cpp
index cc074bb97d..72a4c0d7de 100644
--- a/src/SPIN/pair_spin_exchange.cpp
+++ b/src/SPIN/pair_spin_exchange.cpp
@@ -323,7 +323,7 @@ void PairSpinExchange::compute_single_pair(int ii, double fmi[3])
   double **x = atom->x;
   double **sp = atom->sp;
   double local_cut2;
-  double xi[3], rij[3];
+  double xi[3];
   double delx,dely,delz;
   double spj[3];
 
diff --git a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp
index d31890ea52..569f911eb9 100644
--- a/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp
+++ b/src/USER-CGDNA/pair_oxdna2_coaxstk.cpp
@@ -103,9 +103,9 @@ PairOxdna2Coaxstk::~PairOxdna2Coaxstk()
 void PairOxdna2Coaxstk::compute(int eflag, int vflag)
 {
 
-  double delf[3],delt[3],delta[3],deltb[3]; // force, torque increment;
+  double delf[3],delta[3],deltb[3]; // force, torque increment;
   double evdwl,fpair,finc,tpair,factor_lj;
-  double v1tmp[3],v2tmp[3],v3tmp[3];
+  double v1tmp[3];
   double delr_ss[3],delr_ss_norm[3],rsq_ss,r_ss,rinv_ss;
   double delr_st[3],delr_st_norm[3],rsq_st,r_st,rinv_st;
   double theta1,theta1p,t1dir[3],cost1;
@@ -114,12 +114,6 @@ void PairOxdna2Coaxstk::compute(int eflag, int vflag)
   double theta6,theta6p,t6dir[3],cost6;
   double cosphi3;
 
-  double gamma,gammacub,rinv_ss_cub,fac;
-  double aybx,azbx,rax,ray,raz,rbx;
-  double dcdr,dcdrbx;
-  double dcdaxbx,dcdaybx,dcdazbx;
-  double dcdrax,dcdray,dcdraz;
-
   // distances COM-backbone site, COM-stacking site
   double d_cs=-0.4, d_cst=+0.34;
   // vectors COM-backbone site, COM-stacking site in lab frame
diff --git a/src/USER-MISC/compute_stress_mop.cpp b/src/USER-MISC/compute_stress_mop.cpp
index e63dff507f..e496fd4dfa 100644
--- a/src/USER-MISC/compute_stress_mop.cpp
+++ b/src/USER-MISC/compute_stress_mop.cpp
@@ -210,7 +210,7 @@ void ComputeStressMop::init()
 
 /* ---------------------------------------------------------------------- */
 
-void ComputeStressMop::init_list(int id, NeighList *ptr)
+void ComputeStressMop::init_list(int /* id */, NeighList *ptr)
 {
   list = ptr;
 }
@@ -246,9 +246,9 @@ void ComputeStressMop::compute_vector()
 void ComputeStressMop::compute_pairs()
 
 {
-  int i,j,m,n,ii,jj,inum,jnum,itype,jtype;
+  int i,j,m,ii,jj,inum,jnum,itype,jtype;
   double delx,dely,delz;
-  double rsq,eng,fpair,factor_coul,factor_lj;
+  double rsq,fpair,factor_coul,factor_lj;
   int *ilist,*jlist,*numneigh,**firstneigh;
 
   double *mass = atom->mass;
@@ -363,8 +363,7 @@ void ComputeStressMop::compute_pairs()
     // counts local particles transfers across the plane
 
     if (which[m] == KIN || which[m] == TOTAL){
-      double vcm[3];
-      double masstotal,sgn;
+      double sgn;
 
       for (int i = 0; i < nlocal; i++){
 
diff --git a/src/USER-MISC/compute_stress_mop_profile.cpp b/src/USER-MISC/compute_stress_mop_profile.cpp
index 02ad3ea453..9189318381 100644
--- a/src/USER-MISC/compute_stress_mop_profile.cpp
+++ b/src/USER-MISC/compute_stress_mop_profile.cpp
@@ -211,7 +211,7 @@ void ComputeStressMopProfile::init()
 
 /* ---------------------------------------------------------------------- */
 
-void ComputeStressMopProfile::init_list(int id, NeighList *ptr)
+void ComputeStressMopProfile::init_list(int /* id */, NeighList *ptr)
 {
   list = ptr;
 }
@@ -253,11 +253,11 @@ void ComputeStressMopProfile::compute_array()
 void ComputeStressMopProfile::compute_pairs()
 
 {
-  int i,j,m,n,ii,jj,inum,jnum,itype,jtype,ibin;
+  int i,j,m,ii,jj,inum,jnum,itype,jtype,ibin;
   double delx,dely,delz;
-  double rsq,eng,fpair,factor_coul,factor_lj;
+  double rsq,fpair,factor_coul,factor_lj;
   int *ilist,*jlist,*numneigh,**firstneigh;
-  double pos,pos1,pos_temp;    
+  double pos,pos1;    
 
   double *mass = atom->mass;
   int *type = atom->type;
@@ -385,8 +385,7 @@ void ComputeStressMopProfile::compute_pairs()
 
     if (which[m] == KIN || which[m] == TOTAL){
 
-      double vcm[3];
-      double masstotal,sgn;
+      double sgn;
 
       for (int i = 0; i < nlocal; i++){
 
@@ -449,8 +448,8 @@ void ComputeStressMopProfile::compute_pairs()
 
 void ComputeStressMopProfile::setup_bins()
 {
-  int i,j,k,m,n;
-  double lo,hi,coord1,coord2;
+  int i,n;
+  double lo = 0.0, hi = 0.0;
 
   double *boxlo,*boxhi,*prd;
   boxlo = domain->boxlo;
diff --git a/src/USER-MISC/compute_stress_mop_profile.h b/src/USER-MISC/compute_stress_mop_profile.h
index 648d86cc7f..0ab774f3db 100644
--- a/src/USER-MISC/compute_stress_mop_profile.h
+++ b/src/USER-MISC/compute_stress_mop_profile.h
@@ -50,7 +50,6 @@ namespace LAMMPS_NS {
     double **coord,**coordp;
     double **values_local,**values_global;
 
-    int ndim;
     double dt,nktv2p,ftm2v;
     double area;
     class NeighList *list;
diff --git a/src/USER-MISC/fix_ffl.cpp b/src/USER-MISC/fix_ffl.cpp
index e2fb0166a2..d2a57fd2d0 100644
--- a/src/USER-MISC/fix_ffl.cpp
+++ b/src/USER-MISC/fix_ffl.cpp
@@ -108,8 +108,6 @@ FixFFL::FixFFL(LAMMPS *lmp, int narg, char **arg) :
   }
 
   t_target=t_start;
-  const double kT = t_target * force->boltz / force->mvv2e;
-
 
   // initialize Marsaglia RNG with processor-unique seed
   // NB: this means runs will not be the same with different numbers of processors
@@ -298,7 +296,7 @@ void FixFFL::ffl_integrate() {
 
 }
 
-void FixFFL::initial_integrate(int vflag) {
+void FixFFL::initial_integrate(int /* vflag */) {
   double dtfm;
 
   // update v and x of atoms in group
@@ -391,7 +389,7 @@ void FixFFL::final_integrate() {
 }
 /* ---------------------------------------------------------------------- */
 
-void FixFFL::initial_integrate_respa(int vflag, int ilevel, int iloop) {
+void FixFFL::initial_integrate_respa(int vflag, int ilevel, int /* iloop */) {
   dtv = step_respa[ilevel];
   dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
 
@@ -406,7 +404,7 @@ void FixFFL::initial_integrate_respa(int vflag, int ilevel, int iloop) {
   }
 }
 
-void FixFFL::final_integrate_respa(int ilevel, int iloop) {
+void FixFFL::final_integrate_respa(int ilevel, int /* iloop */) {
 
   dtv = step_respa[ilevel];
   dtf = 0.5 * step_respa[ilevel] * force->ftm2v;
diff --git a/src/USER-MISC/fix_filter_corotate.cpp b/src/USER-MISC/fix_filter_corotate.cpp
index 56ab2b3df9..717861e06f 100644
--- a/src/USER-MISC/fix_filter_corotate.cpp
+++ b/src/USER-MISC/fix_filter_corotate.cpp
@@ -592,14 +592,13 @@ void FixFilterCorotate::pre_neighbor()
       double c = (del2[0])*(del3[1]) - (del2[1])*(del3[0]);
       int signum = sgn(a*(del1[0]) + b*(del1[1]) + c*(del1[2]));
 
-      if (fabs(signum)!= 1)
+      if (abs(signum) != 1)
         error->all(FLERR,"Wrong orientation in cluster of size 4"
           "in fix filter/corotate!");
       clist_q0[i][8] *= signum;
       clist_q0[i][11] *= signum;
 
-    } else if (N == 5)
-    {
+    } else if (N == 5) {
       oxy = atom->map(shake_atom[m][0]);
       atom1 = atom->map(shake_atom[m][1]);
       atom2 = atom->map(shake_atom[m][2]);
@@ -666,14 +665,12 @@ void FixFilterCorotate::pre_neighbor()
       double c = (del2[0])*(del3[1]) - (del2[1])*(del3[0]);
       int signum = sgn(a*(del1[0]) + b*(del1[1]) + c*(del1[2]));
 
-      if (fabs(signum)!= 1)
+      if (abs(signum)!= 1)
         error->all(FLERR,"Wrong orientation in cluster of size 5"
           "in fix filter/corotate!");
       clist_q0[i][8] *= signum;
       clist_q0[i][11] *= signum;
-    }
-    else
-    {
+    } else {
       error->all(FLERR,"Fix filter/corotate cluster with size > 5"
         "not yet configured...");
     }
diff --git a/src/USER-OMP/fix_omp.cpp b/src/USER-OMP/fix_omp.cpp
index 8be54caada..a4587b1c14 100644
--- a/src/USER-OMP/fix_omp.cpp
+++ b/src/USER-OMP/fix_omp.cpp
@@ -80,7 +80,9 @@ FixOMP::FixOMP(LAMMPS *lmp, int narg, char **arg)
   if (nthreads < 1)
     error->all(FLERR,"Illegal number of OpenMP threads requested");
 
+#if defined(_OPENMP)
   int reset_thr = 0;
+#endif
   if (nthreads != comm->nthreads) {
 #if defined(_OPENMP)
     reset_thr = 1;
diff --git a/src/USER-OMP/thr_omp.h b/src/USER-OMP/thr_omp.h
index 0821f8cea0..87d921290e 100644
--- a/src/USER-OMP/thr_omp.h
+++ b/src/USER-OMP/thr_omp.h
@@ -185,6 +185,7 @@ static inline void loop_setup_thr(int &ifrom, int &ito, int &tid,
   tid = 0;
   ifrom = 0;
   ito = inum;
+  nthreads = 1;
 #endif
 }
 
diff --git a/src/compute_chunk_atom.cpp b/src/compute_chunk_atom.cpp
index ddad7eb62f..61b653b375 100644
--- a/src/compute_chunk_atom.cpp
+++ b/src/compute_chunk_atom.cpp
@@ -66,7 +66,7 @@ ComputeChunkAtom::ComputeChunkAtom(LAMMPS *lmp, int narg, char **arg) :
 
   // chunk style and its args
 
-  int iarg;
+  int iarg = 0;
 
   binflag = 0;
   ncoord = 0;
@@ -248,7 +248,7 @@ ComputeChunkAtom::ComputeChunkAtom(LAMMPS *lmp, int narg, char **arg) :
       iarg += 2;
     } else if (strcmp(arg[iarg],"bound") == 0) {
       if (iarg+4 > narg) error->all(FLERR,"Illegal compute chunk/atom command");
-      int idim;
+      int idim = 0;
       if (strcmp(arg[iarg+1],"x") == 0) idim = 0;
       else if (strcmp(arg[iarg+1],"y") == 0) idim = 1;
       else if (strcmp(arg[iarg+1],"z") == 0) idim = 2;
diff --git a/src/compute_dihedral_local.h b/src/compute_dihedral_local.h
index d5f6a64183..5c50a66e96 100644
--- a/src/compute_dihedral_local.h
+++ b/src/compute_dihedral_local.h
@@ -33,7 +33,7 @@ class ComputeDihedralLocal : public Compute {
   double memory_usage();
 
  private:
-  int nvalues,nvar,ncount,setflag,tflag;
+  int nvalues,nvar,ncount,setflag;
 
   int pvar;
   int *bstyle,*vvar;
diff --git a/src/create_bonds.cpp b/src/create_bonds.cpp
index 751c4746ba..e19b565554 100644
--- a/src/create_bonds.cpp
+++ b/src/create_bonds.cpp
@@ -54,7 +54,7 @@ void CreateBonds::command(int narg, char **arg)
 
   int style;
 
-  int iarg;
+  int iarg = 0;
   if (strcmp(arg[0],"many") == 0) {
     style = MANY;
     if (narg != 6) error->all(FLERR,"Illegal create_bonds command");
diff --git a/src/displace_atoms.cpp b/src/displace_atoms.cpp
index 04088bec8c..7b29b1d3d5 100644
--- a/src/displace_atoms.cpp
+++ b/src/displace_atoms.cpp
@@ -118,7 +118,7 @@ void DisplaceAtoms::command(int narg, char **arg)
 
   if (style == RAMP) {
 
-    int d_dim;
+    int d_dim = 0;
     if (strcmp(arg[2],"x") == 0) d_dim = 0;
     else if (strcmp(arg[2],"y") == 0) d_dim = 1;
     else if (strcmp(arg[2],"z") == 0) d_dim = 2;
@@ -136,7 +136,7 @@ void DisplaceAtoms::command(int narg, char **arg)
       d_hi = zscale*force->numeric(FLERR,arg[4]);
     }
 
-    int coord_dim;
+    int coord_dim = 0;
     if (strcmp(arg[5],"x") == 0) coord_dim = 0;
     else if (strcmp(arg[5],"y") == 0) coord_dim = 1;
     else if (strcmp(arg[5],"z") == 0) coord_dim = 2;
diff --git a/src/dump_image.cpp b/src/dump_image.cpp
index a488f65161..0d63d2e4cb 100644
--- a/src/dump_image.cpp
+++ b/src/dump_image.cpp
@@ -1290,7 +1290,7 @@ int DumpImage::modify_param(int narg, char **arg)
   if (strcmp(arg[0],"amap") == 0) {
     if (narg < 6) error->all(FLERR,"Illegal dump_modify command");
     if (strlen(arg[3]) != 2) error->all(FLERR,"Illegal dump_modify command");
-    int factor;
+    int factor = 0;
     if (arg[3][0] == 's') factor = 1;
     else if (arg[3][0] == 'c') factor = 2;
     else if (arg[3][0] == 'd') factor = 3;
diff --git a/src/fix_deform.cpp b/src/fix_deform.cpp
index c960c310f6..909ead3e2a 100644
--- a/src/fix_deform.cpp
+++ b/src/fix_deform.cpp
@@ -802,7 +802,7 @@ void FixDeform::end_of_step()
       // tilt_target can be large positive or large negative value
       // add/subtract box lengths until tilt_target is closest to current value
 
-      int idenom;
+      int idenom = 0;
       if (i == 5) idenom = 0;
       else if (i == 4) idenom = 0;
       else if (i == 3) idenom = 1;
diff --git a/src/fix_move.cpp b/src/fix_move.cpp
index 2f9fb0ebaa..0a5f506ab2 100644
--- a/src/fix_move.cpp
+++ b/src/fix_move.cpp
@@ -68,7 +68,7 @@ FixMove::FixMove(LAMMPS *lmp, int narg, char **arg) :
 
   // parse args
 
-  int iarg;
+  int iarg = 0;
 
   if (strcmp(arg[3],"linear") == 0) {
     if (narg < 7) error->all(FLERR,"Illegal fix move command");
diff --git a/src/input.cpp b/src/input.cpp
index f9dd1ec314..8af8da26be 100644
--- a/src/input.cpp
+++ b/src/input.cpp
@@ -1138,7 +1138,7 @@ void Input::partition()
 {
   if (narg < 3) error->all(FLERR,"Illegal partition command");
 
-  int yesflag;
+  int yesflag = 0;
   if (strcmp(arg[0],"yes") == 0) yesflag = 1;
   else if (strcmp(arg[0],"no") == 0) yesflag = 0;
   else error->all(FLERR,"Illegal partition command");
diff --git a/src/set.cpp b/src/set.cpp
index 7eca4e9a9c..34b86ea328 100644
--- a/src/set.cpp
+++ b/src/set.cpp
@@ -890,7 +890,7 @@ void Set::set(int keyword)
     // enforce quat rotation vector in z dir for 2d systems
 
     else if (keyword == QUAT) {
-      double *quat;
+      double *quat = NULL;
       if (avec_ellipsoid && atom->ellipsoid[i] >= 0)
         quat = avec_ellipsoid->bonus[atom->ellipsoid[i]].quat;
       else if (avec_tri && atom->tri[i] >= 0)
diff --git a/src/variable.cpp b/src/variable.cpp
index 1595456f33..af5f647b74 100644
--- a/src/variable.cpp
+++ b/src/variable.cpp
@@ -182,7 +182,7 @@ void Variable::set(int narg, char **arg)
     if (find(arg[0]) >= 0) return;
     if (nvar == maxvar) grow();
     style[nvar] = LOOP;
-    int nfirst,nlast;
+    int nfirst = 0,nlast = 0;
     if (narg == 3 || (narg == 4 && strcmp(arg[3],"pad") == 0)) {
       nfirst = 1;
       nlast = force->inumeric(FLERR,arg[2]);
@@ -3983,7 +3983,7 @@ int Variable::special_function(char *word, char *contents, Tree **tree,
       strcmp(word,"max") == 0 || strcmp(word,"ave") == 0 ||
       strcmp(word,"trap") == 0 || strcmp(word,"slope") == 0) {
 
-    int method;
+    int method = 0;
     if (strcmp(word,"sum") == 0) method = SUM;
     else if (strcmp(word,"min") == 0) method = XMIN;
     else if (strcmp(word,"max") == 0) method = XMAX;
diff --git a/src/velocity.cpp b/src/velocity.cpp
index 3a0b95fb4d..6d6027cc3c 100644
--- a/src/velocity.cpp
+++ b/src/velocity.cpp
@@ -641,7 +641,7 @@ void Velocity::ramp(int /*narg*/, char **arg)
 
   // parse args
 
-  int v_dim;
+  int v_dim = 0;
   if (strcmp(arg[0],"vx") == 0) v_dim = 0;
   else if (strcmp(arg[0],"vy") == 0) v_dim = 1;
   else if (strcmp(arg[0],"vz") == 0) v_dim = 2;
@@ -662,7 +662,7 @@ void Velocity::ramp(int /*narg*/, char **arg)
     v_hi = zscale*force->numeric(FLERR,arg[2]);
   }
 
-  int coord_dim;
+  int coord_dim = 0;
   if (strcmp(arg[3],"x") == 0) coord_dim = 0;
   else if (strcmp(arg[3],"y") == 0) coord_dim = 1;
   else if (strcmp(arg[3],"z") == 0) coord_dim = 2;
diff --git a/src/write_dump.cpp b/src/write_dump.cpp
index bb79c654b4..6c7375012e 100644
--- a/src/write_dump.cpp
+++ b/src/write_dump.cpp
@@ -45,7 +45,7 @@ void WriteDump::command(int narg, char **arg)
   // create the Dump instance
   // create dump command line with extra required args
 
-  Dump *dump;
+  Dump *dump = NULL;
 
   char **dumpargs = new char*[modindex+2];
   dumpargs[0] = (char *) "WRITE_DUMP"; // dump id

From 6e225d90fc2926170176821e5ef1b8144bd38e3f Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 15 Nov 2018 16:48:38 -0500
Subject: [PATCH 9/9] fix some minor bugs write data file writing and remove
 dead code and silence compiler warnings

---
 src/USER-COLVARS/group_ndx.cpp                 | 4 ++--
 src/USER-DPD/fix_rx.cpp                        | 6 ++++--
 src/USER-MISC/compute_stress_mop_profile.cpp   | 3 +--
 src/USER-MOFFF/angle_class2_p6.cpp             | 2 +-
 src/USER-MOFFF/angle_cosine_buck6d.cpp         | 2 +-
 src/USER-MOFFF/improper_inversion_harmonic.cpp | 5 +++--
 src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp  | 2 +-
 src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp | 2 +-
 8 files changed, 14 insertions(+), 12 deletions(-)

diff --git a/src/USER-COLVARS/group_ndx.cpp b/src/USER-COLVARS/group_ndx.cpp
index 450c250ffa..858336c9d5 100644
--- a/src/USER-COLVARS/group_ndx.cpp
+++ b/src/USER-COLVARS/group_ndx.cpp
@@ -50,7 +50,7 @@ static int cmptagint(const void *p1, const void *p2)
 static void write_group(FILE *fp, int gid, Atom *atom, Group *group, int me,
                         int np, MPI_Comm world, FILE *screen, FILE *logfile)
 {
-  char fmt[8];
+  char fmt[16];
   tagint *sendlist, *recvlist;
   bigint num = group->count(gid);
   int lnum, cols;
@@ -73,7 +73,7 @@ static void write_group(FILE *fp, int gid, Atom *atom, Group *group, int me,
       ++i;
       j /= 10;
     }
-    sprintf(fmt,"%%%dd ", i);
+    snprintf(fmt,16,"%%%dd ", i);
     cols = 80 / (i+1);
   }
 
diff --git a/src/USER-DPD/fix_rx.cpp b/src/USER-DPD/fix_rx.cpp
index 97668471c8..cb8349786f 100644
--- a/src/USER-DPD/fix_rx.cpp
+++ b/src/USER-DPD/fix_rx.cpp
@@ -758,8 +758,10 @@ void FixRX::pre_force(int /*vflag*/)
     memory->create( diagnosticCounterPerODE[FuncSum], nlocal, "FixRX::diagnosticCounterPerODE");
   }
 
-  //#pragma omp parallel \
-  //   reduction(+: nSteps, nIters, nFuncs, nFails )
+#if 0
+  #pragma omp parallel \
+     reduction(+: nSteps, nIters, nFuncs, nFails )
+#endif
   {
     double *rwork = new double[8*nspecies];
 
diff --git a/src/USER-MISC/compute_stress_mop_profile.cpp b/src/USER-MISC/compute_stress_mop_profile.cpp
index 9189318381..76bf487630 100644
--- a/src/USER-MISC/compute_stress_mop_profile.cpp
+++ b/src/USER-MISC/compute_stress_mop_profile.cpp
@@ -451,10 +451,9 @@ void ComputeStressMopProfile::setup_bins()
   int i,n;
   double lo = 0.0, hi = 0.0;
 
-  double *boxlo,*boxhi,*prd;
+  double *boxlo,*boxhi;
   boxlo = domain->boxlo;
   boxhi = domain->boxhi;
-  prd = domain->prd;
 
   if (originflag == LOWER) origin = boxlo[dir];
   else if (originflag == UPPER) origin = boxhi[dir];
diff --git a/src/USER-MOFFF/angle_class2_p6.cpp b/src/USER-MOFFF/angle_class2_p6.cpp
index c821c9d883..d2a6e21e6b 100644
--- a/src/USER-MOFFF/angle_class2_p6.cpp
+++ b/src/USER-MOFFF/angle_class2_p6.cpp
@@ -429,7 +429,7 @@ void AngleClass2P6::read_restart(FILE *fp)
 void AngleClass2P6::write_data(FILE *fp)
 {
   for (int i = 1; i <= atom->nangletypes; i++)
-    fprintf(fp,"%d %g %g %g %g\n",
+    fprintf(fp,"%d %g %g %g %g %g %g\n",
             i,theta0[i]/MY_PI*180.0,k2[i],k3[i],k4[i],k5[i],k6[i]);
 
   fprintf(fp,"\nBondBond Coeffs\n\n");
diff --git a/src/USER-MOFFF/angle_cosine_buck6d.cpp b/src/USER-MOFFF/angle_cosine_buck6d.cpp
index 3f87aeb757..f358097802 100644
--- a/src/USER-MOFFF/angle_cosine_buck6d.cpp
+++ b/src/USER-MOFFF/angle_cosine_buck6d.cpp
@@ -353,7 +353,7 @@ void AngleCosineBuck6d::read_restart(FILE *fp)
 void AngleCosineBuck6d::write_data(FILE *fp)
 {
   for (int i = 1; i <= atom->nangletypes; i++) {
-    fprintf(fp,"%d %g %d %d\n",i,k[i],multiplicity[i],th0[i]);
+    fprintf(fp,"%d %g %d %g\n",i,k[i],multiplicity[i],th0[i]);
   }
 }
 
diff --git a/src/USER-MOFFF/improper_inversion_harmonic.cpp b/src/USER-MOFFF/improper_inversion_harmonic.cpp
index 9608d58054..8404984b53 100644
--- a/src/USER-MOFFF/improper_inversion_harmonic.cpp
+++ b/src/USER-MOFFF/improper_inversion_harmonic.cpp
@@ -241,8 +241,8 @@ void ImproperInversionHarmonic::invang(const int &i1,const int &i2,
     f[i4][2] += f4[2];
   }
 
-  double rb3x, rb3y, rb3z;
-  if (evflag)
+  if (evflag) {
+    double rb3x, rb3y, rb3z;
 
     rb3x = vb1x - vb2x;
     rb3y = vb1y - vb2y;
@@ -252,6 +252,7 @@ void ImproperInversionHarmonic::invang(const int &i1,const int &i2,
              vb3x,vb3y,vb3z,
              vb2x,vb2y,vb2z,
              rb3x,rb3y,rb3z);
+  }
 }
 
 /* ---------------------------------------------------------------------- */
diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp b/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp
index f434d03858..46af95470c 100644
--- a/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp
+++ b/src/USER-MOFFF/pair_buck6d_coul_gauss_dsf.cpp
@@ -83,7 +83,7 @@ void PairBuck6dCoulGaussDSF::compute(int eflag, int vflag)
   double r,rsq,r2inv,r6inv,r14inv,rexp,forcecoul,forcebuck6d,factor_coul,factor_lj;
   double term1,term2,term3,term4,term5;
   double rcu,rqu,sme,smf,ebuck6d;
-  double prefactor,erfcc,erfcd,t,arg;
+  double prefactor,erfcc,erfcd,arg;
   int *ilist,*jlist,*numneigh,**firstneigh;
 
   evdwl = ecoul = 0.0;
diff --git a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp b/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp
index 9902896d18..3c54d64770 100644
--- a/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp
+++ b/src/USER-MOFFF/pair_buck6d_coul_gauss_long.cpp
@@ -85,7 +85,7 @@ void PairBuck6dCoulGaussLong::compute(int eflag, int vflag)
   double grij,expm2,erf;
   double term1,term2,term3,term4,term5;
   double rcu,rqu,sme,smf,ebuck6d,ealpha;
-  double prefactor,erfa,expa,t,arg,falpha;
+  double prefactor,erfa,expa,arg,falpha;
   int *ilist,*jlist,*numneigh,**firstneigh;
 
   evdwl = ecoul = 0.0;