diff --git a/cmake/CMakeLists.txt b/cmake/CMakeLists.txt
index e36d7259a5dc351c7f47744722ee8225d475b8fa..253cee6465852be38810917bf71ea9b01a75ab92 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}")
diff --git a/doc/github-development-workflow.md b/doc/github-development-workflow.md
new file mode 100644
index 0000000000000000000000000000000000000000..31fd3f23f0b3c8c068ead68f33ff78dc6f1b478a
--- /dev/null
+++ b/doc/github-development-workflow.md
@@ -0,0 +1,184 @@
+# 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)
+ * [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](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, 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
+
+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 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
+
+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.
+
+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.
+
diff --git a/src/BODY/pair_body_rounded_polygon.cpp b/src/BODY/pair_body_rounded_polygon.cpp
index 6a176f1083542857951051d2cf6d456991663854..90408177726a33191129fefc791e30f3e60fe1f0 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 ce077a7a045f6de8d31eb51d720638357018286d..4b1611b13779bc3f9874583107c59210fdf39c3e 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 b807bc972bfd9c5ab9e620b2c8e88e763ecd1135..999fab1d6e7065c35b93b4e0ed5292982e787653 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 325f3da0033c78dafd85e759112ccd0056dec4d6..fb82436dba8ca6059118d22c6a93c6331abde9e6 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/atom_vec_molecular.cpp b/src/MOLECULE/atom_vec_molecular.cpp
index 6e903a936eb8177db81606880bd23655739f64dc..cdd3f025058f14f2b1bd3b8dc12fc51ba570f502 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;
diff --git a/src/MOLECULE/fix_cmap.cpp b/src/MOLECULE/fix_cmap.cpp
index a889a8d0db71e7eff23f457d4e4ea06be5108770..ec2588e61b8bc9201d6a484000aecb0396c2d773 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 f345d52aabfd12e68be37c0e4b115120e7884764..a01878bffd23d5e59224eac7d5eb310dd6912024 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 dac88a8efa7e1fd3b92247b36e80c0c0497a888b..4868cd75deb0015e68ae9c08779276e9f5bdeff4 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 9fe4d03fb9c3ff121ab4e6fc38a51930723c7419..967101837e4ea065b40eb6699ffeb3734c93840f 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 cc074bb97d9b9dd91d2bfcc8e378d7cd56a7ba5e..72a4c0d7de4f52b514a4f4e187bd359a5c4be503 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 d31890ea52b9dbfad89e5aec7088fb1826752369..569f911eb9dd3b89f35cc7bba71b59d04e7d553c 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-COLVARS/group_ndx.cpp b/src/USER-COLVARS/group_ndx.cpp
index 450c250ffa4fcbe23aef74fd10cda0887ecfb3dd..858336c9d505d460377dac00d4ce488abad818fc 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 97668471c885ce3215324b38daae58b3d4c4cf35..cb8349786f324e8e0fcd86fa27bd30c114d468b8 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.cpp b/src/USER-MISC/compute_stress_mop.cpp
index e63dff507f4aab135d8d4db7a6749033ca9262ac..e496fd4dfaba6d72e3969076bc826252fd65831b 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 02ad3ea453971f27092266e90857d535f7da79a4..76bf487630a2dba8becec567e69cdd89ee8c62fe 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++){
@@ -449,13 +448,12 @@ 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;
+ 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-MISC/compute_stress_mop_profile.h b/src/USER-MISC/compute_stress_mop_profile.h
index 648d86cc7f98d6a289c418627d1760257bf48a20..0ab774f3db387bb3f2b3809bce4a9776767115c7 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 e2fb0166a28473be73e33ddba4e5c746b2d6679d..d2a57fd2d0106b95e6ecae6712a6f1e17d556f21 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 56ab2b3df9698edd26898fe0c1cbacb8001eebe0..717861e06f10e74ecefc67f52dce7ddee6af25e3 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-MOFFF/angle_class2_p6.cpp b/src/USER-MOFFF/angle_class2_p6.cpp
index c821c9d883ed611661dffb1ddeefea86c6d0ba77..d2a6e21e6be42c3e877e988a0fed430fde9c3aba 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 3f87aeb7574a00b0fa5b83e8a76d038202fc329d..f3580978023edd627399b682173c2e22a08b403c 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 9608d58054fa49d99443f915dbe5c78af055d34a..8404984b53a8d012dd37b73fe6949b05007d3c1e 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 f434d03858b3d370c63e03a2b911e9554d9763e9..46af95470ca5ae7d48f97e964a49f0fb70f0bd81 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 9902896d18ece26a6e49f461e613182b4440b0b5..3c54d6477026582759eba565f73560705514d72e 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;
diff --git a/src/USER-OMP/fix_omp.cpp b/src/USER-OMP/fix_omp.cpp
index 8be54caada2d4b92f4e5f8ba524b088cbd87bd09..a4587b1c145555607b0cd9bfe9ddade6c78f3e09 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 0821f8cea039bec9e11ccf180c524746e0a52910..87d921290efd93e5ed14d158188617e5ca0bf50c 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 ddad7eb62fd6e323756795b376a5fa9daa080915..61b653b3750ab75b184f30803136c7c85c5b47af 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 d5f6a641833435a4f97de69f650df94e357aae63..5c50a66e96f9b047ea4ca9785b1918c4dcce40ac 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 751c4746ba5286aaa39a2b9089a4e4d1ec217a49..e19b56555420e907c192d29c8c3ca7b59ec66113 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 04088bec8ce76233552a9f39da188d853eb0e7e1..7b29b1d3d51e0c4877b31b00fd9431c91c3a8a27 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 a488f65161909a05b598832c3d15a109f346eb21..0d63d2e4cba5b45b7b464d611c55b2d5f608eee4 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 c960c310f618fda3816cd658768505161611d2e5..909ead3e2a9052ba27ecc3405d47074344ad5bf0 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 2f9fb0ebaa596bdbc37553f6e2f2344c49e6f515..0a5f506ab265ff14b6070b6c537b9ae4bd180f56 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 f9dd1ec314840cc142559f0b1e5b31a62aeb452a..8af8da26be5df0a694a8001584abaf4e2d4c98a4 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/read_data.cpp b/src/read_data.cpp
index 26c406c1d6822de7a412736b50cc64572d787a12..373ba30151d3ca77df132e2a37a78443742b78cc 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
@@ -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;
@@ -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
diff --git a/src/read_restart.cpp b/src/read_restart.cpp
index 252c48d251ec8aefb414779752c6699e21d539ec..6b9ea8d77316b867bb193bc2264ee9b392e51b00 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();
diff --git a/src/set.cpp b/src/set.cpp
index 7eca4e9a9c64c0db21618933d8747d903441cea6..34b86ea328bcea334c0cf7b99d83ec3db9161a21 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 1595456f3314debb00fe13038a51d8d5276f9342..af5f647b74a086cc9978504491efc6033e0b15d7 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 3a0b95fb4da91ea6e77d6ff24a012e493137d610..6d6027cc3c7aeb8e77e8c2c2896dd8e7bfcb7c90 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 bb79c654b418569101a1f601f31fe93ce420bd97..6c7375012e8a15c569035acfd69f1f2c12aff706 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