diff --git a/doc/.gitignore b/doc/.gitignore
index 7d30949237..b20157057c 100644
--- a/doc/.gitignore
+++ b/doc/.gitignore
@@ -1,4 +1,5 @@
 /html
+/latex
 /spelling
 /LAMMPS.epub
 /LAMMPS.mobi
diff --git a/doc/src/Install_windows.txt b/doc/src/Install_windows.txt
index 78de4f09f7..7d5aab34f5 100644
--- a/doc/src/Install_windows.txt
+++ b/doc/src/Install_windows.txt
@@ -12,7 +12,7 @@ Download an executable for Windows :h3
 Pre-compiled Windows installers which install LAMMPS executables on a
 Windows system can be downloaded from this site:
 
-"http://rpm.lammps.org/windows.html"_http://rpm.lammps.org/windows.html
+"http://packages.lammps.org/windows.html"_http://packages.lammps.org/windows.html
 
 Note that each installer package has a date in its name, which
 corresponds to the LAMMPS version of the same date.  Installers for
diff --git a/doc/src/Manual.txt b/doc/src/Manual.txt
index b477ce9cf0..f5c6f914c7 100644
--- a/doc/src/Manual.txt
+++ b/doc/src/Manual.txt
@@ -37,27 +37,21 @@ LAMMPS is an open-source code, distributed freely under the terms of
 the GNU Public License (GPL).
 
 The "LAMMPS website"_lws has a variety of information about the code.
-It includes links to an on-line version of this manual, a "mail
+It includes links to an on-line version of this manual, a "mailing
 list"_http://lammps.sandia.gov/mail.html where users can post
-questions, and a "GitHub site"https://github.com/lammps/lammps where
+questions, and a "GitHub site"_https://github.com/lammps/lammps where
 all LAMMPS development is coordinated.
 
 :line
 
-"PDF file"_Manual.pdf of the entire manual, generated by
-"htmldoc"_http://freecode.com/projects/htmldoc
-
 The content for this manual is part of the LAMMPS distribution.  You
 can build a local copy of the Manual as HTML pages or a PDF file, by
 following the steps on the "Manual build"_Manual_build.html doc page.
-
 There is also a "Developer.pdf"_Developer.pdf document which gives
 a brief description of the basic code structure of LAMMPS.
 
 :line
 
-This manual is organized into the following sections.
-
 Once you are familiar with LAMMPS, you may want to bookmark "this
 page"_Commands.html since it gives quick access to a doc page for
 every LAMMPS command.
diff --git a/doc/utils/sphinx-config/conf.py b/doc/utils/sphinx-config/conf.py
index 3056687ff8..8a8b887a5e 100644
--- a/doc/utils/sphinx-config/conf.py
+++ b/doc/utils/sphinx-config/conf.py
@@ -219,7 +219,7 @@ latex_elements = {
 #  author, documentclass [howto, manual, or own class]).
 latex_documents = [
   ('Manual', 'LAMMPS.tex', 'LAMMPS Documentation',
-   'Steve Plimpton', 'manual'),
+   'The LAMMPS Developers', 'manual'),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
diff --git a/src/BODY/fix_wall_body_polygon.cpp b/src/BODY/fix_wall_body_polygon.cpp
index 0c9bd3e741..221937461b 100644
--- a/src/BODY/fix_wall_body_polygon.cpp
+++ b/src/BODY/fix_wall_body_polygon.cpp
@@ -206,7 +206,7 @@ void FixWallBodyPolygon::setup(int vflag)
 
 void FixWallBodyPolygon::post_force(int /*vflag*/)
 {
-  double vwall[3],dx,dy,dz,del1,del2,delxy,delr,rsq,eradi,rradi,wall_pos;
+  double vwall[3],dx,dy,dz,del1,del2,delxy,delr,rsq,eradi,wall_pos;
   int i,ni,npi,ifirst,nei,iefirst,side;
   double facc[3];
 
@@ -316,7 +316,6 @@ void FixWallBodyPolygon::post_force(int /*vflag*/)
       nei = ednum[i];
       iefirst = edfirst[i];
       eradi = enclosing_radius[i];
-      rradi = rounded_radius[i];
 
       // reset vertex and edge forces
 
@@ -332,14 +331,14 @@ void FixWallBodyPolygon::post_force(int /*vflag*/)
         edge[iefirst+ni][4] = 0;
       }
 
-      int interact, num_contacts, done;
+      int num_contacts, done;
       double delta_a, delta_ua, j_a;
       Contact contact_list[MAX_CONTACTS];
 
       num_contacts = 0;
       facc[0] = facc[1] = facc[2] = 0;
-      interact = vertex_against_wall(i, wall_pos, x, f, torque, side,
-                                     contact_list, num_contacts, facc);
+      vertex_against_wall(i, wall_pos, x, f, torque, side,
+                          contact_list, num_contacts, facc);
 
       if (num_contacts >= 2) {
 
@@ -475,12 +474,11 @@ int FixWallBodyPolygon::vertex_against_wall(int i, double wall_pos,
                 Contact* contact_list, int &num_contacts, double* /*facc*/)
 {
   int ni, npi, ifirst, interact;
-  double xpi[3], eradi, rradi;
+  double xpi[3], rradi;
   double fx, fy, fz;
 
   npi = dnum[i];
   ifirst = dfirst[i];
-  eradi = enclosing_radius[i];
   rradi = rounded_radius[i];
 
   interact = 0;
diff --git a/src/BODY/fix_wall_body_polyhedron.cpp b/src/BODY/fix_wall_body_polyhedron.cpp
index 295608a444..24a9e51dad 100644
--- a/src/BODY/fix_wall_body_polyhedron.cpp
+++ b/src/BODY/fix_wall_body_polyhedron.cpp
@@ -213,8 +213,8 @@ void FixWallBodyPolyhedron::setup(int vflag)
 
 void FixWallBodyPolyhedron::post_force(int /*vflag*/)
 {
-  double vwall[3],dx,dy,dz,del1,del2,rsq,eradi,rradi,wall_pos;
-  int i,ni,npi,ifirst,nei,iefirst,nfi,iffirst,side;
+  double vwall[3],dx,dy,dz,del1,del2,rsq,wall_pos;
+  int i,ni,npi,ifirst,nei,iefirst,side;
   double facc[3];
 
   // set position of wall to initial settings and velocity to 0.0
@@ -330,10 +330,6 @@ void FixWallBodyPolyhedron::post_force(int /*vflag*/)
       ifirst = dfirst[i];
       nei = ednum[i];
       iefirst = edfirst[i];
-      nfi = facnum[i];
-      iffirst = facfirst[i];
-      eradi = enclosing_radius[i];
-      rradi = rounded_radius[i];
 
       if (npi == 1) {
         sphere_against_wall(i, wall_pos, side, vwall, x, v, f, angmom, torque);
@@ -356,13 +352,13 @@ void FixWallBodyPolyhedron::post_force(int /*vflag*/)
         edge[iefirst+ni][5] = 0;
       }
 
-      int interact, num_contacts;
+      int num_contacts;
       Contact contact_list[MAX_CONTACTS];
 
       num_contacts = 0;
       facc[0] = facc[1] = facc[2] = 0;
-      interact = edge_against_wall(i, wall_pos, side, vwall, x, f, torque,
-                                   contact_list, num_contacts, facc);
+      edge_against_wall(i, wall_pos, side, vwall, x, f, torque,
+                        contact_list, num_contacts, facc);
 
     } // group bit
   }
@@ -544,7 +540,7 @@ int FixWallBodyPolyhedron::edge_against_wall(int i, double wall_pos,
      int side, double* vwall, double** x, double** /*f*/, double** /*torque*/,
      Contact* /*contact_list*/, int &/*num_contacts*/, double* /*facc*/)
 {
-  int ni, nei, mode, contact;
+  int ni, nei, contact;
   double rradi;
 
   nei = ednum[i];
@@ -555,8 +551,7 @@ int FixWallBodyPolyhedron::edge_against_wall(int i, double wall_pos,
   // loop through body i's edges
 
   for (ni = 0; ni < nei; ni++)
-    mode = compute_distance_to_wall(i, ni, x[i], rradi, wall_pos, side, vwall,
-                                    contact);
+    compute_distance_to_wall(i, ni, x[i], rradi, wall_pos, side, vwall, contact);
 
   return contact;
 }
diff --git a/src/GPU/pair_born_coul_long_cs_gpu.cpp b/src/GPU/pair_born_coul_long_cs_gpu.cpp
index 13cf5f643a..587c7b5215 100644
--- a/src/GPU/pair_born_coul_long_cs_gpu.cpp
+++ b/src/GPU/pair_born_coul_long_cs_gpu.cpp
@@ -212,8 +212,8 @@ double PairBornCoulLongCSGPU::memory_usage()
 /* ---------------------------------------------------------------------- */
 
 void PairBornCoulLongCSGPU::cpu_compute(int start, int inum, int eflag,
-                                      int vflag, int *ilist, int *numneigh,
-                                      int **firstneigh)
+                                      int /* vflag */, int *ilist,
+                                      int *numneigh, int **firstneigh)
 {
   int i,j,ii,jj,jnum,itable,itype,jtype;
   double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
diff --git a/src/GPU/pair_born_coul_long_gpu.cpp b/src/GPU/pair_born_coul_long_gpu.cpp
index c3c3fee40c..1549ed79af 100644
--- a/src/GPU/pair_born_coul_long_gpu.cpp
+++ b/src/GPU/pair_born_coul_long_gpu.cpp
@@ -207,8 +207,8 @@ double PairBornCoulLongGPU::memory_usage()
 /* ---------------------------------------------------------------------- */
 
 void PairBornCoulLongGPU::cpu_compute(int start, int inum, int eflag,
-                                      int vflag, int *ilist, int *numneigh,
-                                      int **firstneigh)
+                                      int /* vflag */, int *ilist,
+                                      int *numneigh, int **firstneigh)
 {
   int i,j,ii,jj,jnum,itype,jtype;
   double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
diff --git a/src/GPU/pair_born_coul_wolf_cs_gpu.cpp b/src/GPU/pair_born_coul_wolf_cs_gpu.cpp
index 90ddf825a9..bf23007bca 100644
--- a/src/GPU/pair_born_coul_wolf_cs_gpu.cpp
+++ b/src/GPU/pair_born_coul_wolf_cs_gpu.cpp
@@ -193,9 +193,9 @@ double PairBornCoulWolfCSGPU::memory_usage()
 
 /* ---------------------------------------------------------------------- */
 
-void PairBornCoulWolfCSGPU::cpu_compute(int start, int inum, int eflag, int vflag,
-                                      int *ilist, int *numneigh,
-                                      int **firstneigh) {
+void PairBornCoulWolfCSGPU::cpu_compute(int start, int inum, int eflag,
+                                      int /* vflag */, int *ilist,
+                                      int *numneigh, int **firstneigh) {
   int i,j,ii,jj,jnum,itype,jtype;
   double xtmp,ytmp,ztmp,qtmp,delx,dely,delz,evdwl,ecoul,fpair;
   double rsq,r2inv,r6inv,forcecoul,forceborn,factor_coul,factor_lj;
diff --git a/src/GPU/pair_buck_coul_long_gpu.cpp b/src/GPU/pair_buck_coul_long_gpu.cpp
index 73821cee8a..a2d14ea25f 100644
--- a/src/GPU/pair_buck_coul_long_gpu.cpp
+++ b/src/GPU/pair_buck_coul_long_gpu.cpp
@@ -201,8 +201,8 @@ double PairBuckCoulLongGPU::memory_usage()
 /* ---------------------------------------------------------------------- */
 
 void PairBuckCoulLongGPU::cpu_compute(int start, int inum, int eflag,
-                                       int vflag, int *ilist, int *numneigh,
-                                       int **firstneigh)
+                                       int /* vflag */, int *ilist,
+                                       int *numneigh, int **firstneigh)
 {
   int i,j,ii,jj,jnum,itype,jtype;
   double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
diff --git a/src/GPU/pair_colloid_gpu.cpp b/src/GPU/pair_colloid_gpu.cpp
index 7bbac32ed3..03e5aac5d5 100644
--- a/src/GPU/pair_colloid_gpu.cpp
+++ b/src/GPU/pair_colloid_gpu.cpp
@@ -184,8 +184,9 @@ double PairColloidGPU::memory_usage()
 
 /* ---------------------------------------------------------------------- */
 
-void PairColloidGPU::cpu_compute(int start, int inum, int eflag, int vflag,
-                                 int *ilist, int *numneigh, int **firstneigh)
+void PairColloidGPU::cpu_compute(int start, int inum, int eflag,
+                                 int /* vflag */, int *ilist,
+                                 int *numneigh, int **firstneigh)
 {
   int i,j,ii,jj,jnum,itype,jtype;
   double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
diff --git a/src/GPU/pair_coul_long_cs_gpu.cpp b/src/GPU/pair_coul_long_cs_gpu.cpp
index cbb9c73ceb..be2a090786 100644
--- a/src/GPU/pair_coul_long_cs_gpu.cpp
+++ b/src/GPU/pair_coul_long_cs_gpu.cpp
@@ -153,7 +153,7 @@ void PairCoulLongCSGPU::init_style()
   for (int i = 1; i <= atom->ntypes; i++) {
     for (int j = i; j <= atom->ntypes; j++) {
       if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) {
-        double cut = init_one(i,j);
+        init_one(i,j);
       }
     }
   }
@@ -208,8 +208,8 @@ double PairCoulLongCSGPU::memory_usage()
 /* ---------------------------------------------------------------------- */
 
 void PairCoulLongCSGPU::cpu_compute(int start, int inum, int eflag,
-                                  int vflag, int *ilist, int *numneigh,
-                                  int **firstneigh)
+                                  int /* vflag */, int *ilist,
+                                  int *numneigh, int **firstneigh)
 {
   int i,j,ii,jj,jnum,itable,itype,jtype;
   double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair;
diff --git a/src/GPU/pair_coul_long_gpu.cpp b/src/GPU/pair_coul_long_gpu.cpp
index 2f12e41b0c..684b0049c0 100644
--- a/src/GPU/pair_coul_long_gpu.cpp
+++ b/src/GPU/pair_coul_long_gpu.cpp
@@ -148,7 +148,7 @@ void PairCoulLongGPU::init_style()
   for (int i = 1; i <= atom->ntypes; i++) {
     for (int j = i; j <= atom->ntypes; j++) {
       if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0)) {
-        double cut = init_one(i,j);
+        init_one(i,j);
       }
     }
   }
@@ -203,8 +203,8 @@ double PairCoulLongGPU::memory_usage()
 /* ---------------------------------------------------------------------- */
 
 void PairCoulLongGPU::cpu_compute(int start, int inum, int eflag,
-                                  int vflag, int *ilist, int *numneigh,
-                                  int **firstneigh)
+                                  int /* vflag */, int *ilist,
+                                  int *numneigh, int **firstneigh)
 {
   int i,j,ii,jj,jnum,itable;
   double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,ecoul,fpair;
diff --git a/src/GPU/pair_eam_alloy_gpu.cpp b/src/GPU/pair_eam_alloy_gpu.cpp
index 11af562f15..20bf6dc50d 100644
--- a/src/GPU/pair_eam_alloy_gpu.cpp
+++ b/src/GPU/pair_eam_alloy_gpu.cpp
@@ -192,8 +192,8 @@ void PairEAMAlloyGPU::init_style()
 /* ---------------------------------------------------------------------- */
 
 double PairEAMAlloyGPU::single(int i, int j, int itype, int jtype,
-                       double rsq, double factor_coul, double factor_lj,
-                       double &fforce)
+                               double rsq, double /* factor_coul */,
+                               double /* factor_lj */, double &fforce)
 {
   int m;
   double r,p,rhoip,rhojp,z2,z2p,recip,phi,phip,psip;
@@ -235,7 +235,7 @@ double PairEAMAlloyGPU::single(int i, int j, int itype, int jtype,
 /* ---------------------------------------------------------------------- */
 
 int PairEAMAlloyGPU::pack_forward_comm(int n, int *list, double *buf,
-                                  int pbc_flag,int *pbc)
+                                       int /* pbc_flag */, int * /* pbc */)
 {
   int i,j,m;
 
diff --git a/src/GPU/pair_eam_fs_gpu.cpp b/src/GPU/pair_eam_fs_gpu.cpp
index ef8dd09e23..821bb1af1c 100644
--- a/src/GPU/pair_eam_fs_gpu.cpp
+++ b/src/GPU/pair_eam_fs_gpu.cpp
@@ -192,8 +192,8 @@ void PairEAMFSGPU::init_style()
 /* ---------------------------------------------------------------------- */
 
 double PairEAMFSGPU::single(int i, int j, int itype, int jtype,
-                       double rsq, double factor_coul, double factor_lj,
-                       double &fforce)
+                            double rsq, double /* factor_coul */,
+                            double /* factor_lj */, double &fforce)
 {
   int m;
   double r,p,rhoip,rhojp,z2,z2p,recip,phi,phip,psip;
@@ -235,7 +235,7 @@ double PairEAMFSGPU::single(int i, int j, int itype, int jtype,
 /* ---------------------------------------------------------------------- */
 
 int PairEAMFSGPU::pack_forward_comm(int n, int *list, double *buf,
-                                  int pbc_flag,int *pbc)
+                                    int /* pbc_flag */, int * /* pbc */)
 {
   int i,j,m;
 
diff --git a/src/GPU/pair_eam_gpu.cpp b/src/GPU/pair_eam_gpu.cpp
index e2eb9daced..515a349ad2 100644
--- a/src/GPU/pair_eam_gpu.cpp
+++ b/src/GPU/pair_eam_gpu.cpp
@@ -195,8 +195,8 @@ void PairEAMGPU::init_style()
 /* ---------------------------------------------------------------------- */
 
 double PairEAMGPU::single(int i, int j, int itype, int jtype,
-                       double rsq, double factor_coul, double factor_lj,
-                       double &fforce)
+                          double rsq, double /* factor_coul */,
+                          double /* factor_lj */, double &fforce)
 {
   int m;
   double r,p,rhoip,rhojp,z2,z2p,recip,phi,phip,psip;
@@ -238,7 +238,7 @@ double PairEAMGPU::single(int i, int j, int itype, int jtype,
 /* ---------------------------------------------------------------------- */
 
 int PairEAMGPU::pack_forward_comm(int n, int *list, double *buf,
-                                  int pbc_flag,int *pbc)
+                                  int /* pbc_flag */, int * /* pbc */)
 {
   int i,j,m;
 
diff --git a/src/GPU/pair_gayberne_gpu.cpp b/src/GPU/pair_gayberne_gpu.cpp
index 8bd5eb073f..32b8b979cd 100644
--- a/src/GPU/pair_gayberne_gpu.cpp
+++ b/src/GPU/pair_gayberne_gpu.cpp
@@ -221,8 +221,9 @@ double PairGayBerneGPU::memory_usage()
 
 /* ---------------------------------------------------------------------- */
 
-void PairGayBerneGPU::cpu_compute(int start, int inum, int eflag, int vflag,
-                                  int *ilist, int *numneigh, int **firstneigh)
+void PairGayBerneGPU::cpu_compute(int start, int inum, int eflag,
+                                  int /* vflag */, int *ilist,
+                                  int *numneigh, int **firstneigh)
 {
   int i,j,ii,jj,jnum,itype,jtype;
   double evdwl,one_eng,rsq,r2inv,r6inv,forcelj,factor_lj;
diff --git a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp
index 8c806053d4..ebc9f88943 100644
--- a/src/GPU/pair_lj_charmm_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_charmm_coul_long_gpu.cpp
@@ -151,11 +151,10 @@ void PairLJCharmmCoulLongGPU::init_style()
 
   // Repeat cutsq calculation because done after call to init_style
 
-  double cut;
   for (int i = 1; i <= atom->ntypes; i++) {
     for (int j = i; j <= atom->ntypes; j++) {
       if (setflag[i][j] != 0 || (setflag[i][i] != 0 && setflag[j][j] != 0))
-        cut = init_one(i,j);
+        init_one(i,j);
     }
   }
 
@@ -219,7 +218,7 @@ double PairLJCharmmCoulLongGPU::memory_usage()
 /* ---------------------------------------------------------------------- */
 
 void PairLJCharmmCoulLongGPU::cpu_compute(int start, int inum, int eflag,
-                                          int vflag, int *ilist,
+                                          int /* vflag */, int *ilist,
                                           int *numneigh, int **firstneigh)
 {
   int i,j,ii,jj,jnum,itype,jtype,itable;
diff --git a/src/GPU/pair_lj_class2_coul_long_gpu.cpp b/src/GPU/pair_lj_class2_coul_long_gpu.cpp
index 214ff306db..797680c032 100644
--- a/src/GPU/pair_lj_class2_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_class2_coul_long_gpu.cpp
@@ -197,8 +197,8 @@ double PairLJClass2CoulLongGPU::memory_usage()
 /* ---------------------------------------------------------------------- */
 
 void PairLJClass2CoulLongGPU::cpu_compute(int start, int inum, int eflag,
-                                       int vflag, int *ilist, int *numneigh,
-                                       int **firstneigh)
+                                          int /* vflag */, int *ilist,
+                                          int *numneigh, int **firstneigh)
 {
   int i,j,ii,jj,jnum,itype,jtype;
   double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
diff --git a/src/GPU/pair_lj_cut_coul_long_gpu.cpp b/src/GPU/pair_lj_cut_coul_long_gpu.cpp
index 3cccb898cc..943d12b0fe 100644
--- a/src/GPU/pair_lj_cut_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_long_gpu.cpp
@@ -215,8 +215,8 @@ double PairLJCutCoulLongGPU::memory_usage()
 /* ---------------------------------------------------------------------- */
 
 void PairLJCutCoulLongGPU::cpu_compute(int start, int inum, int eflag,
-                                       int vflag, int *ilist, int *numneigh,
-                                       int **firstneigh)
+                                       int /* vflag */, int *ilist,
+                                       int *numneigh, int **firstneigh)
 {
   int i,j,ii,jj,jnum,itype,jtype,itable;
   double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
diff --git a/src/GPU/pair_lj_cut_coul_msm_gpu.cpp b/src/GPU/pair_lj_cut_coul_msm_gpu.cpp
index 04ffe245b2..46cf6f19bc 100644
--- a/src/GPU/pair_lj_cut_coul_msm_gpu.cpp
+++ b/src/GPU/pair_lj_cut_coul_msm_gpu.cpp
@@ -192,8 +192,9 @@ double PairLJCutCoulMSMGPU::memory_usage()
 
 /* ---------------------------------------------------------------------- */
 
-void PairLJCutCoulMSMGPU::cpu_compute(int start, int inum, int eflag, int vflag,
-                               int *ilist, int *numneigh, int **firstneigh) {
+void PairLJCutCoulMSMGPU::cpu_compute(int start, int inum, int eflag,
+                                      int /* vflag */, int *ilist,
+                                      int *numneigh, int **firstneigh) {
   int i,j,ii,jj,jnum,itype,jtype,itable;
   double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
   double fraction,table;
diff --git a/src/GPU/pair_lj_cut_dipole_long_gpu.cpp b/src/GPU/pair_lj_cut_dipole_long_gpu.cpp
index 870dc8ba6d..b209fa0ee7 100644
--- a/src/GPU/pair_lj_cut_dipole_long_gpu.cpp
+++ b/src/GPU/pair_lj_cut_dipole_long_gpu.cpp
@@ -216,7 +216,7 @@ void PairLJCutDipoleLongGPU::cpu_compute(int start, int inum, int eflag, int vfl
   double qtmp,xtmp,ytmp,ztmp,delx,dely,delz;
   double rsq,r,rinv,r2inv,r6inv;
   double forcecoulx,forcecouly,forcecoulz,fforce;
-  double tixcoul,tiycoul,tizcoul,tjxcoul,tjycoul,tjzcoul;
+  double tixcoul,tiycoul,tizcoul;
   double fx,fy,fz,fdx,fdy,fdz,fax,fay,faz;
   double pdotp,pidotr,pjdotr,pre1,pre2,pre3;
   double grij,expm2,t,erfc;
@@ -378,14 +378,9 @@ void PairLJCutDipoleLongGPU::cpu_compute(int start, int inum, int eflag, int vfl
           tixcoul = mu[i][1]*(zdiz + zaiz) - mu[i][2]*(zdiy + zaiy);
           tiycoul = mu[i][2]*(zdix + zaix) - mu[i][0]*(zdiz + zaiz);
           tizcoul = mu[i][0]*(zdiy + zaiy) - mu[i][1]*(zdix + zaix);
-          tjxcoul = mu[j][1]*(zdjz + zajz) - mu[j][2]*(zdjy + zajy);
-          tjycoul = mu[j][2]*(zdjx + zajx) - mu[j][0]*(zdjz + zajz);
-          tjzcoul = mu[j][0]*(zdjy + zajy) - mu[j][1]*(zdjx + zajx);
-
         } else {
           forcecoulx = forcecouly = forcecoulz = 0.0;
           tixcoul = tiycoul = tizcoul = 0.0;
-          tjxcoul = tjycoul = tjzcoul = 0.0;
         }
 
         // LJ interaction
diff --git a/src/GPU/pair_lj_expand_coul_long_gpu.cpp b/src/GPU/pair_lj_expand_coul_long_gpu.cpp
index 49e8be5879..4161155980 100644
--- a/src/GPU/pair_lj_expand_coul_long_gpu.cpp
+++ b/src/GPU/pair_lj_expand_coul_long_gpu.cpp
@@ -215,8 +215,8 @@ double PairLJExpandCoulLongGPU::memory_usage()
 /* ---------------------------------------------------------------------- */
 
 void PairLJExpandCoulLongGPU::cpu_compute(int start, int inum, int eflag,
-                                       int vflag, int *ilist, int *numneigh,
-                                       int **firstneigh)
+                                       int /* vflag */, int *ilist,
+                                       int *numneigh, int **firstneigh)
 {
   int i,j,ii,jj,jnum,itype,jtype,itable;
   double qtmp,xtmp,ytmp,ztmp,delx,dely,delz,evdwl,ecoul,fpair;
diff --git a/src/GPU/pair_mie_cut_gpu.cpp b/src/GPU/pair_mie_cut_gpu.cpp
index 5919b05466..e52577ee4c 100644
--- a/src/GPU/pair_mie_cut_gpu.cpp
+++ b/src/GPU/pair_mie_cut_gpu.cpp
@@ -172,8 +172,8 @@ double PairMIECutGPU::memory_usage()
 
 /* ---------------------------------------------------------------------- */
 
-void PairMIECutGPU::cpu_compute(int start, int inum, int eflag, int vflag,
-                               int *ilist, int *numneigh, int **firstneigh) {
+void PairMIECutGPU::cpu_compute(int start, int inum, int eflag, int /* vflag */,
+                                int *ilist, int *numneigh, int **firstneigh) {
   int i,j,ii,jj,jnum,itype,jtype;
   double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
   double rsq,r2inv,rgamR,rgamA,forcemie,factor_mie;
diff --git a/src/GPU/pair_morse_gpu.cpp b/src/GPU/pair_morse_gpu.cpp
index 81ea7c818a..7abf78ff30 100644
--- a/src/GPU/pair_morse_gpu.cpp
+++ b/src/GPU/pair_morse_gpu.cpp
@@ -168,7 +168,7 @@ double PairMorseGPU::memory_usage()
 
 /* ---------------------------------------------------------------------- */
 
-void PairMorseGPU::cpu_compute(int start, int inum, int eflag, int vflag,
+void PairMorseGPU::cpu_compute(int start, int inum, int eflag, int /* vflag */,
                                int *ilist, int *numneigh, int **firstneigh)
 {
   int i,j,ii,jj,jnum,itype,jtype;
diff --git a/src/GPU/pair_resquared_gpu.cpp b/src/GPU/pair_resquared_gpu.cpp
index 34bd0ec22f..b6fada0897 100644
--- a/src/GPU/pair_resquared_gpu.cpp
+++ b/src/GPU/pair_resquared_gpu.cpp
@@ -219,8 +219,9 @@ double PairRESquaredGPU::memory_usage()
 
 /* ---------------------------------------------------------------------- */
 
-void PairRESquaredGPU::cpu_compute(int start, int inum, int eflag, int vflag,
-                                  int *ilist, int *numneigh, int **firstneigh)
+void PairRESquaredGPU::cpu_compute(int start, int inum, int eflag,
+                                   int /* vflag */, int *ilist,
+                                   int *numneigh, int **firstneigh)
 {
   int i,j,ii,jj,jnum,itype,jtype;
   double evdwl,one_eng,rsq,r2inv,r6inv,forcelj,factor_lj;
diff --git a/src/GPU/pair_soft_gpu.cpp b/src/GPU/pair_soft_gpu.cpp
index cc0ea72633..eed1bd5db3 100644
--- a/src/GPU/pair_soft_gpu.cpp
+++ b/src/GPU/pair_soft_gpu.cpp
@@ -182,8 +182,8 @@ double PairSoftGPU::memory_usage()
 
 /* ---------------------------------------------------------------------- */
 
-void PairSoftGPU::cpu_compute(int start, int inum, int eflag, int vflag,
-                               int *ilist, int *numneigh, int **firstneigh) {
+void PairSoftGPU::cpu_compute(int start, int inum, int eflag, int /* vflag */,
+                              int *ilist, int *numneigh, int **firstneigh) {
   int i,j,ii,jj,jnum,itype,jtype;
   double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
   double r,rsq,arg,factor_lj;
diff --git a/src/GPU/pair_table_gpu.cpp b/src/GPU/pair_table_gpu.cpp
index c5aef996db..d0185b85e8 100644
--- a/src/GPU/pair_table_gpu.cpp
+++ b/src/GPU/pair_table_gpu.cpp
@@ -246,7 +246,7 @@ double PairTableGPU::memory_usage()
 
 /* ---------------------------------------------------------------------- */
 
-void PairTableGPU::cpu_compute(int start, int inum, int eflag, int vflag,
+void PairTableGPU::cpu_compute(int start, int inum, int eflag, int /* vflag */,
                                int *ilist, int *numneigh, int **firstneigh) {
   int i,j,ii,jj,jnum,itype,jtype,itable;
   double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
diff --git a/src/GPU/pair_ufm_gpu.cpp b/src/GPU/pair_ufm_gpu.cpp
index 40e8df3323..688e3ef4dc 100644
--- a/src/GPU/pair_ufm_gpu.cpp
+++ b/src/GPU/pair_ufm_gpu.cpp
@@ -186,8 +186,8 @@ double PairUFMGPU::memory_usage()
 
 /* ---------------------------------------------------------------------- */
 
-void PairUFMGPU::cpu_compute(int start, int inum, int eflag, int vflag,
-                               int *ilist, int *numneigh, int **firstneigh) {
+void PairUFMGPU::cpu_compute(int start, int inum, int eflag, int /* vflag */,
+                             int *ilist, int *numneigh, int **firstneigh) {
   int i,j,ii,jj,jnum,itype,jtype;
   double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
   double rsq,expuf,factor_lj;
diff --git a/src/GPU/pair_vashishta_gpu.cpp b/src/GPU/pair_vashishta_gpu.cpp
index 00dbac5f1e..84936f2c26 100644
--- a/src/GPU/pair_vashishta_gpu.cpp
+++ b/src/GPU/pair_vashishta_gpu.cpp
@@ -151,7 +151,7 @@ void PairVashishtaGPU::init_style()
   if (force->newton_pair != 0)
     error->all(FLERR,"Pair style vashishta/gpu requires newton pair off");
 
-  double *cutsq, *r0, *r0eps, *gamma, *eta;
+  double *cutsq, *r0, *gamma, *eta;
   double *lam1inv, *lam4inv, *zizj, *mbigd;
   double *dvrc, *big6w, *heta, *bigh;
   double *bigw, *c0, *costheta, *bigb;
diff --git a/src/GPU/pair_yukawa_colloid_gpu.cpp b/src/GPU/pair_yukawa_colloid_gpu.cpp
index 0332e5f755..556dece7f8 100644
--- a/src/GPU/pair_yukawa_colloid_gpu.cpp
+++ b/src/GPU/pair_yukawa_colloid_gpu.cpp
@@ -179,8 +179,8 @@ double PairYukawaColloidGPU::memory_usage()
 /* ---------------------------------------------------------------------- */
 
 void PairYukawaColloidGPU::cpu_compute(int start, int inum, int eflag,
-                                       int vflag, int *ilist, int *numneigh,
-                                       int **firstneigh) {
+                                       int /* vflag */, int *ilist,
+                                       int *numneigh, int **firstneigh) {
   int i,j,ii,jj,jnum,itype,jtype;
   double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair,radi,radj;
   double r,rsq,rinv,screening,forceyukawa,factor;
diff --git a/src/GPU/pair_yukawa_gpu.cpp b/src/GPU/pair_yukawa_gpu.cpp
index dda4250f07..9d3ea6f5a7 100644
--- a/src/GPU/pair_yukawa_gpu.cpp
+++ b/src/GPU/pair_yukawa_gpu.cpp
@@ -170,8 +170,8 @@ double PairYukawaGPU::memory_usage()
 
 /* ---------------------------------------------------------------------- */
 
-void PairYukawaGPU::cpu_compute(int start, int inum, int eflag, int vflag,
-                               int *ilist, int *numneigh, int **firstneigh) {
+void PairYukawaGPU::cpu_compute(int start, int inum, int eflag, int /* vflag */,
+                                int *ilist, int *numneigh, int **firstneigh) {
   int i,j,ii,jj,jnum,itype,jtype;
   double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
   double rsq,r2inv,r,rinv,screening,forceyukawa,factor;
diff --git a/src/GPU/pair_zbl_gpu.cpp b/src/GPU/pair_zbl_gpu.cpp
index daca79c8e3..c9b8dd75a1 100644
--- a/src/GPU/pair_zbl_gpu.cpp
+++ b/src/GPU/pair_zbl_gpu.cpp
@@ -177,7 +177,7 @@ double PairZBLGPU::memory_usage()
 
 /* ---------------------------------------------------------------------- */
 
-void PairZBLGPU::cpu_compute(int start, int inum, int eflag, int vflag,
+void PairZBLGPU::cpu_compute(int start, int inum, int eflag, int /* vflag */,
                              int *ilist, int *numneigh, int **firstneigh) {
   int i,j,ii,jj,jnum,itype,jtype;
   double xtmp,ytmp,ztmp,delx,dely,delz,evdwl,fpair;
diff --git a/src/MANYBODY/pair_bop.cpp b/src/MANYBODY/pair_bop.cpp
index ca0f229068..6540dedf98 100644
--- a/src/MANYBODY/pair_bop.cpp
+++ b/src/MANYBODY/pair_bop.cpp
@@ -4988,7 +4988,7 @@ void PairBOP::read_table(char *filename)
       fgets(s,MAXLINE,fp);
       nws=0;
       ws=1;
-      for(j=0;j<strlen(s);j++) {
+      for(j=0;j<(int)strlen(s);j++) {
         if(ws==1) {
           if(isspace(s[j])) {
             ws=1;
@@ -5015,7 +5015,7 @@ void PairBOP::read_table(char *filename)
     nws=0;
     ws=1;
     fgets(s,MAXLINE,fp);
-    for(j=0;j<strlen(s);j++) {
+    for(j=0;j<(int)strlen(s);j++) {
       if(ws==1) {
         if(isspace(s[j])) {
           ws=1;
diff --git a/src/PYTHON/pair_python.cpp b/src/PYTHON/pair_python.cpp
index 02c82535fe..4899e5e2ef 100644
--- a/src/PYTHON/pair_python.cpp
+++ b/src/PYTHON/pair_python.cpp
@@ -401,9 +401,9 @@ double PairPython::init_one(int, int)
 
 /* ---------------------------------------------------------------------- */
 
-double PairPython::single(int i, int j, int itype, int jtype, double rsq,
-                         double factor_coul, double factor_lj,
-                         double &fforce)
+double PairPython::single(int /* i */, int /* j */, int itype, int jtype,
+                         double rsq, double /* factor_coul */,
+                         double factor_lj, double &fforce)
 {
   // with hybrid/overlay we might get called for skipped types
   if (skip_types[itype] || skip_types[jtype]) {
diff --git a/src/USER-PTM/README b/src/USER-PTM/README
new file mode 100644
index 0000000000..42b8738f86
--- /dev/null
+++ b/src/USER-PTM/README
@@ -0,0 +1,26 @@
+
+This package provides the compute ptm/atom command for LAMMPS which implements the
+Polyhedral Template Matching algorithm for analysis of molecular dynamics simulation data
+
+The method is currently (Fall 2018) included in OVITO, LAMMPS, and ASAP.
+
+OVITO PTM documentation: http://www.ovito.org/manual/particles.modifiers.polyhedral_template_matching.html
+
+LAMMPS PTM documentation: http://lammps.sandia.gov/doc/compute_ptm_atom.html
+
+ASAP PTM documentation: http://wiki.fysik.dtu.dk/asap/Local%20crystalline%20order
+
+
+If you use PTM in a publication, please reference:
+
+Peter Mahler Larsen and Søren Schmidt and Jakob Schiøtz
+Robust structural identification via polyhedral template matching
+Modelling Simul. Mater. Sci. Eng. 24 (2016) 055007
+
+Article available at:
+http://stacks.iop.org/0965-0393/24/i=5/a=055007
+
+Preprint available at:
+http://arxiv.org/abs/1603.05143
+
+
diff --git a/src/USER-REAXC/fix_qeq_reax.cpp b/src/USER-REAXC/fix_qeq_reax.cpp
index 6f0b93235f..b37c8fff83 100644
--- a/src/USER-REAXC/fix_qeq_reax.cpp
+++ b/src/USER-REAXC/fix_qeq_reax.cpp
@@ -126,14 +126,12 @@ FixQEqReax::FixQEqReax(LAMMPS *lmp, int narg, char **arg) :
   reaxc = NULL;
   reaxc = (PairReaxC *) force->pair_match("reax/c",0);
 
-  if (reaxc) {
-    s_hist = t_hist = NULL;
-    grow_arrays(atom->nmax);
-    atom->add_callback(0);
-    for (int i = 0; i < atom->nmax; i++)
-      for (int j = 0; j < nprev; ++j)
-        s_hist[i][j] = t_hist[i][j] = 0;
-  }
+  s_hist = t_hist = NULL;
+  grow_arrays(atom->nmax);
+  atom->add_callback(0);
+  for (int i = 0; i < atom->nmax; i++)
+    for (int j = 0; j < nprev; ++j)
+      s_hist[i][j] = t_hist[i][j] = 0;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -557,17 +555,11 @@ void FixQEqReax::init_matvec()
       b_s[i]      = -chi[ atom->type[i] ];
       b_t[i]      = -1.0;
 
-      /* linear extrapolation for s & t from previous solutions */
-      //s[i] = 2 * s_hist[i][0] - s_hist[i][1];
-      //t[i] = 2 * t_hist[i][0] - t_hist[i][1];
-
       /* quadratic extrapolation for s & t from previous solutions */
-      //s[i] = s_hist[i][2] + 3 * ( s_hist[i][0] - s_hist[i][1] );
       t[i] = t_hist[i][2] + 3 * ( t_hist[i][0] - t_hist[i][1]);
 
       /* cubic extrapolation for s & t from previous solutions */
       s[i] = 4*(s_hist[i][0]+s_hist[i][2])-(6*s_hist[i][1]+s_hist[i][3]);
-      //t[i] = 4*(t_hist[i][0]+t_hist[i][2])-(6*t_hist[i][1]+t_hist[i][3]);
     }
   }
 
@@ -615,6 +607,7 @@ void FixQEqReax::compute_H()
 
       for (jj = 0; jj < jnum; jj++) {
         j = jlist[jj];
+        j &= NEIGHMASK;
 
         dx = x[j][0] - x[i][0];
         dy = x[j][1] - x[i][1];
diff --git a/src/atom.cpp b/src/atom.cpp
index 9958fefc88..be4d12d52e 100644
--- a/src/atom.cpp
+++ b/src/atom.cpp
@@ -2290,7 +2290,7 @@ int Atom::memcheck(const char *str)
     return 0;
   }
 
-  if (strlen(memstr) + n >= memlength) {
+  if ((int)strlen(memstr) + n >= memlength) {
     memlength += DELTA_MEMSTR;
     memory->grow(memstr,memlength,"atom:memstr");
   }
diff --git a/src/compute_reduce_region.cpp b/src/compute_reduce_region.cpp
index 3dd671ce2b..8e91a299e8 100644
--- a/src/compute_reduce_region.cpp
+++ b/src/compute_reduce_region.cpp
@@ -78,7 +78,6 @@ double ComputeReduceRegion::compute_one(int m, int flag)
     n = value2index[m];
   }
 
-  int aidx = argindex[m];
   int j = argindex[m];
 
   double one = 0.0;
diff --git a/src/create_atoms.cpp b/src/create_atoms.cpp
index 83175b9afb..ba04de026d 100644
--- a/src/create_atoms.cpp
+++ b/src/create_atoms.cpp
@@ -727,26 +727,6 @@ void CreateAtoms::add_lattice()
   domain->lattice->bbox(1,bboxhi[0],bboxhi[1],bboxhi[2],
                         xmin,ymin,zmin,xmax,ymax,zmax);
 
-  // narrow down min/max further by extent of the region, if possible
-
-  if ((style == REGION) && domain->regions[nregion]->bboxflag) {
-    double rxmin = domain->regions[nregion]->extent_xlo;
-    double rxmax = domain->regions[nregion]->extent_xhi;
-    double rymin = domain->regions[nregion]->extent_ylo;
-    double rymax = domain->regions[nregion]->extent_yhi;
-    double rzmin = domain->regions[nregion]->extent_zlo;
-    double rzmax = domain->regions[nregion]->extent_zhi;
-    domain->lattice->box2lattice(rxmin,rymin,rzmin);
-    domain->lattice->box2lattice(rxmax,rymax,rzmax);
-
-    if (rxmin > xmin) xmin = (rxmin > xmax) ? xmax : rxmin;
-    if (rxmax < xmax) xmax = (rxmax < xmin) ? xmin : rxmax;
-    if (rymin > ymin) ymin = (rymin > ymax) ? ymax : rymin;
-    if (rymax < ymax) ymax = (rymax < ymin) ? ymin : rymax;
-    if (rzmin > zmin) zmin = (rzmin > zmax) ? zmax : rzmin;
-    if (rzmax < zmax) zmax = (rzmax < zmin) ? zmin : rzmax;
-  }
-
   // ilo:ihi,jlo:jhi,klo:khi = loop bounds for lattice overlap of my subbox
   // overlap = any part of a unit cell (face,edge,pt) in common with my subbox
   // in lattice space, subbox is a tilted box
diff --git a/src/lmpwindows.h b/src/lmpwindows.h
index ae2a545717..546fa62535 100644
--- a/src/lmpwindows.h
+++ b/src/lmpwindows.h
@@ -4,6 +4,7 @@
 #endif
 #include <direct.h>
 #include <cmath>
+#include <cstring>
 // LAMMPS uses usleep with 100 ms arguments, no microsecond precision needed
 #if !defined(__MINGW32__)
 #include "sleep.h"
@@ -15,6 +16,7 @@
 #define ATOBIGINT _atoi64
 
 #define pclose _pclose
+#define strdup _strdup
 
 // the following functions ared defined to get rid of
 // 'ambiguous call to overloaded function' error in VSS for mismathched type arguments
diff --git a/src/pair.cpp b/src/pair.cpp
index cc066713c9..62d8f6049c 100644
--- a/src/pair.cpp
+++ b/src/pair.cpp
@@ -151,13 +151,13 @@ void Pair::modify_params(int narg, char **arg)
     } else if (strcmp(arg[iarg],"table") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal pair_modify command");
       ncoultablebits = force->inumeric(FLERR,arg[iarg+1]);
-      if (ncoultablebits > sizeof(float)*CHAR_BIT)
+      if (ncoultablebits > (int)sizeof(float)*CHAR_BIT)
         error->all(FLERR,"Too many total bits for bitmapped lookup table");
       iarg += 2;
     } else if (strcmp(arg[iarg],"table/disp") == 0) {
       if (iarg+2 > narg) error->all(FLERR,"Illegal pair_modify command");
       ndisptablebits = force->inumeric(FLERR,arg[iarg+1]);
-      if (ndisptablebits > sizeof(float)*CHAR_BIT)
+      if (ndisptablebits > (int)sizeof(float)*CHAR_BIT)
         error->all(FLERR,"Too many total bits for bitmapped lookup table");
       iarg += 2;
     } else if (strcmp(arg[iarg],"tabinner") == 0) {
@@ -1695,7 +1695,7 @@ void Pair::init_bitmap(double inner, double outer, int ntablebits,
   if (sizeof(int) != sizeof(float))
     error->all(FLERR,"Bitmapped lookup tables require int/float be same size");
 
-  if (ntablebits > sizeof(float)*CHAR_BIT)
+  if (ntablebits > (int)sizeof(float)*CHAR_BIT)
     error->all(FLERR,"Too many total bits for bitmapped lookup table");
 
   if (inner >= outer)
@@ -1719,7 +1719,7 @@ void Pair::init_bitmap(double inner, double outer, int ntablebits,
 
   int nmantbits = ntablebits - nexpbits;
 
-  if (nexpbits > sizeof(float)*CHAR_BIT - FLT_MANT_DIG)
+  if (nexpbits > (int)sizeof(float)*CHAR_BIT - FLT_MANT_DIG)
     error->all(FLERR,"Too many exponent bits for lookup table");
   if (nmantbits+1 > FLT_MANT_DIG)
     error->all(FLERR,"Too many mantissa bits for lookup table");
diff --git a/src/read_data.cpp b/src/read_data.cpp
index 373ba30151..4d7c855065 100644
--- a/src/read_data.cpp
+++ b/src/read_data.cpp
@@ -1963,7 +1963,7 @@ void ReadData::parse_keyword(int first)
     }
     while (eof == 0 && done == 0) {
       int blank = strspn(line," \t\n\r");
-      if ((blank == strlen(line)) || (line[blank] == '#')) {
+      if ((blank == (int)strlen(line)) || (line[blank] == '#')) {
         if (fgets(line,MAXLINE,fp) == NULL) eof = 1;
       } else done = 1;
     }
diff --git a/src/read_restart.cpp b/src/read_restart.cpp
index 82028d8316..73dc37f4cb 100644
--- a/src/read_restart.cpp
+++ b/src/read_restart.cpp
@@ -627,7 +627,7 @@ void ReadRestart::file_search(char *infile, char *outfile)
     if ((ptr = strstr(&ep->d_name[nbegin],end)) == NULL) continue;
     if (strlen(end) == 0) ptr = ep->d_name + strlen(ep->d_name);
     *ptr = '\0';
-    if (strlen(&ep->d_name[nbegin]) < n) {
+    if ((int)strlen(&ep->d_name[nbegin]) < n) {
       strcpy(middle,&ep->d_name[nbegin]);
       if (ATOBIGINT(middle) > maxnum) maxnum = ATOBIGINT(middle);
     }