Merge pull request #2705 from akohlmey/collected-small-changes

Collected small changes and fixes

cmake/CMakeLists.txt

@@ -269,6 +269,7 @@ endif()
 set(ENABLE_IWYU OFF CACHE BOOL "Add 'iwyu' build target to call the include-what-you-use tool")
 mark_as_advanced(ENABLE_IWYU)
 if(ENABLE_IWYU)
+  set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
   find_program(IWYU_EXE NAMES include-what-you-use iwyu)
   find_program(IWYU_TOOL NAMES iwyu_tool iwyu-tool iwyu_tool.py)
   if (IWYU_EXE AND IWYU_TOOL)
@@ -730,7 +731,7 @@ get_target_property(DEFINES lammps COMPILE_DEFINITIONS)
 include(FeatureSummary)
 feature_summary(DESCRIPTION "The following tools and libraries have been found and configured:" WHAT PACKAGES_FOUND)
 message(STATUS "<<< Build configuration >>>
-   Operating System: ${CMAKE_SYSTEM_NAME}
+   Operating System: ${CMAKE_SYSTEM_NAME} ${CMAKE_LINUX_DISTRO} ${CMAKE_DISTRO_VERSION}
    Build type:       ${CMAKE_BUILD_TYPE}
    Install path:     ${CMAKE_INSTALL_PREFIX}
    Generator:        ${CMAKE_GENERATOR} using ${CMAKE_MAKE_PROGRAM}")

cmake/Modules/LAMMPSUtils.cmake

@@ -104,3 +104,13 @@ function(FetchPotentials pkgfolder potfolder)
     endforeach()
   endif()
 endfunction(FetchPotentials)
+
+# set CMAKE_LINUX_DISTRO and CMAKE_DISTRO_VERSION on Linux
+if((CMAKE_SYSTEM_NAME STREQUAL Linux) AND (EXISTS /etc/os-release))
+  file(STRINGS /etc/os-release distro REGEX "^NAME=")
+  string(REGEX REPLACE "NAME=\"?([^\"]*)\"?" "\\1" distro "${distro}")
+  file(STRINGS /etc/os-release disversion REGEX "^VERSION_ID=")
+  string(REGEX REPLACE "VERSION_ID=\"?([^\"]*)\"?" "\\1" disversion "${disversion}")
+  set(CMAKE_LINUX_DISTRO ${distro})
+  set(CMAKE_DISTRO_VERSION ${disversion})
+endif()

cmake/Modules/Packages/USER-PLUMED.cmake

@@ -54,8 +54,9 @@ if(DOWNLOAD_PLUMED)
     set(PLUMED_BUILD_BYPRODUCTS "<INSTALL_DIR>/lib/libplumedWrapper.a")
   endif()
 
-  set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.0/plumed-src-2.7.0.tgz" CACHE STRING "URL for PLUMED tarball")
+  set(PLUMED_URL "https://github.com/plumed/plumed2/releases/download/v2.7.1/plumed-src-2.7.1.tgz" CACHE STRING "URL for PLUMED tarball")
-  set(PLUMED_MD5 "95f29dd0c067577f11972ff90dfc7d12" CACHE STRING "MD5 checksum of PLUMED tarball")
+  set(PLUMED_MD5 "4eac6a462ec84dfe0cec96c82421b8e8" CACHE STRING "MD5 checksum of PLUMED tarball")
+
   mark_as_advanced(PLUMED_URL)
   mark_as_advanced(PLUMED_MD5)
 

cmake/Modules/Testing.cmake

@@ -16,11 +16,14 @@ if(ENABLE_TESTING)
   set(MEMORYCHECK_COMMAND "${VALGRIND_BINARY}" CACHE FILEPATH "Memory Check Command")
   set(MEMORYCHECK_COMMAND_OPTIONS "${VALGRIND_DEFAULT_OPTIONS}" CACHE STRING "Memory Check Command Options")
 
-  # check if a faster linker is available.
+  # we need to build and link a LOT of tester executables, so it is worth checking if
-  # only verified with GNU and Clang compilers and new CMake
+  # a faster linker is available. requires GNU or Clang compiler, newer CMake.
-  if(CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
+  # also only verified with Fedora Linux > 30 and Ubuntu <= 18.04 (Ubuntu 20.04 fails)
-    if((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
+  if((CMAKE_SYSTEM_NAME STREQUAL Linux) AND (CMAKE_VERSION VERSION_GREATER_EQUAL 3.13)
-        OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang"))
+      AND ((${CMAKE_CXX_COMPILER_ID} STREQUAL "GNU")
+        OR (${CMAKE_CXX_COMPILER_ID} STREQUAL "Clang")))
+    if (((CMAKE_LINUX_DISTRO STREQUAL Ubuntu) AND (CMAKE_DISTRO_VERSION VERSION_LESS_EQUAL 18.04))
+        OR ((CMAKE_LINUX_DISTRO STREQUAL Fedora) AND (CMAKE_DISTRO_VERSION VERSION_GREATER 30)))
       include(CheckCXXCompilerFlag)
       set(CMAKE_CUSTOM_LINKER_DEFAULT default)
       check_cxx_compiler_flag(-fuse-ld=lld HAVE_LLD_LINKER_FLAG)

doc/src/fix_qeq.rst

@@ -56,27 +56,28 @@ Examples
 Description
 """""""""""
 
-Perform the charge equilibration (QEq) method as described in :ref:`(Rappe and Goddard) <Rappe1>` and formulated in :ref:`(Nakano) <Nakano1>` (also known
+Perform the charge equilibration (QEq) method as described in
-as the matrix inversion method) and in :ref:`(Rick and Stuart) <Rick1>` (also
+:ref:`(Rappe and Goddard) <Rappe1>` and formulated in :ref:`(Nakano)
-known as the extended Lagrangian method) based on the
+<Nakano1>` (also known as the matrix inversion method) and in
-electronegativity equilization principle.
+:ref:`(Rick and Stuart) <Rick1>` (also known as the extended Lagrangian
+method) based on the electronegativity equilization principle.
 
 These fixes can be used with any :doc:`pair style <pair_style>` in
 LAMMPS, so long as per-atom charges are defined.  The most typical
 use-case is in conjunction with a :doc:`pair style <pair_style>` that
 performs charge equilibration periodically (e.g. every timestep), such
-as the ReaxFF or Streitz-Mintmire potential.
+as the ReaxFF or Streitz-Mintmire potential.  But these fixes can also
-But these fixes can also be used with
+be used with potentials that normally assume per-atom charges are fixed,
-potentials that normally assume per-atom charges are fixed, e.g. a
+e.g. a :doc:`Buckingham <pair_buck>` or :doc:`LJ/Coulombic <pair_lj>`
-:doc:`Buckingham <pair_buck>` or :doc:`LJ/Coulombic <pair_lj>` potential.
+potential.
 
-Because the charge equilibration calculation is effectively
+Because the charge equilibration calculation is effectively independent
-independent of the pair style, these fixes can also be used to perform
+of the pair style, these fixes can also be used to perform a one-time
-a one-time assignment of charges to atoms.  For example, you could
+assignment of charges to atoms.  For example, you could define the QEq
-define the QEq fix, perform a zero-timestep run via the :doc:`run <run>`
+fix, perform a zero-timestep run via the :doc:`run <run>` command
-command without any pair style defined which would set per-atom
+without any pair style defined which would set per-atom charges (based
-charges (based on the current atom configuration), then remove the fix
+on the current atom configuration), then remove the fix via the
-via the :doc:`unfix <unfix>` command before performing further dynamics.
+:doc:`unfix <unfix>` command before performing further dynamics.
 
 .. note::
 
@@ -87,11 +88,14 @@ via the :doc:`unfix <unfix>` command before performing further dynamics.
 
 .. note::
 
-   The :doc:`fix qeq/comb <fix_qeq_comb>` command must still be used
+   The :doc:`fix qeq/comb <fix_qeq_comb>` command must still be used to
-   to perform charge equilibration with the :doc:`COMB potential <pair_comb>`.  The :doc:`fix qeq/reax <fix_qeq_reax>`
+   perform charge equilibration with the :doc:`COMB potential
-   command can be used to perform charge equilibration with the :doc:`ReaxFF force field <pair_reaxc>`, although fix qeq/shielded yields the
+   <pair_comb>`.  The :doc:`fix qeq/reax <fix_qeq_reax>` command can be
-   same results as fix qeq/reax if *Nevery*\ , *cutoff*\ , and *tolerance*
+   used to perform charge equilibration with the :doc:`ReaxFF force
-   are the same.  Eventually the fix qeq/reax command will be deprecated.
+   field <pair_reaxc>`, although fix qeq/shielded yields the same
+   results as fix qeq/reax if *Nevery*\ , *cutoff*\ , and *tolerance*
+   are the same.  Eventually the fix qeq/reax command will be
+   deprecated.
 
 The QEq method minimizes the electrostatic energy of the system (or
 equalizes the derivative of energy with respect to charge of all the
@@ -134,55 +138,57 @@ usually a good number.
 The *qeq/shielded* style describes partial charges on atoms also as
 point charges, but uses a shielded Coulomb potential to describe the
 interaction between a pair of charged particles.  Interaction through
-the shielded Coulomb is given by equation (13) of the :ref:`ReaxFF force field <vanDuin>` paper.  The shielding accounts for charge overlap
+the shielded Coulomb is given by equation (13) of the :ref:`ReaxFF force
+field <vanDuin>` paper.  The shielding accounts for charge overlap
 between charged particles at small separation.  This style is the same
-as :doc:`fix qeq/reax <fix_qeq_reax>`, and can be used with :doc:`pair_style reax/c <pair_reaxc>`.  Only the *chi*\ , *eta*\ , and *gamma*
+as :doc:`fix qeq/reax <fix_qeq_reax>`, and can be used with
-parameters from the *qfile* file are used. When using the string
+:doc:`pair_style reax/c <pair_reaxc>`.  Only the *chi*\ , *eta*\ , and
-*reax/c* as filename, these parameters are extracted directly from
+*gamma* parameters from the *qfile* file are used. When using the string
-an active *reax/c* pair style.  This style solves partial
+*reax/c* as filename, these parameters are extracted directly from an
-charges on atoms via the matrix inversion method.  A tolerance of
+active *reax/c* pair style.  This style solves partial charges on atoms
-1.0e-6 is usually a good number.
+via the matrix inversion method.  A tolerance of 1.0e-6 is usually a
+good number.
 
 The *qeq/slater* style describes partial charges on atoms as spherical
 charge densities centered around atoms via the Slater 1\ *s* orbital, so
-that the interaction between a pair of charged particles is the
+that the interaction between a pair of charged particles is the product
-product of two Slater 1\ *s* orbitals.  The expression for the Slater
+of two Slater 1\ *s* orbitals.  The expression for the Slater 1\ *s*
-1\ *s* orbital is given under equation (6) of the
+orbital is given under equation (6) of the :ref:`Streitz-Mintmire
-:ref:`Streitz-Mintmire <Streitz1>` paper.  Only the *chi*\ , *eta*\ , *zeta*\ , and
+<Streitz1>` paper.  Only the *chi*\ , *eta*\ , *zeta*\ , and *qcore*
-*qcore* parameters from the *qfile* file are used. When using the string
+parameters from the *qfile* file are used. When using the string
 *coul/streitz* as filename, these parameters are extracted directly from
-an active *coul/streitz* pair style.  This style solves
+an active *coul/streitz* pair style.  This style solves partial charges
-partial charges on atoms via the matrix inversion method.  A tolerance
+on atoms via the matrix inversion method.  A tolerance of 1.0e-6 is
-of 1.0e-6 is usually a good number.  Keyword *alpha* can be used to
+usually a good number.  Keyword *alpha* can be used to change the Slater
-change the Slater type orbital exponent.
+type orbital exponent.
 
 The *qeq/dynamic* style describes partial charges on atoms as point
-charges that interact through 1/r, but the extended Lagrangian method
+charges that interact through 1/r, but the extended Lagrangian method is
-is used to solve partial charges on atoms.  Only the *chi* and *eta*
+used to solve partial charges on atoms.  Only the *chi* and *eta*
 parameters from the *qfile* file are used.  Note that Coulomb
-catastrophe can occur if repulsion between the pair of charged
+catastrophe can occur if repulsion between the pair of charged particles
-particles is too weak.  A tolerance of 1.0e-3 is usually a good
+is too weak.  A tolerance of 1.0e-3 is usually a good number.  Keyword
-number.  Keyword *qdamp* can be used to change the damping factor, while
+*qdamp* can be used to change the damping factor, while keyword *qstep*
-keyword *qstep* can be used to change the time step size.
+can be used to change the time step size.
 
-The :ref:`\ *qeq/fire*\ <Shan>` style describes the same charge model and charge
+The :ref:`\ *qeq/fire*\ <Shan>` style describes the same charge model
-solver as the *qeq/dynamic* style, but employs a FIRE minimization
+and charge solver as the *qeq/dynamic* style, but employs a FIRE
-algorithm to solve for equilibrium charges.
+minimization algorithm to solve for equilibrium charges.  Keyword
-Keyword *qdamp* can be used to change the damping factor, while
+*qdamp* can be used to change the damping factor, while keyword *qstep*
-keyword *qstep* can be used to change the time step size.
+can be used to change the time step size.
 
 Note that *qeq/point*\ , *qeq/shielded*\ , and *qeq/slater* describe
 different charge models, whereas the matrix inversion method and the
 extended Lagrangian method (\ *qeq/dynamic* and *qeq/fire*\ ) are
 different solvers.
 
-Note that *qeq/point*\ , *qeq/dynamic* and *qeq/fire* styles all describe
+Note that *qeq/point*\ , *qeq/dynamic* and *qeq/fire* styles all
-charges as point charges that interact through 1/r relationship, but
+describe charges as point charges that interact through 1/r
-solve partial charges on atoms using different solvers.  These three
+relationship, but solve partial charges on atoms using different
-styles should yield comparable results if
+solvers.  These three styles should yield comparable results if the QEq
-the QEq parameters and *Nevery*\ , *cutoff*\ , and *tolerance* are the
+parameters and *Nevery*\ , *cutoff*\ , and *tolerance* are the same.
-same.  Style *qeq/point* is typically faster, *qeq/dynamic* scales
+Style *qeq/point* is typically faster, *qeq/dynamic* scales better on
-better on larger sizes, and *qeq/fire* is faster than *qeq/dynamic*\ .
+larger sizes, and *qeq/fire* is faster than *qeq/dynamic*\ .
 
 .. note::
 
@@ -200,9 +206,11 @@ better on larger sizes, and *qeq/fire* is faster than *qeq/dynamic*\ .
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about these fixes is written to :doc:`binary restart files <restart>`.  No global scalar or vector or per-atom
+No information about these fixes is written to :doc:`binary restart
-quantities are stored by these fixes for access by various :doc:`output commands <Howto_output>`.  No parameter of these fixes can be used
+files <restart>`.  No global scalar or vector or per-atom quantities are
-with the *start/stop* keywords of the :doc:`run <run>` command.
+stored by these fixes for access by various :doc:`output commands
+<Howto_output>`.  No parameter of these fixes can be used with the
+*start/stop* keywords of the :doc:`run <run>` command.
 
 Thexe fixes are invoked during :doc:`energy minimization <minimize>`.
 
@@ -210,7 +218,8 @@ Restrictions
 """"""""""""
 
 These fixes are part of the QEQ package.  They are only enabled if
-LAMMPS was built with that package.  See the :doc:`Build package <Build_package>` doc page for more info.
+LAMMPS was built with that package.  See the :doc:`Build package
+<Build_package>` doc page for more info.
 
 Related commands
 """"""""""""""""

lib/plumed/Install.py

@@ -17,7 +17,7 @@ parser = ArgumentParser(prog='Install.py',
 
 # settings
 
-version = "2.7.0"
+version = "2.7.1"
 mode = "static"
 
 # help message
@@ -47,9 +47,12 @@ checksums = { \
         '2.5.2' : 'bd2f18346c788eb54e1e52f4f6acf41a', \
         '2.5.3' : 'de30d6e7c2dcc0973298e24a6da24286', \
         '2.5.4' : 'f31b7d16a4be2e30aa7d5c19c3d37853', \
+        '2.5.7' : '1ca36226fdb8110b1009aa61d615d4e5', \
         '2.6.0' : '204d2edae58d9b10ba3ad460cad64191', \
         '2.6.1' : '89a9a450fc6025299fe16af235957163', \
+        '2.6.3' : 'a9f8028fd74528c2024781ea1fdefeee', \
         '2.7.0' : '95f29dd0c067577f11972ff90dfc7d12', \
+        '2.7.1' : '4eac6a462ec84dfe0cec96c82421b8e8', \
         }
 
 # parse and process arguments

python/install.py

@@ -10,7 +10,7 @@ build target in the conventional and CMake based build systems
 # copy LAMMPS shared library and lammps package to system dirs
 
 from __future__ import print_function
-import sys,os,shutil
+import sys,os,shutil,time
 from argparse import ArgumentParser
 
 parser = ArgumentParser(prog='install.py',
@@ -80,13 +80,15 @@ if args.dir:
 
   sys.exit()
 
-# extract version string from header
+# extract LAMMPS version string from header
+# and convert to python packaging compatible version
 def get_lammps_version(header):
     with open(header, 'r') as f:
         line = f.readline()
         start_pos = line.find('"')+1
         end_pos = line.find('"', start_pos)
-        return "".join(line[start_pos:end_pos].split())
+        t = time.strptime("".join(line[start_pos:end_pos].split()), "%d%b%Y")
+        return "{}.{}.{}".format(t.tm_year,t.tm_mon,t.tm_mday)
 
 verstr = get_lammps_version(args.version)
 

python/lammps/__init__.py

@@ -13,10 +13,16 @@ from .core import *
 from .data import *
 from .pylammps import *
 
-# convert module string version to numeric version
+# convert installed module string version to numeric version
 def get_version_number():
     import time
+    from os.path import join
     from sys import version_info
+
+    # must report 0 when inside LAMMPS source tree
+    if __file__.find(join('python', 'lammps', '__init__.py')) > 0:
+        return 0
+
     vstring = None
     if version_info.major == 3 and version_info.minor >= 8:
         from importlib.metadata import version
@@ -32,7 +38,7 @@ def get_version_number():
     if not vstring:
         return 0
 
-    t = time.strptime(vstring, "%d%b%Y")
+    t = time.strptime(vstring, "%Y.%m.%d")
     return t.tm_year*10000 + t.tm_mon*100 + t.tm_mday
 
 __version__ = get_version_number()

python/setup.py

@@ -1,7 +1,8 @@
 # this only installs the LAMMPS python package
 # it assumes the LAMMPS shared library is already installed
 from distutils.core import setup
-import os
+from sys import version_info
+import os,time
 
 LAMMPS_PYTHON_DIR = os.path.dirname(os.path.realpath(__file__))
 LAMMPS_DIR = os.path.dirname(LAMMPS_PYTHON_DIR)
@@ -12,7 +13,13 @@ def get_lammps_version():
         line = f.readline()
         start_pos = line.find('"')+1
         end_pos = line.find('"', start_pos)
-        return "".join(line[start_pos:end_pos].split())
+        t = time.strptime("".join(line[start_pos:end_pos].split()), "%d%b%Y")
+        return "{}.{}.{}".format(t.tm_year,t.tm_mon,t.tm_mday)
+
+if version_info.major >= 3:
+    pkgs = ['lammps', 'lammps.mliap']
+else:
+    pkgs = ['lammps']
 
 setup(
     name = "lammps",
@@ -22,5 +29,5 @@ setup(
     url = "https://lammps.sandia.gov",
     description = "LAMMPS Molecular Dynamics Python package",
     license = "GPL",
-    packages=["lammps","lammps.mliap"],
+    packages=pkgs,
 )

src/MANYBODY/fix_qeq_comb.cpp

@@ -17,21 +17,21 @@
 
 #include "fix_qeq_comb.h"
 
-#include <cmath>
-#include <cstring>
-#include "pair_comb.h"
-#include "pair_comb3.h"
-#include "neigh_list.h"
 #include "atom.h"
 #include "comm.h"
+#include "error.h"
 #include "force.h"
 #include "group.h"
+#include "memory.h"
+#include "neigh_list.h"
 #include "respa.h"
 #include "update.h"
-#include "memory.h"
-#include "error.h"
 
+#include <cmath>
+#include <cstring>
 
+#include "pair_comb.h"
+#include "pair_comb3.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
@@ -85,9 +85,6 @@ FixQEQComb::FixQEQComb(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
   int nlocal = atom->nlocal;
   for (int i = 0; i < nlocal; i++) qf[i] = 0.0;
 
-  comb = nullptr;
-  comb3 = nullptr;
-
   comm_forward = 1;
 }
 
@@ -119,8 +116,9 @@ void FixQEQComb::init()
   if (!atom->q_flag)
     error->all(FLERR,"Fix qeq/comb requires atom attribute q");
 
-  comb = (PairComb *) force->pair_match("^comb",0);
   comb3 = (PairComb3 *) force->pair_match("^comb3",0);
+  if (!comb3) comb = (PairComb *) force->pair_match("^comb",0);
+
   if (comb == nullptr && comb3 == nullptr)
     error->all(FLERR,"Must use pair_style comb or comb3 with fix qeq/comb");
 
@@ -207,11 +205,14 @@ void FixQEQComb::post_force(int /*vflag*/)
   if (comb) {
     inum = comb->list->inum;
     ilist = comb->list->ilist;
-  }
+  } else if (comb3) {
-  if (comb3) {
     inum = comb3->list->inum;
     ilist = comb3->list->ilist;
+  } else {
+    inum = 0;
+    ilist = nullptr;
   }
+
   for (ii = 0; ii < inum; ii++) {
     i = ilist[ii];
     q1[i] = q2[i] = qf[i] = 0.0;
@@ -227,8 +228,9 @@ void FixQEQComb::post_force(int /*vflag*/)
     }
 
     comm->forward_comm_fix(this);
+    enegtot = 0.0;
     if (comb) enegtot = comb->yasu_char(qf,igroup);
-    if (comb3) enegtot = comb3->combqeq(qf,igroup);
+    else if (comb3) enegtot = comb3->combqeq(qf,igroup);
 
     enegtot /= ngroup;
     enegchk = enegmax = 0.0;

src/MC/fix_charge_regulation.cpp

@@ -187,14 +187,7 @@ void FixChargeRegulation::init() {
     // neighbor list exclusion setup
     // turn off interactions between group all and the exclusion group
 
-    int narg = 4;
+    neighbor->modify_params(fmt::format("exclude group {} all",group_id));
-    char **arg = new char*[narg];;
-    arg[0] = (char *) "exclude";
-    arg[1] = (char *) "group";
-    arg[2] = (char *) group_id.c_str();
-    arg[3] = (char *) "all";
-    neighbor->modify_params(narg,arg);
-    delete [] arg;
   }
 
   // check that no deletable atoms are in atom->firstgroup
@@ -356,7 +349,7 @@ void FixChargeRegulation::forward_acid() {
 
   double energy_before = energy_stored;
   double factor;
-  double *dummyp = nullptr;
+  double dummyp[3];
   double pos[3];
   pos[0] = 0;
   pos[1] = 0;
@@ -415,7 +408,7 @@ void FixChargeRegulation::backward_acid() {
   double energy_before = energy_stored;
   double factor;
   int mask_tmp;
-  double *dummyp = nullptr;
+  double dummyp[3];
   double pos[3];
   pos[0] = 0;
   pos[1] = 0;
@@ -488,7 +481,7 @@ void FixChargeRegulation::forward_base() {
 
   double energy_before = energy_stored;
   double factor;
-  double *dummyp = nullptr;
+  double dummyp[3];
   double pos[3];
   pos[0] = 0;
   pos[1] = 0;
@@ -546,7 +539,7 @@ void FixChargeRegulation::backward_base() {
 
   double energy_before = energy_stored;
   double factor;
-  double *dummyp = nullptr;
+  double dummyp[3];
   int mask_tmp;
   double pos[3];
   pos[0] = 0;
@@ -619,7 +612,7 @@ void FixChargeRegulation::forward_ions() {
 
   double energy_before = energy_stored;
   double factor;
-  double *dummyp = nullptr;
+  double dummyp[3];
   int m1 = -1, m2 = -1;
   factor = volume_rx * volume_rx * c10pI_plus * c10pI_minus /
            ((1 + ncation) * (1 + nanion));
@@ -654,7 +647,7 @@ void FixChargeRegulation::backward_ions() {
   double energy_before = energy_stored;
   double factor;
   int mask1_tmp = 0, mask2_tmp = 0;
-  double *dummyp = nullptr;
+  double dummyp[3];
   int m1 = -1, m2 = -1;
 
   m1 = get_random_particle(cation_type, +1, 0, dummyp);
@@ -733,7 +726,7 @@ void FixChargeRegulation::forward_ions_multival() {
 
   double energy_before = energy_stored;
   double factor = 1;
-  double *dummyp = nullptr;
+  double dummyp[3];
   int mm[salt_charge_ratio + 1];// particle ID array for all ions to be inserted
 
   if (salt_charge[0] <= -salt_charge[1]) {
@@ -787,7 +780,7 @@ void FixChargeRegulation::backward_ions_multival() {
 
   double energy_before = energy_stored;
   double factor = 1;
-  double *dummyp = nullptr;  // dummy pointer
+  double dummyp[3];  // dummy particle
   int mm[salt_charge_ratio + 1];  // particle ID array for all deleted ions
   double qq[salt_charge_ratio + 1];  // charge array for all deleted ions
   int mask_tmp[salt_charge_ratio + 1];  // temporary mask array

src/MC/fix_gcmc.cpp

@@ -580,14 +580,7 @@ void FixGCMC::init()
     // neighbor list exclusion setup
     // turn off interactions between group all and the exclusion group
 
-    int narg = 4;
+    neighbor->modify_params(fmt::format("exclude group {} all",group_id));
-    char **arg = new char*[narg];;
-    arg[0] = (char *) "exclude";
-    arg[1] = (char *) "group";
-    arg[2] = (char *) group_id.c_str();
-    arg[3] = (char *) "all";
-    neighbor->modify_params(narg,arg);
-    delete [] arg;
   }
 
   // create a new group for temporary use with selected molecules

src/MC/fix_widom.cpp

@@ -342,14 +342,7 @@ void FixWidom::init()
     // neighbor list exclusion setup
     // turn off interactions between group all and the exclusion group
 
-    int narg = 4;
+    neighbor->modify_params(fmt::format("exclude group {} all",group_id));
-    char **arg = new char*[narg];;
-    arg[0] = (char *) "exclude";
-    arg[1] = (char *) "group";
-    arg[2] = (char *) group_id.c_str();
-    arg[3] = (char *) "all";
-    neighbor->modify_params(narg,arg);
-    delete [] arg;
   }
 
   // create a new group for temporary use with selected molecules

src/PYTHON/fix_python_invoke.cpp

@@ -93,7 +93,7 @@ void FixPythonInvoke::end_of_step()
 {
   PyUtils::GIL lock;
 
-  PyObject * result = PyObject_CallFunction((PyObject*)pFunc, "O", (PyObject*)lmpPtr);
+  PyObject * result = PyObject_CallFunction((PyObject*)pFunc, (char *)"O", (PyObject*)lmpPtr);
 
   if (!result) {
     PyUtils::Print_Errors();
@@ -110,8 +110,9 @@ void FixPythonInvoke::post_force(int vflag)
   if (update->ntimestep % nevery != 0) return;
 
   PyUtils::GIL lock;
+  char fmt[] = "Oi";
 
-  PyObject * result = PyObject_CallFunction((PyObject*)pFunc, "Oi", (PyObject*)lmpPtr, vflag);
+  PyObject * result = PyObject_CallFunction((PyObject*)pFunc, fmt, (PyObject*)lmpPtr, vflag);
 
   if (!result) {
     PyUtils::Print_Errors();

src/PYTHON/fix_python_move.cpp

@@ -75,7 +75,7 @@ FixPythonMove::FixPythonMove(LAMMPS *lmp, int narg, char **arg) :
   }
 
   PyObject *ptr = PY_VOID_POINTER(lmp);
-  PyObject *py_move_obj = PyObject_CallFunction(py_move_type, "O", ptr);
+  PyObject *py_move_obj = PyObject_CallFunction(py_move_type, (char *)"O", ptr);
   Py_CLEAR(ptr);
 
   if (!py_move_obj) {
@@ -112,7 +112,7 @@ int FixPythonMove::setmask()
 void FixPythonMove::init()
 {
   PyUtils::GIL lock;
-  PyObject * result = PyObject_CallMethod((PyObject *)py_move, "init", nullptr);
+  PyObject * result = PyObject_CallMethod((PyObject *)py_move, (char *)"init", nullptr);
 
   if (!result) {
     PyUtils::Print_Errors();
@@ -126,7 +126,7 @@ void FixPythonMove::init()
 void FixPythonMove::initial_integrate(int vflag)
 {
   PyUtils::GIL lock;
-  PyObject * result = PyObject_CallMethod((PyObject*)py_move, "initial_integrate", "i", vflag);
+  PyObject * result = PyObject_CallMethod((PyObject*)py_move, (char *)"initial_integrate", (char *)"i", vflag);
 
   if (!result) {
     PyUtils::Print_Errors();
@@ -140,7 +140,7 @@ void FixPythonMove::initial_integrate(int vflag)
 void FixPythonMove::final_integrate()
 {
   PyUtils::GIL lock;
-  PyObject * result = PyObject_CallMethod((PyObject*)py_move, "final_integrate", nullptr);
+  PyObject * result = PyObject_CallMethod((PyObject*)py_move, (char *)"final_integrate", nullptr);
 
   if (!result) {
     PyUtils::Print_Errors();
@@ -154,7 +154,7 @@ void FixPythonMove::final_integrate()
 void FixPythonMove::initial_integrate_respa(int vflag, int ilevel, int iloop)
 {
   PyUtils::GIL lock;
-  PyObject * result = PyObject_CallMethod((PyObject*)py_move, "initial_integrate_respa", "iii", vflag, ilevel, iloop);
+  PyObject * result = PyObject_CallMethod((PyObject*)py_move, (char *)"initial_integrate_respa", (char *)"iii", vflag, ilevel, iloop);
 
   if (!result) {
     PyUtils::Print_Errors();
@@ -168,7 +168,7 @@ void FixPythonMove::initial_integrate_respa(int vflag, int ilevel, int iloop)
 void FixPythonMove::final_integrate_respa(int ilevel, int iloop)
 {
   PyUtils::GIL lock;
-  PyObject * result = PyObject_CallMethod((PyObject*)py_move, "final_integrate_respa", "ii", ilevel, iloop);
+  PyObject * result = PyObject_CallMethod((PyObject*)py_move, (char *)"final_integrate_respa", (char *)"ii", ilevel, iloop);
 
   if (!result) {
     PyUtils::Print_Errors();
@@ -182,7 +182,7 @@ void FixPythonMove::final_integrate_respa(int ilevel, int iloop)
 void FixPythonMove::reset_dt()
 {
   PyUtils::GIL lock;
-  PyObject * result = PyObject_CallMethod((PyObject*)py_move, "reset_dt", nullptr);
+  PyObject * result = PyObject_CallMethod((PyObject*)py_move, (char *)"reset_dt", nullptr);
 
   if (!result) {
     PyUtils::Print_Errors();

src/PYTHON/pair_python.cpp

@@ -288,7 +288,7 @@ void PairPython::coeff(int narg, char **arg)
 
   py_potential = (void *) py_pair_instance;
 
-  PyObject *py_value = PyObject_CallMethod(py_pair_instance, "check_units", "s", update->unit_style);
+  PyObject *py_value = PyObject_CallMethod(py_pair_instance, (char *)"check_units", (char *)"s", update->unit_style);
   if (!py_value) {
     PyUtils::Print_Errors();
     error->all(FLERR,"Calling 'check_units' function failed");
@@ -306,7 +306,7 @@ void PairPython::coeff(int narg, char **arg)
     } else skip_types[i] = 0;
     const int type = i;
     const char * name = arg[2+i];
-    py_value = PyObject_CallMethod(py_pair_instance, "map_coeff", "si", name, type);
+    py_value = PyObject_CallMethod(py_pair_instance, (char *)"map_coeff", (char *)"si", name, type);
     if (!py_value) {
       PyUtils::Print_Errors();
       error->all(FLERR,"Calling 'map_coeff' function failed");

src/QEQ/fix_qeq.cpp

@@ -18,16 +18,16 @@
 
 #include "fix_qeq.h"
 
-#include <cmath>
-#include <cstring>
 #include "atom.h"
 #include "comm.h"
-#include "neigh_list.h"
+#include "error.h"
-#include "update.h"
 #include "force.h"
 #include "memory.h"
-#include "error.h"
+#include "neigh_list.h"
+#include "update.h"
 
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
@@ -386,13 +386,11 @@ int FixQEq::CG( double *b, double *x )
     vector_sum( d, 1., p, beta, d, inum );
   }
 
-  if (loop >= maxiter && comm->me == 0) {
+  if ((comm->me == 0) && (loop >= maxiter))
-    char str[128];
+    error->warning(FLERR,fmt::format("Fix qeq CG convergence failed ({}) "
-    sprintf(str,"Fix qeq CG convergence failed (%g) after %d iterations "
+                                     "after {} iterations at step {}",
-            "at " BIGINT_FORMAT " step",sqrt(sig_new)/b_norm,loop,update->ntimestep);
+                                     sqrt(sig_new)/b_norm,loop,
-    error->warning(FLERR,str);
+                                     update->ntimestep));
-  }
-
   return loop;
 }
 
@@ -708,11 +706,9 @@ void FixQEq::read_file(char *file)
   FILE *fp;
   if (comm->me == 0) {
     fp = utils::open_potential(file,lmp,nullptr);
-    if (fp == nullptr) {
+    if (fp == nullptr)
-      char str[128];
+      error->one(FLERR,fmt::format("Cannot open fix qeq parameter file {}: {}",
-      snprintf(str,128,"Cannot open fix qeq parameter file %s",file);
+                                   file,utils::getsyserror()));
-      error->one(FLERR,str);
-    }
   }
 
   // read each line out of file, skipping blank lines or leading '#'

src/QEQ/fix_qeq_dynamic.cpp

@@ -17,20 +17,20 @@
 
 #include "fix_qeq_dynamic.h"
 
-#include <cmath>
-
-#include <cstring>
 #include "atom.h"
 #include "comm.h"
-#include "neighbor.h"
+#include "error.h"
-#include "neigh_list.h"
-#include "neigh_request.h"
-#include "update.h"
 #include "force.h"
 #include "group.h"
 #include "kspace.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "respa.h"
-#include "error.h"
+#include "update.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 
@@ -154,14 +154,9 @@ void FixQEqDynamic::pre_force(int /*vflag*/)
     }
   }
 
-  if (comm->me == 0) {
+  if ((comm->me == 0) && (iloop >= maxiter))
-    if (iloop == maxiter) {
+      error->warning(FLERR,fmt::format("Charges did not converge at step "
-      char str[128];
+                                       "{}: {}",update->ntimestep,enegchk));
-      sprintf(str,"Charges did not converge at step " BIGINT_FORMAT
-                  ": %lg",update->ntimestep,enegchk);
-      error->warning(FLERR,str);
-    }
-  }
 
   if (force->kspace) force->kspace->qsum_qsq();
 }

src/QEQ/fix_qeq_fire.cpp

@@ -17,22 +17,22 @@
 
 #include "fix_qeq_fire.h"
 
-#include <cmath>
-
-#include <cstring>
 #include "atom.h"
 #include "comm.h"
-#include "neighbor.h"
+#include "error.h"
-#include "neigh_list.h"
-#include "neigh_request.h"
-#include "update.h"
 #include "force.h"
 #include "group.h"
+#include "kspace.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
 #include "pair_comb.h"
 #include "pair_comb3.h"
-#include "kspace.h"
 #include "respa.h"
-#include "error.h"
+#include "update.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
@@ -47,7 +47,7 @@ using namespace FixConst;
 /* ---------------------------------------------------------------------- */
 
 FixQEqFire::FixQEqFire(LAMMPS *lmp, int narg, char **arg) :
-  FixQEq(lmp, narg, arg)
+  FixQEq(lmp, narg, arg), comb(nullptr), comb3(nullptr)
 {
   qdamp = 0.20;
   qstep = 0.20;
@@ -65,9 +65,6 @@ FixQEqFire::FixQEqFire(LAMMPS *lmp, int narg, char **arg) :
       iarg += 2;
     } else error->all(FLERR,"Illegal fix qeq/fire command");
   }
-
-  comb = nullptr;
-  comb3 = nullptr;
 }
 
 /* ---------------------------------------------------------------------- */
@@ -94,9 +91,8 @@ void FixQEqFire::init()
   if (utils::strmatch(update->integrate_style,"^respa"))
     nlevels_respa = ((Respa *) update->integrate)->nlevels;
 
-  comb = (PairComb *) force->pair_match("comb",1);
+  comb3 = (PairComb3 *) force->pair_match("^comb3",0);
-  comb3 = (PairComb3 *) force->pair_match("comb3",1);
+  if (!comb3) comb = (PairComb *) force->pair_match("^comb",0);
-
 }
 
 /* ---------------------------------------------------------------------- */
@@ -218,14 +214,9 @@ void FixQEqFire::pre_force(int /*vflag*/)
     if (enegchk < tolerance) break;
   }
 
-  if (comm->me == 0) {
+  if ((comm->me == 0) && (iloop >= maxiter))
-    if (iloop == maxiter) {
+    error->warning(FLERR,fmt::format("Charges did not converge at step "
-      char str[128];
+                                     "{}: {}",update->ntimestep,enegchk));
-      sprintf(str,"Charges did not converge at step " BIGINT_FORMAT
-                  ": %lg",update->ntimestep,enegchk);
-      error->warning(FLERR,str);
-    }
-  }
 
   if (force->kspace) force->kspace->qsum_qsq();
 }

src/QEQ/fix_qeq_point.cpp

@@ -16,20 +16,22 @@
 ------------------------------------------------------------------------- */
 
 #include "fix_qeq_point.h"
-#include <cmath>
+
-#include <cstring>
 #include "atom.h"
 #include "comm.h"
-#include "neighbor.h"
+#include "error.h"
-#include "neigh_list.h"
-#include "neigh_request.h"
-#include "update.h"
 #include "force.h"
 #include "group.h"
 #include "kspace.h"
-#include "respa.h"
 #include "memory.h"
-#include "error.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
+#include "respa.h"
+#include "update.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 
@@ -158,13 +160,9 @@ void FixQEqPoint::compute_H()
     }
   }
 
-  if (m_fill >= H.m) {
+  if (m_fill >= H.m)
-    char str[128];
+    error->all(FLERR,fmt::format("Fix qeq/point has insufficient H matrix "
-    sprintf(str,"H matrix size has been exceeded: m_fill=%d H.m=%d\n",
+                                 "size: m_fill={} H.m={}\n",m_fill, H.m));
-             m_fill, H.m );
-    error->warning(FLERR,str);
-    error->all(FLERR,"Fix qeq/point has insufficient QEq matrix size");
-  }
 }
 
 /* ---------------------------------------------------------------------- */

src/QEQ/fix_qeq_shielded.cpp

@@ -16,21 +16,23 @@
 ------------------------------------------------------------------------- */
 
 #include "fix_qeq_shielded.h"
-#include <cmath>
+
-#include <cstring>
 #include "atom.h"
 #include "comm.h"
-#include "neighbor.h"
+#include "error.h"
-#include "neigh_list.h"
-#include "neigh_request.h"
-#include "update.h"
 #include "force.h"
 #include "group.h"
-#include "pair.h"
 #include "kspace.h"
-#include "respa.h"
 #include "memory.h"
-#include "error.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
+#include "pair.h"
+#include "respa.h"
+#include "update.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 
@@ -223,13 +225,9 @@ void FixQEqShielded::compute_H()
     }
   }
 
-  if (m_fill >= H.m) {
+  if (m_fill >= H.m)
-    char str[128];
+    error->all(FLERR,fmt::format("Fix qeq/shielded has insufficient H matrix "
-    sprintf(str,"H matrix size has been exceeded: m_fill=%d H.m=%d\n",
+                                 "size: m_fill={} H.m={}\n",m_fill,H.m));
-             m_fill, H.m );
-    error->warning(FLERR,str);
-    error->all(FLERR,"Fix qeq/shielded has insufficient QEq matrix size");
-  }
 }
 
 /* ---------------------------------------------------------------------- */
@@ -247,7 +245,7 @@ double FixQEqShielded::calculate_H( double r, double gamma )
   Taper = Taper * r + Tap[0];
 
   denom = r * r * r + gamma;
-  denom = pow(denom,0.3333333333333);
+  denom = pow(denom,1.0/3.0);
 
   return Taper * EV_TO_KCAL_PER_MOL / denom;
 }

src/QEQ/fix_qeq_slater.cpp

@@ -16,22 +16,23 @@
 ------------------------------------------------------------------------- */
 
 #include "fix_qeq_slater.h"
-#include <cmath>
 
-#include <cstring>
 #include "atom.h"
 #include "comm.h"
-#include "neighbor.h"
+#include "error.h"
-#include "neigh_list.h"
-#include "neigh_request.h"
-#include "update.h"
 #include "force.h"
 #include "group.h"
-#include "pair.h"
 #include "kspace.h"
-#include "respa.h"
 #include "math_const.h"
-#include "error.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
+#include "pair.h"
+#include "respa.h"
+#include "update.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace MathConst;
@@ -207,14 +208,9 @@ void FixQEqSlater::compute_H()
     chizj[i] = zjtmp;
   }
 
-  if (m_fill >= H.m) {
+  if (m_fill >= H.m)
-    char str[128];
+    error->all(FLERR,fmt::format(FLERR,"Fix qeq/slater has insufficient H "
-    sprintf(str,"H matrix size has been exceeded: m_fill=%d H.m=%d\n",
+                                 "matrix size:m_fill={} H.m={}\n",m_fill,H.m));
-             m_fill, H.m );
-    error->warning(FLERR,str);
-    error->all(FLERR,"Fix qeq/slater has insufficient QEq matrix size");
-  }
-
 }
 
 /* ---------------------------------------------------------------------- */

src/USER-COLVARS/ndx_group.h

@@ -31,6 +31,7 @@ class Ndx2Group : public Command {
  public:
   Ndx2Group(class LAMMPS *lmp) : Command(lmp) {};
   void command(int, char **);
+ private:
   void create(const std::string &, const std::vector<tagint> &);
 };
 

src/USER-MISC/fix_srp.cpp

@@ -128,20 +128,10 @@ void FixSRP::init()
   // bond particles do not interact with other types
   // type bptype only interacts with itself
 
-  char* arg1[4];
-  arg1[0] = (char *) "exclude";
-  arg1[1] = (char *) "type";
-  char c0[20];
-  char c1[20];
-
   for (int z = 1; z < atom->ntypes; z++) {
     if (z == bptype)
       continue;
-    sprintf(c0, "%d", z);
+    neighbor->modify_params(fmt::format("exclude type {} {}",z,bptype));
-    arg1[2] = c0;
-    sprintf(c1, "%d", bptype);
-    arg1[3] = c1;
-    neighbor->modify_params(4, arg1);
   }
 }
 

src/body.cpp

@@ -12,7 +12,6 @@
 ------------------------------------------------------------------------- */
 
 #include "body.h"
-#include <cstring>
 
 using namespace LAMMPS_NS;
 

src/compute.cpp

@@ -22,7 +22,6 @@
 #include "modify.h"
 
 #include <cstring>
-#include <cctype>
 
 using namespace LAMMPS_NS;
 

src/compute_chunk_spread_atom.cpp

@@ -23,6 +23,8 @@
 #include "modify.h"
 #include "update.h"
 
+#include <cstring>
+
 using namespace LAMMPS_NS;
 
 /* ---------------------------------------------------------------------- */

src/compute_reduce.cpp

@@ -25,6 +25,8 @@
 #include "update.h"
 #include "variable.h"
 
+#include <cstring>
+
 using namespace LAMMPS_NS;
 
 #define BIG 1.0e20

src/compute_temp_region.cpp

@@ -13,15 +13,14 @@
 
 #include "compute_temp_region.h"
 
-#include <cstring>
 #include "atom.h"
-#include "update.h"
-#include "force.h"
 #include "domain.h"
-#include "region.h"
+#include "error.h"
+#include "force.h"
 #include "group.h"
 #include "memory.h"
-#include "error.h"
+#include "region.h"
+#include "update.h"
 
 using namespace LAMMPS_NS;
 

src/fix.cpp

@@ -21,7 +21,6 @@
 #include "memory.h"
 
 #include <cstring>
-#include <cctype>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/fix_controller.cpp

@@ -21,8 +21,6 @@
 #include "update.h"
 #include "variable.h"
 
-#include <cstring>
-
 using namespace LAMMPS_NS;
 using namespace FixConst;
 

src/fix_enforce2d.cpp

@@ -12,14 +12,13 @@
 ------------------------------------------------------------------------- */
 
 #include "fix_enforce2d.h"
-#include <cstring>
+
 #include "atom.h"
-#include "update.h"
 #include "domain.h"
+#include "error.h"
 #include "modify.h"
 #include "respa.h"
-#include "error.h"
+#include "update.h"
-
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/fix_lineforce.cpp

@@ -19,7 +19,6 @@
 #include "update.h"
 
 #include <cmath>
-#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/fix_nph_sphere.cpp

@@ -16,8 +16,6 @@
 #include "error.h"
 #include "modify.h"
 
-#include <cstring>
-
 using namespace LAMMPS_NS;
 using namespace FixConst;
 

src/fix_npt_sphere.cpp

@@ -16,8 +16,6 @@
 #include "error.h"
 #include "modify.h"
 
-#include <cstring>
-
 using namespace LAMMPS_NS;
 using namespace FixConst;
 

src/fix_nve_limit.cpp

@@ -13,16 +13,15 @@
 
 #include "fix_nve_limit.h"
 
-#include <cmath>
-#include <cstring>
 #include "atom.h"
-#include "force.h"
-#include "update.h"
-#include "respa.h"
-#include "modify.h"
 #include "comm.h"
 #include "error.h"
+#include "force.h"
+#include "modify.h"
+#include "respa.h"
+#include "update.h"
 
+#include <cmath>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/fix_nve_noforce.cpp

@@ -12,11 +12,11 @@
 ------------------------------------------------------------------------- */
 
 #include "fix_nve_noforce.h"
-#include <cstring>
+
 #include "atom.h"
-#include "update.h"
-#include "respa.h"
 #include "error.h"
+#include "respa.h"
+#include "update.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/fix_planeforce.cpp

@@ -19,7 +19,6 @@
 #include "update.h"
 
 #include <cmath>
-#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/fix_store_force.cpp

@@ -12,12 +12,12 @@
 ------------------------------------------------------------------------- */
 
 #include "fix_store_force.h"
-#include <cstring>
+
 #include "atom.h"
-#include "update.h"
-#include "respa.h"
-#include "memory.h"
 #include "error.h"
+#include "memory.h"
+#include "respa.h"
+#include "update.h"
 
 using namespace LAMMPS_NS;
 using namespace FixConst;

src/fix_vector.cpp

@@ -22,8 +22,6 @@
 #include "update.h"
 #include "variable.h"
 
-#include <cstring>
-
 using namespace LAMMPS_NS;
 using namespace FixConst;
 

src/group.cpp

@@ -35,7 +35,6 @@
 #include <cstring>
 #include <map>
 #include <utility>
-#include <vector>
 
 using namespace LAMMPS_NS;
 

src/imbalance_store.cpp

@@ -16,8 +16,6 @@
 #include "atom.h"
 #include "error.h"
 
-#include <cstring>
-
 using namespace LAMMPS_NS;
 
 /* -------------------------------------------------------------------- */

src/imbalance_var.cpp

@@ -20,8 +20,6 @@
 #include "memory.h"
 #include "variable.h"
 
-#include <cstring>
-
 using namespace LAMMPS_NS;
 
 /* -------------------------------------------------------------------- */

src/info.cpp

@@ -39,7 +39,6 @@
 #include "pair.h"
 #include "pair_hybrid.h"
 #include "region.h"
-#include "universe.h"
 #include "update.h"
 #include "variable.h"
 

src/library.cpp

@@ -31,7 +31,6 @@
 #include "group.h"
 #include "info.h"
 #include "input.h"
-#include "integrate.h"
 #include "memory.h"
 #include "modify.h"
 #include "molecule.h"

src/math_eigen.cpp

@@ -19,6 +19,8 @@
 #include "math_eigen_impl.h"
 
 #include <array>
+#include <utility>
+#include <vector>
 
 using std::vector;
 using std::array;

src/math_special.cpp

@@ -4,8 +4,6 @@
 #include <cstdint> // IWYU pragma: keep
 #include <limits>
 
-#include "error.h"
-
 using namespace LAMMPS_NS;
 
 static constexpr int nmaxfactorial = 167;

src/my_pool_chunk.cpp

@@ -14,7 +14,6 @@
 #include "my_pool_chunk.h"
 
 #include <cstdlib>
-#include <cstdio>
 
 #if defined(LMP_USER_INTEL) && !defined(LAMMPS_MEMALIGN) && !defined(_WIN32)
 #define LAMMPS_MEMALIGN 64

src/neighbor.cpp

@@ -2356,6 +2356,22 @@ void Neighbor::modify_params(int narg, char **arg)
   }
 }
 
+/* ----------------------------------------------------------------------
+   convenience function to allow modifying parameters from a single string
+------------------------------------------------------------------------- */
+
+void Neighbor::modify_params(const std::string &modcmd)
+{
+  auto args = utils::split_words(modcmd);
+  char **newarg = new char*[args.size()];
+  int i=0;
+  for (const auto &arg : args) {
+    newarg[i++] = (char *)arg.c_str();
+  }
+  modify_params(args.size(),newarg);
+  delete[] newarg;
+}
+
 /* ----------------------------------------------------------------------
    remove the first group-group exclusion matching group1, group2
 ------------------------------------------------------------------------- */

src/neighbor.h

@@ -118,6 +118,7 @@ class Neighbor : protected Pointers {
   void set(int, char **);           // set neighbor style and skin distance
   void reset_timestep(bigint);      // reset of timestep counter
   void modify_params(int, char**);  // modify params that control builds
+  void modify_params(const std::string &); // convenience overload
 
   void exclusion_group_group_delete(int, int);  // rm a group-group exclusion
   int exclude_setting();            // return exclude value to accelerator pkg

src/npair_full_bin_atomonly.cpp

@@ -12,11 +12,11 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_full_bin_atomonly.h"
-#include "neigh_list.h"
+
 #include "atom.h"
-#include "atom_vec.h"
-#include "my_page.h"
 #include "error.h"
+#include "my_page.h"
+#include "neigh_list.h"
 
 using namespace LAMMPS_NS;
 

src/npair_half_bin_atomonly_newton.cpp

@@ -12,11 +12,11 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_half_bin_atomonly_newton.h"
-#include "neigh_list.h"
+
 #include "atom.h"
-#include "atom_vec.h"
-#include "my_page.h"
 #include "error.h"
+#include "my_page.h"
+#include "neigh_list.h"
 
 using namespace LAMMPS_NS;
 

src/npair_half_size_bin_newtoff.cpp

@@ -12,11 +12,11 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_half_size_bin_newtoff.h"
-#include "neigh_list.h"
+
 #include "atom.h"
-#include "atom_vec.h"
-#include "my_page.h"
 #include "error.h"
+#include "my_page.h"
+#include "neigh_list.h"
 
 using namespace LAMMPS_NS;
 

src/npair_half_size_bin_newton.cpp

@@ -12,11 +12,11 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_half_size_bin_newton.h"
-#include "neigh_list.h"
+
 #include "atom.h"
-#include "atom_vec.h"
-#include "my_page.h"
 #include "error.h"
+#include "my_page.h"
+#include "neigh_list.h"
 
 using namespace LAMMPS_NS;
 

src/npair_half_size_bin_newton_tri.cpp

@@ -12,11 +12,11 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_half_size_bin_newton_tri.h"
-#include "neigh_list.h"
+
 #include "atom.h"
-#include "atom_vec.h"
-#include "my_page.h"
 #include "error.h"
+#include "my_page.h"
+#include "neigh_list.h"
 
 using namespace LAMMPS_NS;
 

src/npair_half_size_multi_newtoff.cpp

@@ -12,11 +12,11 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_half_size_multi_newtoff.h"
-#include "neigh_list.h"
+
 #include "atom.h"
-#include "atom_vec.h"
-#include "my_page.h"
 #include "error.h"
+#include "my_page.h"
+#include "neigh_list.h"
 
 using namespace LAMMPS_NS;
 

src/npair_half_size_multi_newton.cpp

@@ -12,11 +12,11 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_half_size_multi_newton.h"
-#include "neigh_list.h"
+
 #include "atom.h"
-#include "atom_vec.h"
-#include "my_page.h"
 #include "error.h"
+#include "my_page.h"
+#include "neigh_list.h"
 
 using namespace LAMMPS_NS;
 

src/npair_half_size_multi_newton_tri.cpp

@@ -12,11 +12,11 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_half_size_multi_newton_tri.h"
-#include "neigh_list.h"
+
 #include "atom.h"
-#include "atom_vec.h"
-#include "my_page.h"
 #include "error.h"
+#include "my_page.h"
+#include "neigh_list.h"
 
 using namespace LAMMPS_NS;
 

src/npair_half_size_nsq_newtoff.cpp

@@ -12,12 +12,12 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_half_size_nsq_newtoff.h"
-#include "neigh_list.h"
+
 #include "atom.h"
-#include "atom_vec.h"
+#include "error.h"
 #include "group.h"
 #include "my_page.h"
-#include "error.h"
+#include "neigh_list.h"
 
 using namespace LAMMPS_NS;
 

src/npair_half_size_nsq_newton.cpp

@@ -12,12 +12,12 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_half_size_nsq_newton.h"
-#include "neigh_list.h"
+
 #include "atom.h"
-#include "atom_vec.h"
+#include "error.h"
 #include "group.h"
 #include "my_page.h"
-#include "error.h"
+#include "neigh_list.h"
 
 using namespace LAMMPS_NS;
 

src/npair_halffull_newtoff.cpp

@@ -12,10 +12,10 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_halffull_newtoff.h"
-#include "neigh_list.h"
+
-#include "atom_vec.h"
-#include "my_page.h"
 #include "error.h"
+#include "my_page.h"
+#include "neigh_list.h"
 
 using namespace LAMMPS_NS;
 

src/npair_halffull_newton.cpp

@@ -12,11 +12,11 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_halffull_newton.h"
-#include "neigh_list.h"
+
 #include "atom.h"
-#include "atom_vec.h"
-#include "my_page.h"
 #include "error.h"
+#include "my_page.h"
+#include "neigh_list.h"
 
 using namespace LAMMPS_NS;
 

src/npair_skip.cpp

@@ -12,11 +12,11 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_skip.h"
-#include "neigh_list.h"
+
 #include "atom.h"
-#include "atom_vec.h"
-#include "my_page.h"
 #include "error.h"
+#include "my_page.h"
+#include "neigh_list.h"
 
 using namespace LAMMPS_NS;
 

src/npair_skip_respa.cpp

@@ -12,11 +12,11 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_skip_respa.h"
-#include "neigh_list.h"
+
 #include "atom.h"
-#include "atom_vec.h"
-#include "my_page.h"
 #include "error.h"
+#include "my_page.h"
+#include "neigh_list.h"
 
 using namespace LAMMPS_NS;
 

src/npair_skip_size.cpp

@@ -12,11 +12,11 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_skip_size.h"
-#include "neigh_list.h"
+
 #include "atom.h"
-#include "atom_vec.h"
-#include "my_page.h"
 #include "error.h"
+#include "my_page.h"
+#include "neigh_list.h"
 
 using namespace LAMMPS_NS;
 

src/npair_skip_size_off2on.cpp

@@ -12,11 +12,11 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_skip_size_off2on.h"
-#include "neigh_list.h"
+
 #include "atom.h"
-#include "atom_vec.h"
-#include "my_page.h"
 #include "error.h"
+#include "my_page.h"
+#include "neigh_list.h"
 
 using namespace LAMMPS_NS;
 

src/npair_skip_size_off2on_oneside.cpp

@@ -12,12 +12,12 @@
 ------------------------------------------------------------------------- */
 
 #include "npair_skip_size_off2on_oneside.h"
-#include "neigh_list.h"
+
 #include "atom.h"
-#include "atom_vec.h"
 #include "domain.h"
-#include "my_page.h"
 #include "error.h"
+#include "my_page.h"
+#include "neigh_list.h"
 
 using namespace LAMMPS_NS;
 

src/output.cpp

@@ -14,18 +14,15 @@
 #include "output.h"
 #include "style_dump.h"         // IWYU pragma: keep
 
-#include "atom.h"
 #include "comm.h"
 #include "domain.h"
 #include "dump.h"
 #include "error.h"
-#include "force.h"
 #include "group.h"
 #include "info.h"
 #include "input.h"
 #include "memory.h"
 #include "modify.h"
-#include "neighbor.h"
 #include "thermo.h"
 #include "update.h"
 #include "variable.h"

src/pair_hybrid_scaled.cpp

@@ -396,6 +396,9 @@ double PairHybridScaled::single(int i, int j, int itype, int jtype, double rsq,
     double *vals = new double[nvars];
     for (i = 0; i < nvars; ++i) {
       j = input->variable->find(scalevars[i].c_str());
+      if (j < 0)
+        error->all(FLERR,fmt::format("Variable '{}' not found when updating "
+                                     "scale factors",scalevars[i]));
       vals[i] = input->variable->compute_equal(j);
     }
     for (i = 0; i < nstyles; ++i) {
@@ -457,8 +460,6 @@ void PairHybridScaled::coeff(int narg, char **arg)
       if (multiple[m]) {
         multflag = 1;
         if (narg < 4) error->all(FLERR,"Incorrect args for pair coefficients");
-        if (!isdigit(arg[3][0]))
-          error->all(FLERR,"Incorrect args for pair coefficients");
         int index = utils::inumeric(FLERR,arg[3],false,lmp);
         if (index == multiple[m]) break;
         else continue;

src/pair_lj96_cut.cpp

@@ -17,20 +17,19 @@
 
 #include "pair_lj96_cut.h"
 
-#include <cmath>
-#include <cstring>
 #include "atom.h"
 #include "comm.h"
+#include "error.h"
 #include "force.h"
-#include "neighbor.h"
-#include "neigh_list.h"
-#include "neigh_request.h"
-#include "update.h"
-#include "respa.h"
 #include "math_const.h"
 #include "memory.h"
-#include "error.h"
+#include "neigh_list.h"
+#include "neigh_request.h"
+#include "neighbor.h"
+#include "respa.h"
+#include "update.h"
 
+#include <cmath>
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/pair_lj_relres.cpp

@@ -26,7 +26,6 @@
 #include "memory.h"
 
 #include <cmath>
-#include <cstdlib>
 
 using namespace LAMMPS_NS;
 
@@ -608,18 +607,18 @@ void PairLJRelRes::read_restart(FILE *fp)
   int me = comm->me;
   for (i = 1; i <= atom->ntypes; i++)
     for (j = i; j <= atom->ntypes; j++) {
-      if (me == 0) fread(&setflag[i][j],sizeof(int),1,fp);
+      if (me == 0) utils::sfread(FLERR,&setflag[i][j],sizeof(int),1,fp,nullptr,error);
       MPI_Bcast(&setflag[i][j],1,MPI_INT,0,world);
       if (setflag[i][j]) {
         if (me == 0) {
-          fread(&epsilonf[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilonf[i][j],sizeof(double),1,fp,nullptr,error);
-          fread(&sigmaf[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&sigmaf[i][j],sizeof(double),1,fp,nullptr,error);
-          fread(&epsilon[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&epsilon[i][j],sizeof(double),1,fp,nullptr,error);
-          fread(&sigma[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&sigma[i][j],sizeof(double),1,fp,nullptr,error);
-          fread(&cutf_inner[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&cutf_inner[i][j],sizeof(double),1,fp,nullptr,error);
-          fread(&cutf[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&cutf[i][j],sizeof(double),1,fp,nullptr,error);
-          fread(&cut_inner[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&cut_inner[i][j],sizeof(double),1,fp,nullptr,error);
-          fread(&cut[i][j],sizeof(double),1,fp);
+          utils::sfread(FLERR,&cut[i][j],sizeof(double),1,fp,nullptr,error);
         }
         MPI_Bcast(&epsilonf[i][j],1,MPI_DOUBLE,0,world);
         MPI_Bcast(&sigmaf[i][j],1,MPI_DOUBLE,0,world);
@@ -655,12 +654,12 @@ void PairLJRelRes::read_restart_settings(FILE *fp)
 {
   int me = comm->me;
   if (me == 0) {
-    fread(&cutf_inner_global,sizeof(double),1,fp);
+    utils::sfread(FLERR,&cutf_inner_global,sizeof(double),1,fp,nullptr,error);
-    fread(&cutf_global,sizeof(double),1,fp);
+    utils::sfread(FLERR,&cutf_global,sizeof(double),1,fp,nullptr,error);
-    fread(&cut_inner_global,sizeof(double),1,fp);
+    utils::sfread(FLERR,&cut_inner_global,sizeof(double),1,fp,nullptr,error);
-    fread(&cut_global,sizeof(double),1,fp);
+    utils::sfread(FLERR,&cut_global,sizeof(double),1,fp,nullptr,error);
-    fread(&offset_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&offset_flag,sizeof(int),1,fp,nullptr,error);
-    fread(&mix_flag,sizeof(int),1,fp);
+    utils::sfread(FLERR,&mix_flag,sizeof(int),1,fp,nullptr,error);
   }
   MPI_Bcast(&cutf_inner_global,1,MPI_DOUBLE,0,world);
   MPI_Bcast(&cutf_global,1,MPI_DOUBLE,0,world);

src/pair_morse.cpp

@@ -13,14 +13,15 @@
 
 #include "pair_morse.h"
 
-#include <cmath>
-#include <cstring>
 #include "atom.h"
 #include "comm.h"
-#include "force.h"
-#include "neigh_list.h"
-#include "memory.h"
 #include "error.h"
+#include "force.h"
+#include "memory.h"
+#include "neigh_list.h"
+
+#include <cmath>
+#include <cstring>
 
 using namespace LAMMPS_NS;
 

src/potential_file_reader.cpp

@@ -62,7 +62,8 @@ PotentialFileReader::PotentialFileReader(LAMMPS *lmp,
   try {
     reader = open_potential(filename);
     if (!reader) {
-      error->one(FLERR, fmt::format("cannot open {} potential file {}", potential_name, filename));
+      error->one(FLERR, fmt::format("cannot open {} potential file {}: {}",
+                                    potential_name, filename, utils::getsyserror()));
     }
   } catch (FileReaderException &e) {
     error->one(FLERR, e.what());

src/read_restart.cpp

@@ -1195,7 +1195,7 @@ void ReadRestart::check_eof_magic()
   if (me == 0) {
     long curpos = ftell(fp);
     fseek(fp,(long)-n,SEEK_END);
-    fread(str,sizeof(char),n,fp);
+    utils::sfread(FLERR,str,sizeof(char),n,fp,nullptr,error);
     fseek(fp,curpos,SEEK_SET);
   }
 

src/reader.cpp

@@ -15,8 +15,6 @@
 
 #include "error.h"
 
-#include <cstring>
-
 using namespace LAMMPS_NS;
 
 // only proc 0 calls methods of this class, except for constructor/destructor

src/region_sphere.cpp

@@ -19,7 +19,6 @@
 #include "variable.h"
 
 #include <cmath>
-#include <cstring>
 
 using namespace LAMMPS_NS;
 

src/text_file_reader.cpp

@@ -46,7 +46,8 @@ TextFileReader::TextFileReader(const std::string &filename, const std::string &f
   fp = fopen(filename.c_str(), "r");
 
   if (fp == nullptr) {
-    throw FileReaderException(fmt::format("cannot open {} file {}", filetype, filename));
+    throw FileReaderException(fmt::format("cannot open {} file {}: {}",
+                              filetype, filename, utils::getsyserror()));
   }
 }
 

src/tokenizer.cpp

@@ -19,7 +19,6 @@
 #include "utils.h"
 #include "fmt/format.h"
 
-#include <exception>
 #include <utility>
 
 using namespace LAMMPS_NS;

src/universe.cpp

@@ -15,9 +15,7 @@
 
 #include "error.h"
 #include "memory.h"
-#include "version.h"
 
-#include <cctype>
 #include <cstring>
 
 using namespace LAMMPS_NS;

src/variable.cpp

@@ -40,7 +40,6 @@
 #include <cstring>
 #include <unistd.h>
 #include <unordered_map>
-#include <vector>
 
 using namespace LAMMPS_NS;
 using namespace MathConst;

src/write_coeff.cpp

@@ -22,7 +22,6 @@
 #include "force.h"
 #include "improper.h"
 #include "pair.h"
-#include "universe.h"
 
 #include <cctype>
 #include <cstring>

src/write_data.cpp

@@ -29,7 +29,6 @@
 #include "output.h"
 #include "pair.h"
 #include "thermo.h"
-#include "universe.h"
 #include "update.h"
 
 #include <cstring>

src/write_restart.cpp

@@ -32,7 +32,6 @@
 #include "output.h"
 #include "pair.h"
 #include "thermo.h"
-#include "universe.h"
 #include "update.h"
 
 #include <cstring>