Merge pull request #3663 from akohlmey/collected-small-changes

Collected small changes and fixes

cmake/Modules/Packages/GPU.cmake

@@ -98,9 +98,11 @@ if(GPU_API STREQUAL "CUDA")
   # comparison chart according to: https://en.wikipedia.org/wiki/CUDA#GPUs_supported
   if(CUDA_VERSION VERSION_LESS 8.0)
     message(FATAL_ERROR "CUDA Toolkit version 8.0 or later is required")
-  elseif(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
+  elseif(CUDA_VERSION VERSION_GREATER_EQUAL "13.0")
     message(WARNING "Untested CUDA Toolkit version ${CUDA_VERSION}. Use at your own risk")
     set(GPU_CUDA_GENCODE "-arch=all")
+  elseif(CUDA_VERSION VERSION_GREATER_EQUAL "12.0")
+    set(GPU_CUDA_GENCODE "-arch=all")
   else()
     # Kepler (GPU Arch 3.0) is supported by CUDA 5 to CUDA 10.2
     if((CUDA_VERSION VERSION_GREATER_EQUAL "5.0") AND (CUDA_VERSION VERSION_LESS "11.0"))

doc/Makefile

@@ -94,10 +94,11 @@ html: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK) $(MATHJAX)
 		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
 		echo "############################################" ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		rst_anchor_check src/*.rst ;\
-		python $(BUILDDIR)/utils/check-packages.py -s ../src -d src ;\
+		$(PYTHON) $(BUILDDIR)/utils/check-packages.py -s ../src -d src ;\
 		env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
 		env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
-		python $(BUILDDIR)/utils/check-styles.py -s ../src -d src ;\
+		env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\
+		$(PYTHON) $(BUILDDIR)/utils/check-styles.py -s ../src -d src ;\
 		echo "############################################" ;\
 		deactivate ;\
 	)
@@ -174,10 +175,11 @@ pdf: xmlgen $(VENV) $(SPHINXCONFIG)/conf.py $(ANCHORCHECK)
 		rm -f $(BUILDDIR)/doxygen/xml/run.stamp;\
 		echo "############################################" ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
 		rst_anchor_check src/*.rst ;\
-		python utils/check-packages.py -s ../src -d src ;\
+		$(PYTHON) utils/check-packages.py -s ../src -d src ;\
 		env LC_ALL=C grep -n '[^ -~]' $(RSTDIR)/*.rst ;\
 		env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst ;\
-		python utils/check-styles.py -s ../src -d src ;\
+		env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst ;\
+		$(PYTHON) utils/check-styles.py -s ../src -d src ;\
 		echo "############################################" ;\
 		deactivate ;\
 	)
@@ -208,14 +210,14 @@ anchor_check : $(ANCHORCHECK)
 style_check : $(VENV)
 	@(\
 		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
-		python utils/check-styles.py -s ../src -d src ;\
+		$(PYTHON) utils/check-styles.py -s ../src -d src ;\
 		deactivate ;\
 	)
 
 package_check : $(VENV)
 	@(\
 		. $(VENV)/bin/activate ; env PYTHONWARNINGS= PYTHONDONTWRITEBYTECODE=1 \
-		python utils/check-packages.py -s ../src -d src ;\
+		$(PYTHON) utils/check-packages.py -s ../src -d src ;\
 		deactivate ;\
 	)
 
@@ -224,6 +226,7 @@ char_check :
 
 role_check :
 	@( env LC_ALL=C grep -n ' :[a-z]\+`' $(RSTDIR)/*.rst && exit 1 || : )
+	@( env LC_ALL=C grep -n ' `[^`]\+<[a-z][^`]\+`[^_]' $(RSTDIR)/*.rst && exit 1 || : )
 
 link_check : $(VENV) html
 	@(\

doc/msi2lmp.1

@@ -1,11 +1,11 @@
-.TH MSI2LMP "1" "v3.9.9" "2018-11-05"
+.TH MSI2LMP "1" "v3.9.10" "2023-03-10"
 .SH NAME
 .B MSI2LMP
 \- Converter for Materials Studio files to LAMMPS
 
 .SH SYNOPSIS
 .B msi2lmp
-<ROOTNAME> [-class <I|1|II|2|O|0>] [-frc <path to frc file>] [-print #] [-ignore] [-nocenter] [-oldstyle] [-shift <x> <y> <z>]
+[-help] <ROOTNAME> [-class <I|1|II|2|O|0>] [-frc <path to frc file>] [-print #] [-ignore] [-nocenter] [-oldstyle] [-shift <x> <y> <z>]
 
 .SH DESCRIPTION
 .PP
@@ -22,6 +22,9 @@ needed between .frc and .car/.mdf files are the atom types.
 
 .SH OPTIONS
 .TP
+\fB\-h\fR, \fB\-help\fR,
+Print detailed help message to the screen and stop.
+.TP
 \fB\<ROOTNAME>\fR
 This has to be the first argument and is a
 .B mandatory

doc/src/Build_extras.rst

@@ -274,7 +274,7 @@ To enable GPU binning via CUDA performance primitives set the Makefile variable
 most modern GPUs.
 
 To support the CUDA multiprocessor server you can set the define
-``-DCUDA_PROXY``.  Please note that in this case you must **not** use
+``-DCUDA_MPS_SUPPORT``.  Please note that in this case you must **not** use
 the CUDA performance primitives and thus set the variable ``CUDPP_OPT``
 to empty.
 
@@ -1964,10 +1964,10 @@ OPENMP package
    Apple offers the `Xcode package and IDE
    <https://developer.apple.com/xcode/>`_ for compiling software on
    macOS, so you have likely installed it to compile LAMMPS.  Their
-   compiler is based on `Clang <https://clang.llvm.org/>`, but while it
+   compiler is based on `Clang <https://clang.llvm.org/>`_, but while it
    is capable of processing OpenMP directives, the necessary header
    files and OpenMP runtime library are missing.  The `R developers
-   <https://www.r-project.org/>` have figured out a way to build those
+   <https://www.r-project.org/>`_ have figured out a way to build those
    in a compatible fashion. One can download them from
    `https://mac.r-project.org/openmp/
    <https://mac.r-project.org/openmp/>`_.  Simply adding those files as

doc/src/Howto.rst

@@ -70,6 +70,7 @@ Force fields howto
    Howto_amoeba
    Howto_tip3p
    Howto_tip4p
+   Howto_tip5p
    Howto_spc
 
 Packages howto

doc/src/Howto_mdi.rst

@@ -63,18 +63,18 @@ The package also provides a :doc:`mdi plugin <mdi>` command, which
 enables LAMMPS to operate as an MDI driver and load an MDI engine as a
 plugin library.
 
-The package furthermore includes a `fix mdi/qm <fix_mdi_qm>` command, in
+The package furthermore includes a :doc:`fix mdi/qm <fix_mdi_qm>`
-which LAMMPS operates as an MDI driver in conjunction with a quantum
+command, in which LAMMPS operates as an MDI driver in conjunction with a
-mechanics code as an MDI engine.  The post_force() method of the
+quantum mechanics code as an MDI engine.  The post_force() method of the
-``fix_mdi_qm.cpp`` file shows how a driver issues MDI commands to another
+``fix_mdi_qm.cpp`` file shows how a driver issues MDI commands to
-code.  This command can be used to couple to an MDI engine, which is
+another code.  This command can be used to couple to an MDI engine,
-either a stand-alone code or a plugin library.
+which is either a stand-alone code or a plugin library.
 
-As explained in the `fix mdi/qm <fix_mdi_qm>` command documentation, it
+As explained in the :doc:`fix mdi/qm <fix_mdi_qm>` command
-can be used to perform *ab initio* MD simulations or energy
+documentation, it can be used to perform *ab initio* MD simulations or
-minimizations, or to evaluate the quantum energy and forces for a series
+energy minimizations, or to evaluate the quantum energy and forces for a
-of independent systems.  The ``examples/mdi`` directory has example
+series of independent systems.  The ``examples/mdi`` directory has
-input scripts for all of these use cases.
+example input scripts for all of these use cases.
 
 ----------
 

doc/src/Howto_spc.rst

@@ -20,7 +20,6 @@ atoms and the water molecule to run a rigid SPC model.
 | LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0
 | :math:`r_0` of OH bond = 1.0
 | :math:`\theta_0` of HOH angle = 109.47\ :math:`^{\circ}`
-|
 
 Note that as originally proposed, the SPC model was run with a 9
 Angstrom cutoff for both LJ and Coulomb terms.  It can also be used
@@ -33,16 +32,123 @@ the partial charge assignments change:
 
 | O charge = -0.8476
 | H charge = 0.4238
-|
 
 See the :ref:`(Berendsen) <howto-Berendsen>` reference for more details on both
 the SPC and SPC/E models.
 
+Below is the code for a LAMMPS input file and a molecule file
+(``spce.mol``) of SPC/E water for use with the :doc:`molecule command
+<molecule>` demonstrating how to set up a small bulk water system for
+SPC/E with rigid bonds.
+
+.. code-block:: LAMMPS
+
+   units real
+   atom_style full
+   region box block -5 5 -5 5 -5 5
+   create_box 2 box  bond/types 1 angle/types 1 &
+                   extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
+
+   mass 1 15.9994
+   mass 2 1.008
+
+   pair_style lj/cut/coul/cut 10.0
+   pair_coeff 1 1 0.1553 3.166
+   pair_coeff 1 2 0.0    1.0
+   pair_coeff 2 2 0.0    1.0
+
+   bond_style zero
+   bond_coeff 1 1.0
+
+   angle_style zero
+   angle_coeff 1 109.47
+
+   molecule water spce.mol
+   create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33
+
+   timestep 1.0
+   fix rigid     all shake 0.0001 10 10000 b 1 a 1
+   minimize 0.0 0.0 1000 10000
+   run 0 post no
+   reset_timestep 0
+   velocity all create 300.0 5463576
+   fix integrate all nvt temp 300.0 300.0 1.0
+
+   thermo_style custom step temp press etotal density pe ke
+   thermo 1000
+   run 20000 upto
+   write_data tip4p.data nocoeff
+
+.. _spce_molecule:
+.. code-block::
+
+   # Water molecule. SPC/E geometry
+
+   3 atoms
+   2 bonds
+   1 angles
+
+   Coords
+
+   1    0.00000  -0.06461   0.00000
+   2    0.81649   0.51275   0.00000
+   3   -0.81649   0.51275   0.00000
+
+   Types
+
+   1        1   # O
+   2        2   # H
+   3        2   # H
+
+   Charges
+
+   1       -0.8476
+   2        0.4238
+   3        0.4238
+
+   Bonds
+
+   1   1      1      2
+   2   1      1      3
+
+   Angles
+
+   1   1      2      1      3
+
+   Shake Flags
+
+   1 1
+   2 1
+   3 1
+
+   Shake Atoms
+
+   1 1 2 3
+   2 1 2 3
+   3 1 2 3
+
+   Shake Bond Types
+
+   1 1 1 1
+   2 1 1 1
+   3 1 1 1
+
+   Special Bond Counts
+
+   1 2 0 0
+   2 1 1 0
+   3 1 1 0
+
+   Special Bonds
+
+   1 2 3
+   2 1 3
+   3 1 2
+
 Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wiki/Water_model>`_.
 
 ----------
 
 .. _howto-Berendsen:
 
-**(Berendsen)** Berendsen, Grigera, Straatsma, J Phys Chem, 91,
+**(Berendsen)** Berendsen, Grigera, Straatsma, J Phys Chem, 91, 6269-6271 (1987).
-6269-6271 (1987).

doc/src/Howto_tip3p.rst

@@ -1,53 +1,211 @@
 TIP3P water model
 =================
 
-The TIP3P water model as implemented in CHARMM
+The TIP3P water model as implemented in CHARMM :ref:`(MacKerell)
-:ref:`(MacKerell) <howto-tip3p>` specifies a 3-site rigid water molecule with
+<howto-tip3p>` specifies a 3-site rigid water molecule with charges and
-charges and Lennard-Jones parameters assigned to each of the 3 atoms.
+Lennard-Jones parameters assigned to each of the 3 atoms.
-In LAMMPS the :doc:`fix shake <fix_shake>` command can be used to hold
-the two O-H bonds and the H-O-H angle rigid.  A bond style of
-*harmonic* and an angle style of *harmonic* or *charmm* should also be
-used.
 
-These are the additional parameters (in real units) to set for O and H
+A suitable pair style with cutoff Coulomb would be:
-atoms and the water molecule to run a rigid TIP3P-CHARMM model with a
-cutoff.  The K values can be used if a flexible TIP3P model (without
-fix shake) is desired.  If the LJ epsilon and sigma for HH and OH are
-set to 0.0, it corresponds to the original 1983 TIP3P model
-:ref:`(Jorgensen) <Jorgensen1>`.
 
-| O mass = 15.9994
+* :doc:`pair_style lj/cut/coul/cut <pair_lj_cut_coul>`
-| H mass = 1.008
-| O charge = -0.834
-| H charge = 0.417
-| LJ :math:`\epsilon` of OO = 0.1521
-| LJ :math:`\sigma` of OO = 3.1507
-| LJ :math:`\epsilon` of HH = 0.0460
-| LJ :math:`\sigma` of HH = 0.4000
-| LJ :math:`\epsilon` of OH = 0.0836
-| LJ :math:`\sigma` of OH = 1.7753
-| K of OH bond = 450
-| :math:`r_0` of OH bond = 0.9572
-| K of HOH angle = 55
-| :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}`
-|
 
-These are the parameters to use for TIP3P with a long-range Coulomb
+or these commands for a long-range Coulomb model:
-solver (e.g. Ewald or PPPM in LAMMPS), see :ref:`(Price) <Price1>` for
+
-details:
+* :doc:`pair_style lj/cut/coul/long <pair_lj_cut_coul>`
+* :doc:`pair_style lj/cut/coul/long/soft <pair_fep_soft>`
+* :doc:`kspace_style pppm <kspace_style>`
+* :doc:`kspace_style pppm/disp <kspace_style>`
+
+In LAMMPS the :doc:`fix shake or fix rattle <fix_shake>` command can be
+used to hold the two O-H bonds and the H-O-H angle rigid.  A bond style
+of :doc:`harmonic <bond_harmonic>` and an angle style of :doc:`harmonic
+<angle_harmonic>` or :doc:`charmm <angle_charmm>` should also be used.
+In case of rigid bonds also bond style :doc:`zero <bond_zero>` and angle
+style :doc:`zero <angle_zero>` can be used.
+
+The table below lists the force field parameters (in real :doc:`units
+<units>`) to for the water molecule atoms to run a rigid or flexible
+TIP3P-CHARMM model with a cutoff, the original 1983 TIP3P model
+:ref:`(Jorgensen) <Jorgensen1>`, or a TIP3P model with parameters
+optimized for a long-range Coulomb solver (e.g. Ewald or PPPM in LAMMPS)
+:ref:`(Price) <Price1>`.   The K values can be used if a flexible TIP3P
+model (without fix shake) is desired, for rigid bonds/angles they are
+ignored.
+
+   .. list-table::
+      :header-rows: 1
+      :widths: auto
+
+      * - Parameter
+        - TIP3P-CHARMM
+        - TIP3P (original)
+        - TIP3P (Ewald)
+      * - O mass (amu)
+        - 15.9994
+        - 15.9994
+        - 15.9994
+      * - H mass (amu)
+        - 1.008
+        - 1.008
+        - 1.008
+      * - O charge (:math:`e`)
+        - -0.834
+        - -0.834
+        - -0.834
+      * - H charge (:math:`e`)
+        - 0.417
+        - 0.417
+        - 0.417
+      * - LJ :math:`\epsilon` of OO (kcal/mole)
+        - 0.1521
+        - 0.1521
+        - 0.1020
+      * - LJ :math:`\sigma` of OO (:math:`\AA`)
+        - 3.1507
+        - 3.1507
+        - 3.188
+      * - LJ :math:`\epsilon` of HH (kcal/mole)
+        - 0.0460
+        - 0.0
+        - 0.0
+      * - LJ :math:`\sigma` of HH (:math:`\AA`)
+        - 0.4
+        - 1.0
+        - 1.0
+      * - LJ :math:`\epsilon` of OH (kcal/mole)
+        - 0.0836
+        - 0.0
+        - 0.0
+      * - LJ :math:`\sigma` of OH (:math:`\AA`)
+        - 1.7753
+        - 1.0
+        - 1.0
+      * - K of OH bond (kcal/mole/:math:`\AA^2`)
+        - 450
+        - 450
+        - 450
+      * - :math:`r_0` of OH bond (:math:`\AA`)
+        - 0.9572
+        - 0.9572
+        - 0.9572
+      * - K of HOH angle (kcal/mole)
+        - 55.0
+        - 55.0
+        - 55.0
+      * - :math:`\theta_0` of HOH angle
+        - 104.52\ :math:`^{\circ}`
+        - 104.52\ :math:`^{\circ}`
+        - 104.52\ :math:`^{\circ}`
+
+Below is the code for a LAMMPS input file and a molecule file
+(``tip3p.mol``) of TIP3P water for use with the :doc:`molecule command
+<molecule>` demonstrating how to set up a small bulk water system for
+TIP3P with rigid bonds.
+
+.. code-block:: LAMMPS
+
+    units real
+    atom_style full
+    region box block -5 5 -5 5 -5 5
+    create_box 2 box bond/types 1 angle/types 1 &
+                extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
+
+    mass 1 15.9994
+    mass 2 1.008
+
+    pair_style lj/cut/coul/cut 8.0
+    pair_coeff 1 1 0.1521 3.1507
+    pair_coeff 2 2 0.0    1.0
+
+    bond_style zero
+    bond_coeff 1 0.9574
+
+    angle_style zero
+    angle_coeff 1 104.52
+
+    molecule water tip3p.mol
+    create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33
+
+    fix rigid all shake 0.001 10 10000 b 1 a 1
+    minimize 0.0 0.0 1000 10000
+    run 0 post no
+
+    reset_timestep 0
+    velocity all create 300.0 5463576
+    fix integrate all nvt temp 300 300 1.0
+
+    thermo_style custom step temp press etotal pe
+
+    thermo 1000
+    run 20000
+    write_data tip3p.data nocoeff
+
+.. _tip3p_molecule:
+.. code-block::
+
+   # Water molecule. TIP3P geometry
+
+   3 atoms
+   2 bonds
+   1 angles
+
+   Coords
+
+   1    0.00000  -0.06556   0.00000
+   2    0.75695   0.52032   0.00000
+   3   -0.75695   0.52032   0.00000
+
+   Types
+
+   1        1   # O
+   2        2   # H
+   3        2   # H
+
+   Charges
+
+   1       -0.834
+   2        0.417
+   3        0.417
+
+   Bonds
+
+   1   1      1      2
+   2   1      1      3
+
+   Angles
+
+   1   1      2      1      3
+
+   Shake Flags
+
+   1 1
+   2 1
+   3 1
+
+   Shake Atoms
+
+   1 1 2 3
+   2 1 2 3
+   3 1 2 3
+
+   Shake Bond Types
+
+   1 1 1 1
+   2 1 1 1
+   3 1 1 1
+
+   Special Bond Counts
+
+   1 2 0 0
+   2 1 1 0
+   3 1 1 0
+
+   Special Bonds
+
+   1 2 3
+   2 1 3
+   3 1 2
 
-| O mass = 15.9994
-| H mass = 1.008
-| O charge = -0.830
-| H charge = 0.415
-| LJ :math:`\epsilon` of OO = 0.102
-| LJ :math:`\sigma` of OO = 3.188
-| LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0
-| K of OH bond = 450
-| :math:`r_0` of OH bond = 0.9572
-| K of HOH angle = 55
-| :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}`
-|
 
 Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wiki/Water_model>`_.
 

doc/src/Howto_tip4p.rst

@@ -2,19 +2,33 @@ TIP4P water model
 =================
 
 The four-point TIP4P rigid water model extends the traditional
-three-point TIP3P model by adding an additional site, usually
+:doc:`three-point TIP3P <Howto_tip3p>` model by adding an additional
-massless, where the charge associated with the oxygen atom is placed.
+site M, usually massless, where the charge associated with the oxygen
-This site M is located at a fixed distance away from the oxygen along
+atom is placed.  This site M is located at a fixed distance away from
-the bisector of the HOH bond angle.  A bond style of *harmonic* and an
+the oxygen along the bisector of the HOH bond angle.  A bond style of
-angle style of *harmonic* or *charmm* should also be used.
+:doc:`harmonic <bond_harmonic>` and an angle style of :doc:`harmonic
+<angle_harmonic>` or :doc:`charmm <angle_charmm>` should also be used.
+In case of rigid bonds also bond style :doc:`zero <bond_zero>` and angle
+style :doc:`zero <angle_zero>` can be used.
 
-A TIP4P model is run with LAMMPS using either these commands
+There are two ways to implement TIP4P water in LAMMPS:
-for a cutoff model:
+
+#. Use a specially written pair style that uses the :ref:`TIP3P geometry
+   <tip3p_molecule>` without the point M. The point M location is then
+   implicitly derived from the other atoms or each water molecule and
+   used during the force computation.  The forces on M are then
+   projected on the oxygen and the two hydrogen atoms.  This is
+   computationally very efficient, but the charge distribution in space
+   is only correct within the tip4p labeled styles.  So all other
+   computations using charges will "see" the negative charge incorrectly
+   on the oxygen atom.
+
+   This can be done with the following pair styles for Coulomb with a cutoff:
 
    * :doc:`pair_style tip4p/cut <pair_lj_cut_tip4p>`
    * :doc:`pair_style lj/cut/tip4p/cut <pair_lj_cut_tip4p>`
 
-or these commands for a long-range model:
+   or these commands for a long-range Coulomb treatment:
 
    * :doc:`pair_style tip4p/long <pair_coul>`
    * :doc:`pair_style lj/cut/tip4p/long <pair_lj_cut_tip4p>`
@@ -31,71 +45,95 @@ parameter sets listed below are all for rigid TIP4P model variants and
    thus the bond and angle force constants are not used and can be set to
    any legal value; only equilibrium length and angle are used.
 
-These are the additional parameters (in real units) to set for O and H
+#. Use an :ref:`explicit 4 point TIP4P geometry <tip4p_molecule>` where
-atoms and the water molecule to run a rigid TIP4P model with a cutoff
+   the oxygen atom carries no charge and the M point no Lennard-Jones
-:ref:`(Jorgensen) <Jorgensen5>`.  Note that the OM distance is specified in
+   interactions.  Since :doc:`fix shake <fix_shake>` or :doc:`fix rattle
-the :doc:`pair_style <pair_style>` command, not as part of the pair
+   <fix_shake>` may not be applied to this kind of geometry, :doc:`fix
-coefficients.
+   rigid or fix rigid/small <fix_rigid>` or its thermostatted variants
+   are required to maintain a rigid geometry.  This avoids some of the
+   issues with respect to analysis and non-tip4p styles, but it is a
+   more costly force computation (more atoms in the same volume and thus
+   more neighbors in the neighbor lists) and requires a much shorter
+   timestep for stable integration of the rigid body motion.  Since no
+   bonds or angles are required, they do not need to be defined and atom
+   style charge would be sufficient for a bulk TIP4P water system.  In
+   order to avoid that LAMMPS produces an error due to the massless M
+   site a tiny non-zero mass needs to be assigned.
 
-| O mass = 15.9994
+The table below lists the force field parameters (in real :doc:`units
-| H mass = 1.008
+<units>`) to for a selection of popular variants of the TIP4P model.
-| O charge = -1.040
+There is the rigid TIP4P model with a cutoff :ref:`(Jorgensen)
-| H charge = 0.520
+<Jorgensen5>`, the TIP4/Ice model :ref:`(Abascal1) <Abascal1>`, the
-| :math:`r_0` of OH bond = 0.9572
+TIP4P/2005 model :ref:`(Abascal2) <Abascal2>` and a version of TIP4P
-| :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}`
+parameters adjusted for use with a long-range Coulombic solver
-| OM distance = 0.15
+(e.g. Ewald or PPPM in LAMMPS).  Note that for implicit TIP4P models the
-| LJ :math:`\epsilon` of O-O = 0.1550
+OM distance is specified in the :doc:`pair_style <pair_style>` command,
-| LJ :math:`\sigma` of O-O = 3.1536
+not as part of the pair coefficients.
-| LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0
-| Coulomb cutoff = 8.5
-|
 
-For the TIP4/Ice model (J Chem Phys, 122, 234511 (2005);
+   .. list-table::
-https://doi.org/10.1063/1.1931662) these values can be used:
+      :header-rows: 1
+      :widths: auto
 
-| O mass = 15.9994
+      * - Parameter
-| H mass =  1.008
+        - TIP4P (original)
-| O charge = -1.1794
+        - TIP4P/Ice
-| H charge =  0.5897
+        - TIP4P/2005
-| :math:`r_0` of OH bond = 0.9572
+        - TIP4P (Ewald)
-| :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}`
+      * - O mass (amu)
-| OM distance = 0.1577
+        - 15.9994
-| LJ :math:`\epsilon` of O-O = 0.21084
+        - 15.9994
-| LJ :math:`\sigma` of O-O = 3.1668
+        - 15.9994
-| LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0
+        - 15.9994
-| Coulomb cutoff = 8.5
+      * - H mass (amu)
-|
+        - 1.008
-
+        - 1.008
-For the TIP4P/2005 model (J Chem Phys, 123, 234505 (2005);
+        - 1.008
-https://doi.org/10.1063/1.2121687), these values can be used:
+        - 1.008
-
+      * - O or M charge (:math:`e`)
-| O mass = 15.9994
+        - -1.040
-| H mass =  1.008
+        - -1.1794
-| O charge = -1.1128
+        - -1.1128
-| H charge = 0.5564
+        - -1.04844
-| :math:`r_0` of OH bond = 0.9572
+      * - H charge (:math:`e`)
-| :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}`
+        - 0.520
-| OM distance = 0.1546
+        - 0.5897
-| LJ :math:`\epsilon` of O-O = 0.1852
+        - 0.5564
-| LJ :math:`\sigma` of O-O = 3.1589
+        - 0.52422
-| LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0
+      * - LJ :math:`\epsilon` of OO (kcal/mole)
-| Coulomb cutoff = 8.5
+        - 0.1550
-|
+        - 0.1577
-
+        - 0.1852
-These are the parameters to use for TIP4P with a long-range Coulombic
+        - 0.16275
-solver (e.g. Ewald or PPPM in LAMMPS):
+      * - LJ :math:`\sigma` of OO (:math:`\AA`)
-
+        - 3.1536
-| O mass = 15.9994
+        - 3.1668
-| H mass = 1.008
+        - 3.1589
-| O charge = -1.0484
+        - 3.16435
-| H charge = 0.5242
+      * - LJ :math:`\epsilon` of HH, MM, OH, OM, HM (kcal/mole)
-| :math:`r_0` of OH bond = 0.9572
+        - 0.0
-| :math:`\theta` of HOH angle = 104.52\ :math:`^{\circ}`
+        - 0.0
-| OM distance = 0.1250
+        - 0.0
-| LJ :math:`\epsilon` of O-O = 0.16275
+        - 0.0
-| LJ :math:`\sigma` of O-O = 3.16435
+      * - LJ :math:`\sigma` of HH, MM, OH, OM, HM (:math:`\AA`)
-| LJ :math:`\epsilon`, :math:`\sigma` of OH, HH = 0.0
+        - 1.0
-|
+        - 1.0
+        - 1.0
+        - 1.0
+      * - :math:`r_0` of OH bond (:math:`\AA`)
+        - 0.9572
+        - 0.9572
+        - 0.9572
+        - 0.9572
+      * - :math:`\theta_0` of HOH angle
+        - 104.52\ :math:`^{\circ}`
+        - 104.52\ :math:`^{\circ}`
+        - 104.52\ :math:`^{\circ}`
+        - 104.52\ :math:`^{\circ}`
+      * - OM distance (:math:`\AA`)
+        - 0.15
+        - 0.1577
+        - 0.1546
+        - 0.1250
 
 Note that the when using the TIP4P pair style, the neighbor list cutoff
 for Coulomb interactions is effectively extended by a distance 2 \* (OM
@@ -108,6 +146,117 @@ trade-off for your model.  The OM distance and the LJ and Coulombic
 cutoffs are set in the :doc:`pair_style lj/cut/tip4p/long
 <pair_lj_cut_tip4p>` command.
 
+Below is the code for a LAMMPS input file using the implicit method and
+the :ref:`TIP3P molecule file <tip3p_molecule>`.  Because the TIP4P
+charges are different from TIP3P they need to be reset (or the molecule
+file changed):
+
+.. code-block:: LAMMPS
+
+    units real
+    atom_style full
+    region box block -5 5 -5 5 -5 5
+    create_box 2 box bond/types 1 angle/types 1 &
+                extra/bond/per/atom 2 extra/angle/per/atom 1 extra/special/per/atom 2
+
+    mass 1 15.9994
+    mass 2 1.008
+
+    pair_style lj/cut/tip4p/cut 1 2 1 1 0.15 8.0
+    pair_coeff 1 1 0.1550 3.1536
+    pair_coeff 2 2 0.0    1.0
+
+    bond_style zero
+    bond_coeff 1 0.9574
+
+    angle_style zero
+    angle_coeff 1 104.52
+
+    molecule water tip3p.mol  # this uses the TIP3P geometry
+    create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33
+    # must change charges for TIP4P
+    set type 1 charge -1.040
+    set type 2 charge  0.520
+
+    fix rigid all shake 0.001 10 10000 b 1 a 1
+    minimize 0.0 0.0 1000 10000
+    run 0 post no
+
+    reset_timestep 0
+    velocity all create 300.0 5463576
+    fix integrate all nvt temp 300 300 1.0
+
+    thermo_style custom step temp press etotal pe
+
+    thermo 1000
+    run 20000
+    write_data tip3p.data nocoeff
+
+Below is the code for a LAMMPS input file using the explicit method and
+a TIP4P molecule file.  Because of using :doc:`fix rigid/nvt/small
+<fix_rigid>` no bonds need to be defined and thus no extra storage needs
+to be reserved for them, but we need to switch to atom style full or use
+:doc:`fix property/atom mol <fix_property_atom>` so that fix
+rigid/nvt/small can identify rigid bodies by their molecule ID:
+
+.. code-block:: LAMMPS
+
+    units real
+    atom_style charge
+    region box block -5 5 -5 5 -5 5
+    create_box 3 box
+
+    mass 1 15.9994
+    mass 2 1.008
+    mass 3 1.0e-100
+
+    pair_style lj/cut/coul/cut 8.0
+    pair_coeff 1 1 0.1550 3.1536
+    pair_coeff 2 2 0.0    1.0
+    pair_coeff 3 3 0.0    1.0
+
+    fix mol all property/atom mol
+    molecule water tip4p.mol
+    create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33
+
+    timestep 0.1
+    fix integrate all rigid/nvt/small molecule temp 300.0 300.0 1.0
+    velocity all create 300.0 5463576
+
+    thermo_style custom step temp press etotal density pe ke
+    thermo 1000
+    run 20000
+    write_data tip4p.data nocoeff
+
+.. _tip4p_molecule:
+.. code-block::
+
+   # Water molecule. Explicit TIP4P geometry for use with fix rigid
+
+   4 atoms
+
+   Coords
+
+   1    0.00000  -0.06556   0.00000
+   2    0.75695   0.52032   0.00000
+   3   -0.75695   0.52032   0.00000
+   4    0.00000   0.08444   0.00000
+
+   Types
+
+   1        1   # O
+   2        2   # H
+   3        2   # H
+   4        3   # M
+
+   Charges
+
+   1        0.000
+   2        0.520
+   3        0.520
+   4       -1.040
+
+
 Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wiki/Water_model>`_.
 
 ----------
@@ -116,3 +265,13 @@ Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wik
 
 **(Jorgensen)** Jorgensen, Chandrasekhar, Madura, Impey, Klein, J Chem
 Phys, 79, 926 (1983).
+
+.. _Abascal1:
+
+**(Abascal1)** Abascal, Sanz, Fernandez, Vega, J Chem Phys, 122, 234511 (2005)
+   https://doi.org/10.1063/1.1931662
+
+.. _Abascal2:
+
+**(Abascal2)** Abascal, J Chem Phys, 123, 234505 (2005)
+   https://doi.org/10.1063/1.2121687

doc/src/Howto_tip5p.rst

@@ -0,0 +1,161 @@
+TIP5P water model
+=================
+
+The five-point TIP5P rigid water model extends the :doc:`three-point
+TIP3P model <Howto_tip3p>` by adding two additional sites L, usually
+massless, where the charge associated with the oxygen atom is placed.
+These sites L are located at a fixed distance away from the oxygen atom,
+forming a tetrahedral angle that is rotated by 90 degrees from the HOH
+plane.  Those sites thus somewhat approximate lone pairs of the oxygen
+and consequently improve the water structure to become even more
+"tetrahedral" in comparison to the :doc:`four-point TIP4P model
+<Howto_tip4p>`.
+
+A suitable pair style with cutoff Coulomb would be:
+
+* :doc:`pair_style lj/cut/coul/cut <pair_lj_cut_coul>`
+
+or these commands for a long-range model:
+
+* :doc:`pair_style lj/cut/coul/long <pair_lj_cut_coul>`
+* :doc:`pair_style lj/cut/coul/long/soft <pair_fep_soft>`
+* :doc:`kspace_style pppm <kspace_style>`
+* :doc:`kspace_style pppm/disp <kspace_style>`
+
+A TIP5P model *must* be run using a :doc:`rigid fix <fix_rigid>` since
+there is no other option to keep this kind of structure rigid in LAMMPS.
+In order to avoid that LAMMPS produces an error due to the massless L
+sites, those need to be assigned a tiny non-zero mass.
+
+The table below lists the force field parameters (in real :doc:`units
+<units>`) to for a the TIP5P model with a cutoff :ref:`(Mahoney)
+<Mahoney>` and the TIP5P-E model :ref:`(Rick) <Rick>` for use with a
+long-range Coulombic solver (e.g. Ewald or PPPM in LAMMPS).
+
+   .. list-table::
+      :header-rows: 1
+      :widths: auto
+
+      * - Parameter
+        - TIP5P
+        - TIP5P-E
+      * - O mass (amu)
+        - 15.9994
+        - 15.9994
+      * - H mass (amu)
+        - 1.008
+        - 1.008
+      * - O charge (:math:`e`)
+        - 0.0
+        - 0.0
+      * - L charge (:math:`e`)
+        - -0.241
+        - -0.241
+      * - H charge (:math:`e`)
+        - 0.241
+        - 0.241
+      * - LJ :math:`\epsilon` of OO (kcal/mole)
+        - 0.1600
+        - 0.1780
+      * - LJ :math:`\sigma` of OO (:math:`\AA`)
+        - 3.1200
+        - 3.0970
+      * - LJ :math:`\epsilon` of HH, LL, OH, OL, HL (kcal/mole)
+        - 0.0
+        - 0.0
+      * - LJ :math:`\sigma` of HH, LL, OH, OL, HL (:math:`\AA`)
+        - 1.0
+        - 1.0
+      * - :math:`r_0` of OH bond (:math:`\AA`)
+        - 0.9572
+        - 0.9572
+      * - :math:`\theta_0` of HOH angle
+        - 104.52\ :math:`^{\circ}`
+        - 104.52\ :math:`^{\circ}`
+      * - OL distance (:math:`\AA`)
+        - 0.70
+        - 0.70
+      * - :math:`\theta_0` of LOL angle
+        - 109.47\ :math:`^{\circ}`
+        - 109.47\ :math:`^{\circ}`
+
+Below is the code for a LAMMPS input file for setting up a simulation of
+TIP5P water with a molecule file.  Because of using :doc:`fix
+rigid/nvt/small <fix_rigid>` no bonds need to be defined and thus no
+extra storage needs to be reserved for them, but we need to switch to
+atom style full or use :doc:`fix property/atom mol <fix_property_atom>`
+so that fix rigid/nvt/small can identify rigid bodies by their molecule
+ID:
+
+.. code-block:: LAMMPS
+
+    units real
+    atom_style charge
+    region box block -5 5 -5 5 -5 5
+    create_box 3 box
+
+    mass 1 15.9994
+    mass 2 1.008
+    mass 3 1.0e-100
+
+    pair_style lj/cut/coul/cut 8.0
+    pair_coeff 1 1 0.160  3.12
+    pair_coeff 2 2 0.0    1.0
+    pair_coeff 3 3 0.0    1.0
+
+    fix mol all property/atom mol
+    molecule water tip5p.mol
+    create_atoms 0 random 33 34564 NULL mol water 25367 overlap 1.33
+
+    timestep 0.20
+    fix integrate all rigid/nvt/small molecule temp 300.0 300.0 1.0
+    reset_timestep 0
+    velocity all create 300.0 5463576
+
+    thermo_style custom step temp press etotal density pe ke
+    thermo 1000
+    run 20000
+    write_data tip5p.data nocoeff
+
+.. _tip5p_molecule:
+.. code-block::
+
+   # Water molecule. Explicit TIP5P geometry for use with fix rigid
+
+   5 atoms
+
+   Coords
+
+   1    0.00000  -0.06556   0.00000
+   2    0.75695   0.52032   0.00000
+   3   -0.75695   0.52032   0.00000
+   4    0.00000  -0.46971   0.57154
+   5    0.00000  -0.46971  -0.57154
+
+   Types
+
+   1        1   # O
+   2        2   # H
+   3        2   # H
+   4        3   # L
+   5        3   # L
+
+   Charges
+
+   1        0.000
+   2        0.241
+   3        0.241
+   4       -0.241
+   5       -0.241
+
+Wikipedia also has a nice article on `water models <https://en.wikipedia.org/wiki/Water_model>`_.
+
+----------
+
+.. _Mahoney:
+
+**(Mahoney)** Mahoney, Jorgensen, J Chem Phys 112, 8910 (2000)
+
+.. _Rick:
+
+**(Rick)** Rick, J Chem Phys 120, 6085 (2004)

doc/src/Install_linux.rst

@@ -42,7 +42,7 @@ static linkage, there is no ``liblammps.so`` library file and thus also the
 LAMMPS python module, which depends on it, is not included.
 
 The compressed tar archives available for download have names following
-the pattern `lammps-linux-x86_64-<version>.tar.gz` and will all unpack
+the pattern ``lammps-linux-x86_64-<version>.tar.gz`` and will all unpack
 into a ``lammps-static`` folder.  The executables are then in the
 ``lammps-static/bin/`` folder.  Since they do not depend on any other
 software, they may be freely moved or copied around.

doc/src/Install_windows.rst

@@ -17,11 +17,12 @@ install the Windows MPI package (MPICH2 from Argonne National Labs),
 needed to run in parallel with MPI.
 
 The LAMMPS binaries contain *all* :doc:`optional packages <Packages>`
-included in the source distribution except: KIM, KOKKOS, MSCG, PYTHON,
+included in the source distribution except: ADIOS, H5MD, KIM, ML-PACE,
-ADIOS, H5MD, NETCDF, QMMM, ML-QUIP, and VTK.
+ML-QUIP, MSCG, NETCDF, PLUMED, QMMM, SCAFACOS, and VTK.  The serial
-The serial version also does not include the MPIIO and
+version also does not include the MPIIO and LATBOLTZ packages.  The
-LATBOLTZ packages.  The GPU package is compiled for OpenCL with
+PYTHON package is only available in the Python installers that bundle a
-mixed precision kernels.
+Python runtime.  The GPU package is compiled for OpenCL with mixed
+precision kernels.
 
 The LAMMPS library is compiled as a shared library and the
 :doc:`LAMMPS Python module <Python_module>` is installed, so that

doc/src/Intro_features.rst

@@ -195,7 +195,7 @@ Multi-replica models
 * :doc:`parallel replica dynamics <prd>`
 * :doc:`temperature accelerated dynamics <tad>`
 * :doc:`parallel tempering <temper>`
-* path-integral MD: `first variant <fix_pimd>`, `second variant <fix_ipi>`
+* path-integral MD: :doc:`first variant <fix_pimd>`, :doc:`second variant <fix_ipi>`
 * multi-walker collective variables with :doc:`Colvars <fix_colvars>` and :doc:`Plumed <fix_plumed>`
 
 .. _prepost:

doc/src/balance.rst

@@ -498,7 +498,7 @@ data to other processors during load-balancing will be random or
 deterministic.  Random is generally faster; deterministic will ensure
 the new ordering of atoms on each processor is the same each time the
 same simulation is run.  This can be useful for debugging purposes.
-Since the balance commmand is a one-time operation, the default is
+Since the balance command is a one-time operation, the default is
 *yes* to perform sorting.
 
 The *out* keyword writes a text file to the specified *filename* with

doc/src/bond_table.rst

@@ -112,8 +112,9 @@ are estimated (less accurately) by the first two and last two force
 values in the table.
 
 The "EQ" parameter is also optional.  If used, it is followed by a the
-equilibrium bond length, which is used, for example, by the :doc:`fix shake <fix_shake>` command.  If not used, the equilibrium bond
+equilibrium bond length, which is used, for example, by the :doc:`fix
-length is to the distance in the table with the lowest potential energy.
+shake <fix_shake>` command.  If not used, the equilibrium bond length is
+to the distance in the table with the lowest potential energy.
 
 Following a blank line, the next N lines list the tabulated values.
 On each line, the first value is the index from 1 to N, the second value is
@@ -135,16 +136,15 @@ one that matches the specified keyword.
 
 ----------
 
-Restart, fix_modify, output, run start/stop, minimize info
+Restart info
-"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
+""""""""""""
 
-This bond style writes the settings for the "bond_style table"
+This bond style writes the settings for the "bond_style table" command
-command to :doc:`binary restart files <restart>`, so a bond_style
+to :doc:`binary restart files <restart>`, so a bond_style command does
-command does not need to specified in an input script that reads a
+not need to specified in an input script that reads a restart file.
-restart file.  However, the coefficient information is not stored in
+However, the coefficient information is not stored in the restart file,
-the restart file, since it is tabulated in the potential files.  Thus,
+since it is tabulated in the potential files.  Thus, bond_coeff commands
-bond_coeff commands do need to be specified in the restart input
+do need to be specified in the restart input script.
-script.
 
 Restrictions
 """"""""""""

doc/src/bond_write.rst

@@ -70,7 +70,7 @@ be specified even if the potential has a finite value at r = 0.0.
 Related commands
 """"""""""""""""
 
-:doc:`bond_style table <bond_table>`, `angle_write <angle_write>`,
+:doc:`bond_style table <bond_table>`, :doc:`angle_write <angle_write>`,
 :doc:`bond_style <bond_style>`, :doc:`bond_coeff <bond_coeff>`
 
 Default

doc/src/dump.rst

@@ -375,7 +375,7 @@ output with each snapshot:
    nx ny nz
 
 The value dim will be 2 or 3 for 2d or 3d simulations.  It is included
-so that post-processing tools like `OVITO <https://www.ovito.org>`,
+so that post-processing tools like `OVITO <https://www.ovito.org>`_,
 which can visualize grid-based quantities know how to draw each grid
 cell.  The grid size will match the input script parameters for
 grid(s) created by the computes or fixes which are referenced by the

doc/src/fix_adapt.rst

@@ -139,7 +139,7 @@ formulas for the meaning of these parameters:
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
 | :doc:`buck/mdf <pair_mdf>`                                                   | a,c                                              | type pairs  |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
-| :doc:`coul/cut <pair_coul>`                                                  | scale                                            | type pairs  |
+| :doc:`coul/cut, coul/cut/global <pair_coul>`                                 | scale                                            | type pairs  |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
 | :doc:`coul/cut/soft <pair_fep_soft>`                                         | lambda                                           | type pairs  |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
@@ -151,10 +151,16 @@ formulas for the meaning of these parameters:
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
 | :doc:`coul/long/soft <pair_fep_soft>`                                        | scale, lambda, coulombic_cutoff                  | type pairs  |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`coul/slater/long <pair_coul_slater>`                                   | scale                                            | type pairs  |
++------------------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`coul/streitz <pair_coul>`                                              | scale                                            | type pairs  |
++------------------------------------------------------------------------------+--------------------------------------------------+-------------+
 | :doc:`eam, eam/alloy, eam/fs <pair_eam>`                                     | scale                                            | type pairs  |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
 | :doc:`gauss <pair_gauss>`                                                    | a                                                | type pairs  |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`harmonic/cut <pair_harmonic_cut>`                                      | k, cutoff                                        | type pairs  |
++------------------------------------------------------------------------------+--------------------------------------------------+-------------+
 | :doc:`lennard/mdf <pair_mdf>`                                                | A,B                                              | type pairs  |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
 | :doc:`lj/class2 <pair_class2>`                                               | epsilon,sigma                                    | type pairs  |
@@ -181,6 +187,8 @@ formulas for the meaning of these parameters:
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
 | :doc:`lubricate <pair_lubricate>`                                            | mu                                               | global      |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`meam <pair_meam>`                                                      | scale                                            | type pairs  |
++------------------------------------------------------------------------------+--------------------------------------------------+-------------+
 | :doc:`mie/cut <pair_mie>`                                                    | epsilon,sigma,gamma_repulsive,gamma_attractive   | type pairs  |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
 | :doc:`morse, morse/smooth/linear <pair_morse>`                               | D0,R0,alpha                                      | type pairs  |
@@ -191,7 +199,7 @@ formulas for the meaning of these parameters:
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
 | :doc:`nm/cut/coul/cut, nm/cut/coul/long <pair_nm>`                           | E0,R0,m,n,coulombic_cutoff                       | type pairs  |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
-| :doc:`reaxff <pair_reaxff>`                                                  | chi, eta, gamma                                  | type global |
+| :doc:`pace, pace/extrapolation <pair_pace>`                                  | scale                                            | type pairs  |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
 | :doc:`snap <pair_snap>`                                                      | scale                                            | type pairs  |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
@@ -203,11 +211,13 @@ formulas for the meaning of these parameters:
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
 | :doc:`spin/neel <pair_spin_neel>`                                            | coulombic_cutoff                                 | type global |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
+| :doc:`soft <pair_soft>`                                                      | a                                                | type pairs  |
++------------------------------------------------------------------------------+--------------------------------------------------+-------------+
 | :doc:`table <pair_table>`                                                    | table_cutoff                                     | type pairs  |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
 | :doc:`ufm <pair_ufm>`                                                        | epsilon,sigma                                    | type pairs  |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
-| :doc:`soft <pair_soft>`                                                      | a                                                | type pairs  |
+| :doc:`wf/cut <pair_wf_cut>`                                                  | epsilon,sigma,nu,mu                              | type pairs  |
 +------------------------------------------------------------------------------+--------------------------------------------------+-------------+
 
 .. note::

doc/src/fix_alchemy.rst

@@ -12,7 +12,7 @@ Syntax
 
 * ID, group-ID are documented in :doc:`fix <fix>` command
 * alchemy = style name of this fix command
-* v_name = variable with name that determines the :math:`\lambda_p` value
+* v_name = variable with name that determines the :math:`\lambda_R` value
 
 Examples
 """"""""
@@ -26,87 +26,126 @@ Description
 
 .. versionadded:: TBD
 
-This fix command enables running an "alchemical transformation" MD
+This fix command enables an "alchemical transformation" to be performed
-simulation between two topologies (i.e. the same number and positions of
+between two systems, whereby one system slowly transforms into the other
-atoms, but differences in atom parameters like type, charge, bonds,
+over the course of a molecular dynamics run.  This is useful for
-angles and so on).  For this a :ref:`multi-partition run <partition>` is
+measuring thermodynamic differences between two different systems.  It
-required with exactly two partitions.  During the MD run, the fix will
+also allows transformations that are not easily possible with the
-will determine a factor, :math:`\lambda_p`, for each partition *p* that
+:doc:`pair style hybrid/scaled <pair_hybrid>`, :doc:`fix adapt
-will be taken from an equal style or equivalent :doc:`variable
+<fix_adapt>` or :doc:`fix adapt/fep <fix_adapt_fep>` commands.
-<variable>`.  Typically, this variable would be chose to linearly ramp
-*down* from 1.0 to 0.0 for the *first* partition (*p=0*) and linearly
-ramp *up* from 0.0 to 1.0 for the *second* partition (*p=1*).  The
-forces used for the propagation of the atoms will be the sum of the
-forces of the two systems combined and scaled with their respective
-:math:`\lambda_p` factor.  This allows to perform transformations that
-are not easily possible with :doc:`pair style hybrid/scaled
-<pair_hybrid>`, :doc:`fix adapt <fix_adapt>` or :doc:`fix adapt/fep
-<fix_adapt_fep>`.
 
-.. note::
+Example inputs are included in the ``examples/PACKAGES/alchemy``
+directory for (a) transforming a pure copper system into a
+copper/aluminum bronze alloy and (b) transforming two water molecules
+in a box of water into a hydronium and a hydroxyl ion.
 
-   Since the definition of the variable to provide the :math:`\lambda_p` is
+The two systems must be defined as :doc:`separate replica
-   independent in the two partitions, no check is made that the two values
+<Howto_replica>` and run in separate partitions of processors using the
-   remain between 0.0 and 1.0 and that they add up to 1.0.  So care needs to
+:doc:`-partition <Run_options>` command-line switch.  Exactly two
-   be taken when defining those variables that this is the case.
+partitions must be specified, and each partition must use the same number
+of processors and the same domain decomposition.
 
-Due to the specifics of the implementation, the initial geometry and
+Because the forces applied to the atoms are the same mix of the forces
-dimensions of the system must be exactly the same and the fix will
+from each partition and the simulation starts with the same atom
-synchronize them during the run.  It is thus not possible to initialize
+positions across both partitions, they will generate the same trajectory
-the two partitions by reading different data files or creating different
+of coordinates for each atom, and the same simulation box size and
-systems from scratch, but rather they have to be started from the same
+shape.  The latter two conditions are *enforced* by this fix; it
-system and then the desired modifications need to be applied to the
+exchanges coordinates and box information between the replicas.  This is
-system of the second partition.  The commands :doc:`pair style
+not strictly required, but since MD simulations are an example of a
-hybrid/scaled <pair_hybrid>`, :doc:`fix adapt <fix_adapt>` or :doc:`fix
+chaotic system, even the tiniest random difference will eventually grow
-adapt/fep <fix_adapt_fep>` could be used for simulations where the
+exponentially into an unwanted divergence.
-requirements for fix alchemy are not given.
 
-The commands below demonstrate how the setup for the second partition
+Otherwise, the properties of each atom (type, charge, bond and angle
-can be done for the example of transforming a pure copper system into a
+partners, etc.), as well as energy and forces between interacting atoms
-copper/aluminum bronze.
+(pair, bond, angle styles, etc.) can be different in the two systems.
+
+This can be initialized in the same input script by using commands which
+only apply to one or the other replica.  The example scripts use a
+world-style :doc:`variable <variable>` command along with
+:doc:`if/then/else <if>` commands for this purpose.  The
+:doc:`partition <partition>` command can also be used.
 
 .. code-block:: LAMMPS
 
-   variable name world pure alloy
-
    create_box 2 box
    create_atoms 1 box
    pair_style eam/alloy
    pair_coeff * * AlCu.eam.alloy Cu Al
 
    # replace 5% of copper with aluminum on the second partition only
+
    variable name world pure alloy
    if "${name} == alloy" then &
      "set type 1 type/fraction 2 0.05 6745234"
 
-   # define ramp variable to combine the two different partitions
+Both replicas must define an instance of this fix, but with a different
-   if "${name} == pure" then             &
+*v_name* variable.  The named variable must be an equal-style or
-     "variable ramp equal ramp(1.0,0.0)"    &
+equivalent :doc:`variable <variable>`.  The two variables should be
-   else                                      &
+defined so that one ramps *down* from 1.0 to 0.0 for the *first* replica
-      "variable ramp equal ramp(0.0,1.0)"
+(*R=0*) and the other ramps *up* from 0.0 to 1.0 for the *second*
+replica (*R=1*).  A simple way is to do this is linearly, which can be
+done using the ramp() function of the :doc:`variable <variable>`
+command.  You could also define a variable which returns a value between
+0.0 and 1.0 as a non-linear function of the timestep.  Here is a linear
+example:
 
+.. code-block:: LAMMPS
+
+   partition yes 1 variable ramp equal ramp(1.0,0.0)
+   partition yes 2 variable ramp equal ramp(0.0,1.0)
    fix 2 all alchemy v_ramp
 
+.. note::
 
-The ``examples/PACKAGES/alchemy`` folder contains complete example
+   For an alchemical transformation, the two variables should sum to
-inputs for this command.
+   exactly 1.0 at any timestep.  LAMMPS does *NOT* check that this is
+   the case.
+
+If you use the ``ramp()`` function to define the two variables, this fix
+can easily be used across successive runs in the same input script by
+ensuring each instance of the :doc:`run <run>` command specifies the
+appropriate *start* or *stop* options.
+
+At each timestep of an MD run, the two instances of this fix evaluate
+their respective variables as a :math:`\lambda_R` factor, where *R* = 0
+or 1 for each replica.  The forces used by each system for the
+propagation of their atoms is set to the sum of the forces for the two
+systems, each scaled by their respective :math:`\lambda_R` factor.  Thus,
+during the MD run, the system will transform incrementally from the
+first system to the second system.
+
+.. note::
+
+   As mentioned above, the coordinates of the atoms and box size/shape
+   must be exactly the same in the two replicas.  Therefore, it is
+   generally not a good idea to initialize the two replicas by reading
+   different data files or creating them individually from scratch.
+   Rather, a single system should be initialized and then desired
+   modifications applied to the system to either replica.  If your
+   input script somehow induces the two systems to become different
+   (e.g. by performing :doc:`atom_modify sort <atom_modify>`
+   differently, or by adding or depositing a different number of atoms),
+   then LAMMPS will detect the mismatch and generate an error.  This is
+   done by ensuring that each step the number and ordering of atoms is
+   identical within each pair of processors in the two replicas.
 
 ----------
 
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.
+No information about this fix is written to :doc:`binary restart files
-None of the :doc:`fix_modify <fix_modify>` options are relevant to this fix.
+<restart>`.  None of the :doc:`fix_modify <fix_modify>` options are
+relevant to this fix.
 
-This fix stores a global scalar (the current value of :math:`\lambda_p`)
+This fix stores a global scalar (the current value of :math:`\lambda_R`)
 and a global vector of length 3 which contains the potential energy of
 the first partition, the second partition and the combined value,
 respectively. The global scalar is unitless and "intensive", the vector
 is in :doc:`energy units <units>` and "extensive".  These values can be
 used by any command that uses a global value from a fix as input.  See
-the :doc:`Howto output <Howto_output>` doc page for an overview of
+the :doc:`output howto <Howto_output>` page for an overview of LAMMPS
-LAMMPS output options.
+output options.
 
 This fix is not invoked during :doc:`energy minimization <minimize>`.
 
@@ -117,12 +156,9 @@ This fix is part of the REPLICA package.  It is only enabled if LAMMPS
 was built with that package.  See the :doc:`Build package
 <Build_package>` page for more info.
 
-There may be only one instance of this fix in use at any time.
+There may be only one instance of this fix in use at a time within
+each replica.
 
-This fix requires to perform a :ref:`multi-partition run <partition>`
-with *exactly* two partitions.
-
-This fix is *not* compatible with :doc:`load balancing <fix_balance>`.
 
 Related commands
 """"""""""""""""

doc/src/fix_balance.rst

@@ -314,7 +314,7 @@ data to other processors during load-balancing will be random or
 deterministic.  Random is generally faster; deterministic will ensure
 the new ordering of atoms on each processor is the same each time the
 same simulation is run.  This can be useful for debugging purposes.
-Since the fix balance commmand is performed during timestepping, the
+Since the fix balance command is performed during timestepping, the
 default is *no* so that sorting is not performed.
 
 The *out* keyword writes text to the specified *filename* with the

doc/src/fix_mscg.rst

@@ -40,15 +40,15 @@ Description
 
 This fix applies the Multi-Scale Coarse-Graining (MSCG) method to
 snapshots from a dump file to generate potentials for coarse-grained
-simulations from all-atom simulations, using a force-matching
+simulations from all-atom simulations, using a force-matching technique
-technique (:ref:`Izvekov <Izvekov>`, :ref:`Noid <Noid>`).
+(:ref:`Izvekov <Izvekov>`, :ref:`Noid <Noid>`).
 
-It makes use of the MS-CG library, written and maintained by Greg
+It makes use of the MS-CG library, written and maintained by Greg Voth's
-Voth's group at the University of Chicago, which is freely available
+group at the University of Chicago, which is freely available on their
-on their `MS-CG GitHub site <https://github.com/uchicago-voth/MSCG-release>`_.  See instructions
+`MS-CG GitHub site <https://github.com/uchicago-voth/MSCG-release>`_.
-on obtaining and installing the MS-CG library in the src/MSCG/README
+See instructions on obtaining and installing the MS-CG library in the
-file, which must be done before you build LAMMPS with this fix command
+src/MSCG/README file, which must be done before you build LAMMPS with
-and use the command in a LAMMPS input script.
+this fix command and use the command in a LAMMPS input script.
 
 An example script using this fix is provided the examples/mscg
 directory.
@@ -65,15 +65,18 @@ simulations is as follows:
 6. Check the results of the force matching.
 7. Run coarse-grained simulations using the new coarse-grained potentials.
 
-This fix can perform the range finding and force matching steps 4 and
+This fix can perform the range finding and force matching steps 4 and 5
-5 of the above workflow when used in conjunction with the
+of the above workflow when used in conjunction with the :doc:`rerun
-:doc:`rerun <rerun>` command.  It does not perform steps 1-3 and 6-7.
+<rerun>` command.  It does not perform steps 1-3 and 6-7.
 
-Step 2 can be performed using a Python script (what is the name?)
+Step 2 can be performed using a Python script (cgmap), which defines the
-provided with the MS-CG library which defines the coarse-grained model
+coarse-grained model and converts a standard LAMMPS dump file for an
-and converts a standard LAMMPS dump file for an all-atom simulation
+all-atom simulation (step 1) into a LAMMPS dump file which has the
-(step 1) into a LAMMPS dump file which has the positions of and forces
+positions of and forces on the coarse-grained beads.  To use cgmap the
-on the coarse-grained beads.
+following repositories need to be downloaded and installed.
+
+#. The custom lammpsdata branch of mdtraj from https://github.com/hockyg/mdtraj/tree/lammpsdata
+#. The master branch of cgmap from https://github.com/uchicago-voth/cgmap
 
 In step 3, an input file named "control.in" is needed by the MS-CG
 library which sets parameters for the range finding and force matching
@@ -83,12 +86,12 @@ info on this file.
 
 When this fix is used to perform steps 4 and 5, the MS-CG library also
 produces additional output files.  The range finder functionality
-(step 4) outputs files defining pair and bonded interaction ranges.
+(step 4) outputs files defining pair and bonded interaction ranges.  The
-The force matching functionality (step 5) outputs tabulated force
+force matching functionality (step 5) outputs tabulated force files for
-files for every interaction in the system. Other diagnostic files can
+every interaction in the system. Other diagnostic files can also be
-also be output depending on the parameters in the MS-CG library input
+output depending on the parameters in the MS-CG library input script.
-script.  Again, see the documentation provided with the MS-CG library
+Again, see the documentation provided with the MS-CG library for more
-for more info.
+info.
 
 ----------
 
@@ -97,8 +100,8 @@ be invoked. If *on*, the step 4 range finder functionality is invoked.
 *off*, the step 5 force matching functionality is invoked.
 
 If the *name* keyword is used, string names are defined to associate
-with the integer atom types in LAMMPS.  *Ntype* names must be
+with the integer atom types in LAMMPS.  *Ntype* names must be provided,
-provided, one for each atom type (1-Ntype).
+one for each atom type (1-Ntype).
 
 The *max* keyword specifies the maximum number of bonds, angles, and
 dihedrals a bead can have in the coarse-grained model.
@@ -107,16 +110,13 @@ Restrictions
 """"""""""""
 
 This fix is part of the MSCG package. It is only enabled if LAMMPS was
-built with that package.  See the :doc:`Build package <Build_package>`
+built with that package.  Building the MSCG package also requires
-doc page for more info.
+external libraries. See the :doc:`Build_package` and :doc:`Build_extras`
-
+pages for more info.
-The MS-CG library uses C++11, which may not be supported by older
-compilers. The MS-CG library also has some additional numeric library
-dependencies, which are described in its documentation.
 
 Currently, the MS-CG library is not set up to run in parallel with MPI,
-so this fix can only be used in a serial LAMMPS build and run
+so this fix can only be used in a serial LAMMPS build and run on a
-on a single processor.
+single processor.
 
 Related commands
 """"""""""""""""

doc/src/fix_mvv_dpd.rst

@@ -65,33 +65,37 @@ a default value of 0.5 is used, which effectively reproduces the
 standard velocity-Verlet (VV) scheme.  For more details, see
 :ref:`Groot <Groot2>`.
 
-Fix *mvv/dpd* updates the position and velocity of each atom.  It can
+Fix *mvv/dpd* updates the position and velocity of each atom.  It can be
-be used with the :doc:`pair_style mdpd <pair_mesodpd>` command or other
+used with the :doc:`pair_style mdpd <pair_mesodpd>` command or other
 pair styles such as :doc:`pair dpd <pair_dpd>`.
 
-Fix *mvv/edpd* updates the per-atom temperature, in addition to
+Fix *mvv/edpd* updates the per-atom temperature, in addition to position
-position and velocity, and must be used with the :doc:`pair_style edpd <pair_mesodpd>` command.
+and velocity, and must be used with the :doc:`pair_style edpd
+<pair_mesodpd>` command.
 
-Fix *mvv/tdpd* updates the per-atom chemical concentration, in
+Fix *mvv/tdpd* updates the per-atom chemical concentration, in addition
-addition to position and velocity, and must be used with the
+to position and velocity, and must be used with the :doc:`pair_style
-:doc:`pair_style tdpd <pair_mesodpd>` command.
+tdpd <pair_mesodpd>` command.
 
 ----------
 
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-No information about this fix is written to :doc:`binary restart files <restart>`.  None of the :doc:`fix_modify <fix_modify>` options
+No information about this fix is written to :doc:`binary restart files
-are relevant to this fix.  No global or per-atom quantities are stored
+<restart>`.  None of the :doc:`fix_modify <fix_modify>` options are
-by this fix for access by various :doc:`output commands <Howto_output>`.
+relevant to this fix.  No global or per-atom quantities are stored by
+this fix for access by various :doc:`output commands <Howto_output>`.
 No parameter of this fix can be used with the *start/stop* keywords of
-the :doc:`run <run>` command.  This fix is not invoked during :doc:`energy minimization <minimize>`.
+the :doc:`run <run>` command.  This fix is not invoked during
+:doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""
 
-This fix is part of the DPD-MESO package. It is only enabled if
+These fixes are part of the DPD-MESO package. They are only enabled if
-LAMMPS was built with that package. See the :doc:`Build package <Build_package>` page for more info.
+LAMMPS was built with that package. See the :doc:`Build package
+<Build_package>` page for more info.
 
 Related commands
 """"""""""""""""

doc/src/fix_nh_uef.rst

@@ -218,10 +218,11 @@ use :doc:`change_box <change_box>` before invoking the fix.
 Related commands
 """"""""""""""""
 
-:doc:`fix nvt <fix_nh>`, :doc:`fix npt <fix_nh>`, `fix nvt/sllod
+:doc:`fix nvt <fix_nh>`, :doc:`fix npt <fix_nh>`,
-:doc:<fix_nvt_sllod>`, `compute temp/uef <compute_temp_uef>`,
+:doc:`fix nvt/sllod <fix_nvt_sllod>`,
-:doc::doc:`compute pressure/uef <compute_pressure_uef>`, `dump cfg/uef
+:doc:`compute temp/uef <compute_temp_uef>`,
-:doc:<dump_cfg_uef>`
+:doc:`compute pressure/uef <compute_pressure_uef>`,
+:doc:`dump cfg/uef <dump_cfg_uef>`
 
 Default
 """""""

doc/src/fix_pimd.rst

@@ -1,7 +1,7 @@
 .. index:: fix pimd/nvt
 
 fix pimd/nvt command
-================
+====================
 
 Syntax
 """"""

doc/src/fix_shake.rst

@@ -63,7 +63,7 @@ however, can *only* be applied during molecular dynamics runs.
 
 .. versionchanged:: 15Sep2022
 
-These fixes may still be used during minimization.  In that case the
+These fixes may now also be used during minimization.  In that case the
 constraints are *approximated* by strong harmonic restraints.
 
 **SHAKE vs RATTLE:**
@@ -133,9 +133,9 @@ constraint lists atom types.  All bonds connected to an atom of the
 specified type will be constrained.  The *m* constraint lists atom
 masses.  All bonds connected to atoms of the specified masses will be
 constrained (within a fudge factor of MASSDELTA specified in
-fix_shake.cpp).  The *a* constraint lists angle types.  If both bonds
+``src/RIGID/fix_shake.cpp``).  The *a* constraint lists angle types.  If
-in the angle are constrained then the angle will also be constrained
+both bonds in the angle are constrained then the angle will also be
-if its type is in the list.
+constrained if its type is in the list.
 
 For all constraints, a particular bond is only constrained if both
 atoms in the bond are in the group specified with the SHAKE fix.
@@ -205,11 +205,11 @@ LAMMPS closely follows (:ref:`Andersen (1983) <Andersen3>`).
    The *fix rattle* command modifies forces and velocities and thus
    should be defined after all other integration fixes in your input
    script.  If you define other fixes that modify velocities or forces
-   after *fix rattle* operates, then *fix rattle* will not take them into
+   after *fix rattle* operates, then *fix rattle* will not take them
-   account and the overall time integration will typically not satisfy
+   into account and the overall time integration will typically not
-   the RATTLE constraints.  You can check whether the constraints work
+   satisfy the RATTLE constraints.  You can check whether the
-   correctly by setting the value of RATTLE_DEBUG in src/fix_rattle.cpp
+   constraints work correctly by setting the value of RATTLE_DEBUG in
-   to 1 and recompiling LAMMPS.
+   ``src/RIGID/fix_rattle.cpp`` to 1 and recompiling LAMMPS.
 
 ----------
 
@@ -275,8 +275,8 @@ reducing the :doc:`timestep <timestep>`.
 Related commands
 """"""""""""""""
 
-`fix rigid <fix_rigid>`, `fix ehex <fix_ehex>`,
+:doc:`fix rigid <fix_rigid>`, :doc:`fix ehex <fix_ehex>`,
-`fix nve/manifold/rattle <fix_nve_manifold_rattle>`
+:doc:`fix nve/manifold/rattle <fix_nve_manifold_rattle>`
 
 
 Default

doc/src/fix_wall.rst

@@ -194,6 +194,8 @@ For style *wall/morse*, the energy E is given by a Morse potential:
    E = D_0 \left[ e^{- 2 \alpha (r - r_0)} - 2 e^{- \alpha (r - r_0)} \right]
        \qquad r < r_c
 
+.. versionadded:: TBD
+
 For style *wall/lepton*, the energy E is provided as an Lepton
 expression string using "r" as the distance variable.  The `Lepton
 library <https://simtk.org/projects/lepton>`_, that the *wall/lepton*
@@ -213,6 +215,8 @@ spring as in fix *wall/harmonic* with a force constant *K* (same as
 :math:`\epsilon` above) of 100 energy units.  More details on the Lepton
 expression strings are given below.
 
+.. versionadded:: TBD
+
 For style *wall/table*, the energy E and forces are determined from
 interpolation tables listed in one or more files as a function of
 distance.  The interpolation tables are used to evaluate energy and
@@ -371,7 +375,7 @@ is *no*, which means the system must be non-periodic when using a wall.
 But you may wish to use a periodic box.  E.g. to allow some particles to
 interact with the wall via the fix group-ID, and others to pass through
 it and wrap around a periodic box.  In this case you should ensure that
-the wall if sufficiently far enough away from the box boundary.  If you
+the wall is sufficiently far enough away from the box boundary.  If you
 do not, then particles may interact with both the wall and with periodic
 images on the other side of the box, which is probably not what you
 want.

doc/src/minimize.rst

@@ -49,19 +49,19 @@ and forces) by pushing the atoms off of each other.
 
    The distance that atoms can move during individual minimization steps
    can be quite large, especially at the beginning of a minimization.
-   Thus `neighbor list settings <neigh_modify>` of *every = 1* and
+   Thus :doc:`neighbor list settings <neigh_modify>` of *every = 1* and
    *delay = 0* are **required**.  This may be combined with either
    *check = no* (always update the neighbor list) or *check = yes* (only
    update the neighbor list if at least one atom has moved more than
-   half the `neighbor list skin <neighbor>` distance since the last
+   half the :doc:`neighbor list skin <neighbor>` distance since the last
    reneighboring).  Using *check = yes* is recommended since it avoids
    unneeded reneighboring steps when the system is closer to the minimum
-   and thus atoms move only small distances.  Using *check = no* may
+   and thus atoms move only small distances.  Using *check = no* may be
-   be required for debugging or when coupling LAMMPS with external
+   required for debugging or when coupling LAMMPS with external codes
-   codes that require a predictable sequence of neighbor list updates.
+   that require a predictable sequence of neighbor list updates.
 
-   If the settings are **not** *every = 1* and *delay = 0*, LAMMPS
+   If the settings are **not** *every = 1* and *delay = 0*, LAMMPS will
-   will temporarily apply a `neigh_modify every 1 delay 0 check yes
+   temporarily apply a :doc:`neigh_modify every 1 delay 0 check yes
    <neigh_modify>` setting during the minimization and restore the
    original setting at the end of the minimization.  A corresponding
    message will be printed to the screen and log file, if this happens.

doc/src/molecule.rst

@@ -121,6 +121,11 @@ molecule (header keyword = inertia).
    ensure space is allocated for storing topology info for molecules that
    are added later.
 
+----------
+
+Format of a molecule file
+"""""""""""""""""""""""""
+
 The format of an individual molecule file is similar but
 (not identical) to the data file read by the :doc:`read_data <read_data>`
 commands, and is as follows.

doc/src/pair_eam.rst

@@ -116,11 +116,12 @@ are parameterized in terms of LAMMPS :doc:`metal units <units>`.
 
 .. note::
 
-   Note that unlike for other potentials, cutoffs for EAM
+   Note that unlike for other potentials, cutoffs for EAM potentials are not
-   potentials are not set in the pair_style or pair_coeff command; they
+   set in the pair_style or pair_coeff command; they are specified in the EAM
-   are specified in the EAM potential files themselves.  Likewise, the
+   potential files themselves.  Likewise, valid EAM potential files usually
-   EAM potential files list atomic masses; thus you do not need to use
+   contain atomic masses; thus you may not need to use the :doc:`mass <mass>`
-   the :doc:`mass <mass>` command to specify them.
+   command to specify them, unless the potential file uses a dummy value (e.g.
+   0.0). LAMMPS will print a warning, if this is the case.
 
 There are web sites that distribute and document EAM potentials stored
 in DYNAMO or other formats:

doc/src/pair_gauss.rst

@@ -103,12 +103,13 @@ Mixing, shift, table, tail correction, restart, rRESPA info
 
 For atom type pairs I,J and I != J, the A, B, H, sigma_h, r_mh
 parameters, and the cutoff distance for these pair styles can be mixed:
-A (energy units)
+
-sqrt(1/B) (distance units, see below)
+* A (energy units)
-H (energy units)
+* :math:`\sqrt{\frac{1}{B}}` (distance units, see below)
-sigma_h (distance units)
+* H (energy units)
-r_mh (distance units)
+* :math:`r_{mh}` (distance units)
-cutoff (distance units):ul
+* :math:`\sigma_h` (distance units)
+* cutoff (distance units)
 
 The default mix value is *geometric*\ .
 Only *arithmetic* and *geometric* mix values are supported.

doc/src/pair_hybrid.rst

@@ -91,7 +91,8 @@ contributions from sub-styles are weighted by their scale factors, which
 may be fractional or even negative.  Furthermore the scale factors may
 be variables that may change during a simulation.  This enables
 switching smoothly between two different pair styles or two different
-parameter sets during a run.
+parameter sets during a run in a similar fashion as could be done
+with :doc:`fix adapt <fix_adapt>` or :doc:`fix alchemy <fix_alchemy>`.
 
 All pair styles that will be used are listed as "sub-styles" following
 the *hybrid* or *hybrid/overlay* keyword, in any order.  In case of the

doc/src/pair_mesodpd.rst

@@ -299,7 +299,7 @@ Restrictions
 """"""""""""
 
 The pair styles *edpd*, *mdpd*, *mdpd/rhosum* and *tdpd* are part of
-the DPD-MESO package. It is only enabled if LAMMPS was built with
+the DPD-MESO package. They are only enabled if LAMMPS was built with
 that package.  See the :doc:`Build package <Build_package>` page for
 more info.
 

doc/src/pair_tersoff_mod.rst

@@ -145,7 +145,7 @@ coefficients in the formulae above:
 * c3
 * c4
 * c5
-* c0 (energy units, tersoff/mod/c only):ul
+* c0 (energy units, tersoff/mod/c only)
 
 The n, :math:`\eta`, :math:`\lambda_2`, B, :math:`\lambda_1`, and A parameters are only used for
 two-body interactions.  The :math:`\beta`, :math:`\alpha`, c1, c2, c3, c4, c5, h

doc/src/pair_ylz.rst

@@ -142,10 +142,11 @@ the :doc:`atom_style ellipsoid <atom_style>` command.
 Related commands
 """"""""""""""""
 
-:doc:`pair_coeff <pair_coeff>`, :doc:`fix nve/asphere
+:doc:`pair_coeff <pair_coeff>`,
-:doc:<fix_nve_asphere>`, `compute temp/asphere <compute_temp_asphere>`,
+:doc:`fix nve/asphere <fix_nve_asphere>`,
-:doc::doc:`pair_style resquared <pair_resquared>`, :doc:`pair_style
+:doc:`compute temp/asphere <compute_temp_asphere>`,
-:doc:gayberne <pair_gayberne>`
+:doc:`pair_style resquared <pair_resquared>`,
+:doc:`pair_style gayberne <pair_gayberne>`
 
 Default
 """""""

doc/src/read_data.rst

@@ -1477,10 +1477,12 @@ The *Triangles* section must appear after the *Atoms* section.
 
 where the keywords have these meanings:
 
+   .. parsed-literal::
+
       vx,vy,vz = translational velocity of atom
       lx,ly,lz = angular momentum of aspherical atom
       wx,wy,wz = angular velocity of spherical atom
-ervel = electron radial velocity (0 for fixed-core):ul
+      ervel = electron radial velocity (0 for fixed-core)
 
 The velocity lines can appear in any order.  This section can only be
 used after an *Atoms* section.  This is because the *Atoms* section

doc/src/run_style.rst

@@ -78,27 +78,41 @@ processors.  See the :doc:`-partition command-line switch <Run_options>`
 for info on how to run LAMMPS with multiple partitions.
 
 Specifically, this style performs all computation except the
-:doc:`kspace_style <kspace_style>` portion of the force field on the first
+:doc:`kspace_style <kspace_style>` portion of the force field on the
-partition.  This include the :doc:`pair style <pair_style>`, :doc:`bond style <bond_style>`, :doc:`neighbor list building <neighbor>`,
+first partition.  This include the :doc:`pair style <pair_style>`,
-:doc:`fixes <fix>` including time integration, and output.  The
+:doc:`bond style <bond_style>`, :doc:`neighbor list building
-:doc:`kspace_style <kspace_style>` portion of the calculation is
+<neighbor>`, :doc:`fixes <fix>` including time integration, and output.
+The :doc:`kspace_style <kspace_style>` portion of the calculation is
 performed on the second partition.
 
-This is most useful for the PPPM kspace_style when its performance on
+This can lead to a significant speedup, if the number of processors can
-a large number of processors degrades due to the cost of communication
+be easily increased and the fraction of time is spent in computing
-in its 3d FFTs.  In this scenario, splitting your P total processors
+Kspace interactions is significant, too.  The two partitions may have a
-into 2 subsets of processors, P1 in the first partition and P2 in the
+different number of processors.  This is most useful for the PPPM
-second partition, can enable your simulation to run faster.  This is
+kspace_style when its performance on a large number of processors
-because the long-range forces in PPPM can be calculated at the same
+degrades due to the cost of communication in its 3d FFTs.  In this
-time as pairwise and bonded forces are being calculated, and the FFTs
+scenario, splitting your P total processors into 2 subsets of
-can actually speed up when running on fewer processors.
+processors, P1 in the first partition and P2 in the second partition,
+can enable your simulation to run faster.  This is because the
+long-range forces in PPPM can be calculated at the same time as pairwise
+and bonded forces are being calculated *and* the parallel 3d FFTs can be
+faster to compute when running on fewer processors.  Please note that
+the scenario of using fewer MPI processes to reduce communication
+overhead can also be implemented through using MPI with OpenMP threads
+via the INTEL, KOKKOS, or OPENMP package.  This alternative option is
+typically more effective in case of a fixed number of available
+processors and less complex to execute.
 
-To use this style, you must define 2 partitions where P1 is a multiple
+To use the *verlet/split* style, you must define 2 partitions with the
-of P2.  Typically having P1 be 3x larger than P2 is a good choice.
+:doc:`-partition command-line switch <Run_options>`, where partition P1
-The 3d processor layouts in each partition must overlay in the
+is either the same size or an integer multiple of the size of the
-following sense.  If P1 is a Px1 by Py1 by Pz1 grid, and P2 = Px2 by
+partition P2.  Typically having P1 be 3x larger than P2 is a good
-Py2 by Pz2, then Px1 must be an integer multiple of Px2, and similarly
+choice, since the (serial) performance of LAMMPS is often best if the
-for Py1 a multiple of Py2, and Pz1 a multiple of Pz2.
+time spent in the ``Pair`` computation versus ``Kspace`` is a 3:1 split.
+The 3d processor layouts in each partition must overlay in the following
+sense.  If P1 is a Px1 by Py1 by Pz1 grid, and P2 = Px2 by Py2 by Pz2,
+then Px1 must be an integer multiple of Px2, and similarly for Py1 a
+multiple of Py2, and Pz1 a multiple of Pz2.
 
 Typically the best way to do this is to let the first partition choose
 its own optimal layout, then require the second partition's layout to
@@ -122,9 +136,10 @@ of 60 and 15 processors each:
 When you run in 2-partition mode with the *verlet/split* style, the
 thermodynamic data for the entire simulation will be output to the log
 and screen file of the first partition, which are log.lammps.0 and
-screen.0 by default; see the :doc:`-plog and -pscreen command-line switches <Run_options>` to change this.  The log and screen file
+screen.0 by default; see the :doc:`-plog and -pscreen command-line
-for the second partition will not contain thermodynamic output beyond the
+switches <Run_options>` to change this.  The log and screen file for the
-first timestep of the run.
+second partition will not contain thermodynamic output beyond the first
+timestep of the run.
 
 See the :doc:`Accelerator packages <Speed_packages>` page for
 performance details of the speed-up offered by the *verlet/split*
@@ -137,70 +152,73 @@ options to support this, and strategies are discussed in :doc:`Section
 ----------
 
 The *respa* style implements the rRESPA multi-timescale integrator
-:ref:`(Tuckerman) <Tuckerman3>` with N hierarchical levels, where level 1 is
+:ref:`(Tuckerman) <Tuckerman3>` with N hierarchical levels, where level
-the innermost loop (shortest timestep) and level N is the outermost
+1 is the innermost loop (shortest timestep) and level N is the outermost
 loop (largest timestep).  The loop factor arguments specify what the
-looping factor is between levels.  N1 specifies the number of
+looping factor is between levels.  N1 specifies the number of iterations
-iterations of level 1 for a single iteration of level 2, N2 is the
+of level 1 for a single iteration of level 2, N2 is the iterations of
-iterations of level 2 per iteration of level 3, etc.  N-1 looping
+level 2 per iteration of level 3, etc.  N-1 looping parameters must be
-parameters must be specified.
+specified.
 
-Thus with a 4-level respa setting of "2 2 2" for the 3 loop factors,
+Thus with a 4-level respa setting of "2 2 2" for the 3 loop factors, you
-you could choose to have bond interactions computed 8x per large
+could choose to have bond interactions computed 8x per large timestep,
-timestep, angle interactions computed 4x, pair interactions computed
+angle interactions computed 4x, pair interactions computed 2x, and
-2x, and long-range interactions once per large timestep.
+long-range interactions once per large timestep.
 
 The :doc:`timestep <timestep>` command sets the large timestep for the
 outermost rRESPA level.  Thus if the 3 loop factors are "2 2 2" for
-4-level rRESPA, and the outer timestep is set to 4.0 fs, then the
+4-level rRESPA, and the outer timestep is set to 4.0 fs, then the inner
-inner timestep would be 8x smaller or 0.5 fs.  All other LAMMPS
+timestep would be 8x smaller or 0.5 fs.  All other LAMMPS commands that
-commands that specify number of timesteps (e.g. :doc:`thermo <thermo>`
+specify number of timesteps (e.g. :doc:`thermo <thermo>` for thermo
-for thermo output every N steps, :doc:`neigh_modify delay/every <neigh_modify>` parameters, :doc:`dump <dump>` every N
+output every N steps, :doc:`neigh_modify delay/every <neigh_modify>`
-steps, etc) refer to the outermost timesteps.
+parameters, :doc:`dump <dump>` every N steps, etc) refer to the
+outermost timesteps.
 
-The rRESPA keywords enable you to specify at what level of the
+The rRESPA keywords enable you to specify at what level of the hierarchy
-hierarchy various forces will be computed.  If not specified, the
+various forces will be computed.  If not specified, the defaults are
-defaults are that bond forces are computed at level 1 (innermost
+that bond forces are computed at level 1 (innermost loop), angle forces
-loop), angle forces are computed where bond forces are, dihedral
+are computed where bond forces are, dihedral forces are computed where
-forces are computed where angle forces are, improper forces are
+angle forces are, improper forces are computed where dihedral forces
-computed where dihedral forces are, pair forces are computed at the
+are, pair forces are computed at the outermost level, and kspace forces
-outermost level, and kspace forces are computed where pair forces are.
+are computed where pair forces are.  The inner, middle, outer forces
-The inner, middle, outer forces have no defaults.
+have no defaults.
 
 For fixes that support it, the rRESPA level at which a given fix is
-active, can be selected through the :doc:`fix_modify <fix_modify>` command.
+active, can be selected through the :doc:`fix_modify <fix_modify>`
+command.
 
-The *inner* and *middle* keywords take additional arguments for
+The *inner* and *middle* keywords take additional arguments for cutoffs
-cutoffs that are used by the pairwise force computations.  If the 2
+that are used by the pairwise force computations.  If the 2 cutoffs for
-cutoffs for *inner* are 5.0 and 6.0, this means that all pairs up to
+*inner* are 5.0 and 6.0, this means that all pairs up to 6.0 apart are
-6.0 apart are computed by the inner force.  Those between 5.0 and 6.0
+computed by the inner force.  Those between 5.0 and 6.0 have their force
-have their force go ramped to 0.0 so the overlap with the next regime
+go ramped to 0.0 so the overlap with the next regime (middle or outer)
-(middle or outer) is smooth.  The next regime (middle or outer) will
+is smooth.  The next regime (middle or outer) will compute forces for
-compute forces for all pairs from 5.0 outward, with those from 5.0 to
+all pairs from 5.0 outward, with those from 5.0 to 6.0 having their
-6.0 having their value ramped in an inverse manner.
+value ramped in an inverse manner.
 
 Note that you can use *inner* and *outer* without using *middle* to
 split the pairwise computations into two portions instead of three.
-Unless you are using a very long pairwise cutoff, a 2-way split is
+Unless you are using a very long pairwise cutoff, a 2-way split is often
-often faster than a 3-way split, since it avoids too much duplicate
+faster than a 3-way split, since it avoids too much duplicate
 computation of pairwise interactions near the intermediate cutoffs.
 
-Also note that only a few pair potentials support the use of the
+Also note that only a few pair potentials support the use of the *inner*
-*inner* and *middle* and *outer* keywords.  If not, only the *pair*
+and *middle* and *outer* keywords.  If not, only the *pair* keyword can
-keyword can be used with that pair style, meaning all pairwise forces
+be used with that pair style, meaning all pairwise forces are computed
-are computed at the same rRESPA level.  See the doc pages for
+at the same rRESPA level.  See the doc pages for individual pair styles
-individual pair styles for details.
+for details.
 
 Another option for using pair potentials with rRESPA is with the
-*hybrid* keyword, which requires the use of the :doc:`pair_style hybrid or hybrid/overlay <pair_hybrid>` command.  In this scenario, different
+*hybrid* keyword, which requires the use of the :doc:`pair_style hybrid
+or hybrid/overlay <pair_hybrid>` command.  In this scenario, different
 sub-styles of the hybrid pair style are evaluated at different rRESPA
-levels.  This can be useful, for example, to set different timesteps
+levels.  This can be useful, for example, to set different timesteps for
-for hybrid coarse-grained/all-atom models.  The *hybrid* keyword
+hybrid coarse-grained/all-atom models.  The *hybrid* keyword requires as
-requires as many level assignments as there are hybrid sub-styles,
+many level assignments as there are hybrid sub-styles, which assigns
-which assigns each sub-style to a rRESPA level, following their order
+each sub-style to a rRESPA level, following their order of definition in
-of definition in the pair_style command. Since the *hybrid* keyword
+the pair_style command. Since the *hybrid* keyword operates on pair
-operates on pair style computations, it is mutually exclusive with
+style computations, it is mutually exclusive with either the *pair* or
-either the *pair* or the *inner*\ /\ *middle*\ /\ *outer* keywords.
+the *inner*\ /\ *middle*\ /\ *outer* keywords.
 
 When using rRESPA (or for any MD simulation) care must be taken to
 choose a timestep size(s) that ensures the Hamiltonian for the chosen

doc/utils/check-packages.py

@@ -49,7 +49,9 @@ pkgs = []
 # folder, and is not called 'MAKE' is a package 
 
 for d in pkgdirs:
-    pkg = dirs.match(d).group(1)
+    match = dirs.match(d)
+    if not match: continue
+    pkg = match.group(1)
     if not os.path.isdir(os.path.join(src_dir, pkg)): continue
     if pkg in ['DEPEND','MAKE','STUBS']: continue
     pkgs.append(pkg)

doc/utils/sphinx-config/false_positives.txt

@@ -1,5 +1,6 @@
 aa
 aat
+Abascal
 abc
 abf
 ABI
@@ -437,6 +438,7 @@ cfile
 CFL
 cgdna
 CGDNA
+cgmap
 cgs
 cgsdk
 CGSDK
@@ -1442,6 +1444,7 @@ hux
 hwloc
 hx
 hy
+hydronium
 hydrophobicity
 hydrostatic
 hydrostatically
@@ -1791,6 +1794,7 @@ lammps
 Lammps
 LAMMPS
 lammpsbin
+lammpsdata
 lammpsplot
 lammpsplugin
 Lamoureux
@@ -1985,6 +1989,7 @@ magelec
 Maginn
 magneton
 magnetons
+Mahoney
 mainboard
 mainboards
 makefile
@@ -2070,6 +2075,7 @@ mdi
 MDI
 mdpd
 mDPD
+mdtraj
 meam
 MEAM
 meamf
@@ -3186,6 +3192,7 @@ Sandia
 sandybrown
 sanitizer
 Sanyal
+Sanz
 Sarath
 sc
 scafacos

examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8

@@ -0,0 +1,2 @@
+LAMMPS (8 Feb 2023)
+Running on 8 partitions of processors

examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.0

@@ -0,0 +1,199 @@
+LAMMPS (8 Feb 2023)
+Processor partition = 0
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+variable ibead uloop 32 pad
+variable out_freq string 100
+variable job_name string H2
+
+units      real
+atom_style full
+pair_style table linear 10000
+
+neighbor 2.0 bin
+neigh_modify every 1 delay 0 check no
+
+read_data H2.data
+Reading data file ...
+  orthogonal box = (0 0 0) to (19.71219 19.71219 19.71219)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  180 atoms
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     0 = max # of 1-2 neighbors
+     0 = max # of 1-3 neighbors
+     0 = max # of 1-4 neighbors
+     1 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
+  read_data CPU = 0.003 seconds
+
+pair_coeff 1 * pair.table PAIR_H2
+WARNING: 5852 of 18000 force values in table PAIR_H2 are inconsistent with -dE/dr.
+WARNING:  Should only be flagged at inflection points (src/pair_table.cpp:466)
+
+timestep        0.001
+
+velocity all create 1.0 1985 rot yes dist gaussian
+
+fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 25.0 nhc 4
+
+thermo_style    custom step temp pe etotal pzz f_1[1] f_1[2] f_1[3]
+thermo_modify   colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial
+thermo          ${out_freq}
+thermo          100
+
+#dump dcd all dcd ${out_freq} ${job_name}_${ibead}.dcd
+
+#restart ${out_freq} ${job_name}_${ibead}.restart1 ${job_name}_${ibead}.restart2
+
+run 10000
+WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Fix pimd/nvt -P/(beta^2 * hbar^2) =       -2.0510430e-01 (kcal/mol/A^2)
+
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 11.55117
+  ghost atom cutoff = 11.55117
+  binsize = 5.775585, bins = 4 4 4
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair table, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 11.97 | 11.97 | 11.97 Mbytes
+   Step          Temp          PotEng         TotEng          Pzz          espring         T_ring         virial    
+         0   1             -50.292986     -49.759421      16.18218       0              2.4190752e-312  4.331435e-14 
+       100   1.0017926     -50.292812     -49.758291      16.197861      4.265072e-05   0.99622709    -0.027624534  
+       200   1.0071966     -50.292414     -49.755009      16.235286      0.00017002327  1.0016011     -0.055248299  
+       300   1.0162913     -50.291757     -49.7495        16.297361      0.00038044032  1.0106453     -0.082873452  
+       400   1.0292116     -50.290849     -49.741697      16.38451       0.00067129747  1.0234938     -0.11047807   
+       500   1.046152      -50.289692     -49.731502      16.497053      0.0010393068   1.0403401     -0.13806207   
+       600   1.0673727     -50.288298     -49.718785      16.634959      0.0014807685   1.0614428     -0.16561253   
+       700   1.0932075     -50.286675     -49.703378      16.798983      0.0019918311   1.0871342     -0.19314289   
+       800   1.1240754     -50.284828     -49.68506       16.990234      0.0025687136   1.1178306     -0.22065895   
+       900   1.1604938     -50.28276      -49.663562      17.210179      0.0032078786   1.1540466     -0.24818038   
+      1000   1.2030968     -50.280481     -49.638551      17.460167      0.0039061562   1.196413      -0.27572028   
+      1100   1.2526583     -50.277991     -49.609616      17.742341      0.0046608267   1.2456991     -0.30331246   
+      1200   1.3101204     -50.275294     -49.576259      18.059364      0.0054696709   1.3028419     -0.33099732   
+      1300   1.3766308     -50.272386     -49.537864      18.415203      0.0063309999   1.3689828     -0.35880748   
+      1400   1.4535894     -50.269262     -49.493677      18.814095      0.007243672    1.4455139     -0.38678366   
+      1500   1.5427084     -50.265919     -49.442783      19.261431      0.0082071044   1.5341378     -0.41499269   
+      1600   1.6460882     -50.262344     -49.384049      19.763852      0.0092212862   1.6369433     -0.44348166   
+      1700   1.7663158     -50.25853      -49.316086      20.329991      0.010286796    1.756503      -0.47232409   
+      1800   1.9065905     -50.254461     -49.237171      20.96974       0.01140483     1.8959983     -0.50158483   
+      1900   2.0708856     -50.250115     -49.145163      21.696809      0.012577241    2.0593807     -0.53134846   
+      2000   2.2641571     -50.245477     -49.037402      22.525956      0.013806592    2.2515785     -0.5617101    
+      2100   2.4926123     -50.240516     -48.910546      23.477847      0.015096239    2.4787644     -0.59276642   
+      2200   2.7640541     -50.2352       -48.760398      24.577541      0.01645042     2.7486983     -0.62463764   
+      2300   3.088323      -50.229491     -48.58167       25.856282      0.017874391    3.0711656     -0.65745388   
+      2400   3.4778567     -50.223344     -48.367681      27.353194      0.01937458     3.4585353     -0.69135912   
+      2500   3.9483938     -50.216703     -48.109978      29.11873       0.020958791    3.9264583     -0.72652121   
+      2600   4.5198403     -50.209503     -47.797875      31.215234      0.02263645     4.4947301     -0.76313188   
+      2700   5.2173107     -50.201663     -47.417889      33.721815      0.024418904    5.1883257     -0.80140558   
+      2800   6.0723283     -50.193089     -46.953107      36.73757       0.026319777    6.0385931     -0.84159436   
+      2900   7.1241213     -50.183668     -46.382487      40.38551       0.028355393    7.0845429     -0.88396874   
+      3000   8.4208727     -50.173266     -45.680183      44.816478      0.030545255    8.3740901     -0.9288431    
+      3100   10.020649     -50.161717     -44.81505       50.212214      0.032912578    9.9649788     -0.97656436   
+      3200   11.991558     -50.148837     -43.750561      56.786471      0.035484852    11.924938     -1.0275116    
+      3300   14.410456     -50.134392     -42.445477      64.781319      0.038294377    14.330398     -1.0821007    
+      3400   17.359303     -50.11813      -40.855813      74.455919      0.041378722    17.262863     -1.14076      
+      3500   20.918126     -50.099744     -38.938564      86.068376      0.044780961    20.801915     -1.2039443    
+      3600   25.153676     -50.078895     -36.657774      99.840861      0.048549564    25.013933     -1.2720773    
+      3700   30.103431     -50.055212     -33.993075      115.91254      0.052737712    29.93619      -1.3455663    
+      3800   35.755845     -50.028299     -30.950232      134.28175      0.057401834    35.557201     -1.4247605    
+      3900   42.029581     -49.997746     -27.572232      154.74519      0.062599126    41.796084     -1.5098692    
+      4000   48.756702     -49.963159     -23.948289      176.84543      0.06838392     48.485832     -1.6010084    
+      4100   55.676392     -49.924188     -20.217214      199.84979      0.074802896    55.367079     -1.6980754    
+      4200   62.445716     -49.880563     -16.561714      222.7783       0.081889414    62.098795     -1.8007866    
+      4300   68.671023     -49.832118     -13.191664      244.49021      0.089657516    68.289518     -1.9086164    
+      4400   73.957826     -49.778843     -10.317535      263.82539      0.098096488    73.546949     -2.0208305    
+      4500   77.969954     -49.7209       -8.1188616      279.77238      0.10716704     77.536788     -2.1364913    
+      4600   80.483598     -49.658617     -6.7153862      291.6285       0.11680011     80.036467     -2.254524     
+      4700   81.421471     -49.592506     -6.1488596      299.10183      0.12689894     80.969129     -2.3737378    
+      4800   80.857888     -49.523204     -6.3802649      302.3328       0.13734453     80.408677     -2.492954     
+      4900   78.994781     -49.451459     -7.3026086      301.83334      0.14800388     78.555921     -2.6110228    
+      5000   76.117367     -49.378045     -8.7644823      298.36557      0.15873983     75.694493     -2.7269278    
+      5100   72.542745     -49.303735     -10.597466      292.79593      0.16942116     72.139729     -2.8398052    
+      5200   68.573953     -49.22923      -12.640569      285.96472      0.17993138     68.192987     -2.949009     
+      5300   64.467624     -49.155126     -14.757458      278.59037      0.19017535     64.10947      -3.0540851    
+      5400   60.41785      -49.081671     -16.844821      271.22804      0.20008281     60.082195     -3.1546148    
+      5500   56.554431     -49.009666     -18.834201      264.2355       0.20960898     56.24024      -3.250862     
+      5600   52.95111      -48.938861     -20.686002      257.84121      0.21873248     52.656937     -3.3428291    
+      5700   49.638794     -48.869827     -22.384304      252.12886      0.22745138     49.363023     -3.4305128    
+      5800   46.619514     -48.801888     -23.927347      247.13356      0.23577844     46.360517     -3.5141755    
+      5900   43.878389     -48.73593      -25.323958      242.80111      0.24373625     43.634621     -3.5942967    
+      6000   41.392437     -48.671406     -26.585851      239.09246      0.25135296     41.162479     -3.6710953    
+      6100   39.136252     -48.60798      -27.726246      235.9541       0.25865905     38.918828     -3.7449553    
+      6200   37.085195     -48.545774     -28.758412      233.32233      0.26568495     36.879167     -3.8159439    
+      6300   35.216896     -48.484909     -29.694407      231.1392       0.27245965     35.021246     -3.884503     
+      6400   33.511732     -48.42458      -30.543893      229.37842      0.2790099      33.325556     -3.9507385    
+      6500   31.952789     -48.365385     -31.316496      227.98228      0.2853599      31.775274     -4.0149897    
+      6600   30.525576     -48.307233     -32.019853      226.91697      0.29153132     30.35599      -4.0774486    
+      6700   29.217672     -48.24981      -32.660283      226.16022      0.29754342     29.055351     -4.1382338    
+      6800   28.018378     -48.192803     -33.243177      225.69366      0.30341329     27.862721     -4.1974677    
+      6900   26.918418     -48.136622     -33.773896      225.48194      0.30915615     26.768871     -4.2553485    
+      7000   25.909681     -48.08096      -34.256461      225.51257      0.31478562     25.765738     -4.311968     
+      7100   24.985015     -48.025534     -34.694405      225.77479      0.32031392     24.84621      -4.3675242    
+      7200   24.138072     -47.970746     -35.091516      226.24048      0.32575216     24.003972     -4.4219335    
+      7300   23.36317      -47.916089     -35.450319      226.90757      0.33111051     23.233375     -4.4754578    
+      7400   22.655198     -47.861976     -35.773956      227.75054      0.33639834     22.529336     -4.5280134    
+      7500   22.009532     -47.808135     -36.064618      228.76407      0.34162439     21.887257     -4.5797622    
+      7600   21.421974     -47.754508     -36.324492      229.93785      0.34679689     21.302963     -4.6307739    
+      7700   20.888691     -47.700827     -36.555352      231.26801      0.35192361     20.772643     -4.6812057    
+      7800   20.406177     -47.64705      -36.759028      232.73618      0.35701201     20.292809     -4.7306795    
+      7900   19.971205     -47.593833     -36.937897      234.33449      0.36206923     19.860254     -4.7798815    
+      8000   19.580795     -47.540435     -37.092808      236.06384      0.36710221     19.472013     -4.8285632    
+      8100   19.232176     -47.487281     -37.225665      237.90655      0.37211768     19.125331     -4.8768578    
+      8200   18.922755     -47.4341       -37.33758       239.86116      0.37712221     18.817628     -4.9247735    
+      8300   18.650078     -47.380856     -37.429827      241.92202      0.38212226     18.546466     -4.972363     
+      8400   18.4118       -47.327508     -37.503616      244.08393      0.38712418     18.309512     -5.0196756    
+      8500   18.205651     -47.273789     -37.559891      246.34742      0.3921342      18.104508     -5.06671      
+      8600   18.029398     -47.219424     -37.599568      248.71065      0.39715848     17.929235     -5.1133124    
+      8700   17.880815     -47.165549     -37.624972      251.14475      0.4022031      17.781477     -5.1600447    
+      8800   17.757645     -47.110958     -37.636101      253.66312      0.40727406     17.658991     -5.2066259    
+      8900   17.657573     -47.056554     -37.635091      256.25454      0.41237724     17.559475     -5.2531731    
+      9000   17.578197     -47.001835     -37.622724      258.91696      0.41751847     17.48054      -5.2996769    
+      9100   17.517006     -46.946535     -37.600073      261.64727      0.42270345     17.41969      -5.3462575    
+      9200   17.471368     -46.890625     -37.568515      264.44427      0.42793776     17.374305     -5.3925966    
+      9300   17.438519     -46.834765     -37.530181      267.28872      0.43322691     17.341639     -5.4391596    
+      9400   17.415579     -46.778464     -37.486121      270.18178      0.43857628     17.318826     -5.485798     
+      9500   17.399563     -46.721685     -37.437887      273.11812      0.44399119     17.302899     -5.5325337    
+      9600   17.387425     -46.664405     -37.387083      276.08982      0.44947693     17.290829     -5.5793912    
+      9700   17.376109     -46.606364     -37.335081      279.09236      0.45503878     17.279575     -5.6264788    
+      9800   17.362615     -46.547755     -37.283671      282.11747      0.46068208     17.266156     -5.6736623    
+      9900   17.344087     -46.488783     -37.234585      285.15699      0.46641232     17.247731     -5.7209993    
+     10000   17.317913     -46.42918      -37.188947      288.20641      0.4722352      17.221703     -5.7685405    
+Loop time of 14.691 on 1 procs for 10000 steps with 180 atoms
+
+Performance: 0.059 ns/day, 408.083 hours/ns, 680.689 timesteps/s, 122.524 katom-step/s
+96.5% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 3.0453     | 3.0453     | 3.0453     |   0.0 | 20.73
+Bond    | 0.00108    | 0.00108    | 0.00108    |   0.0 |  0.01
+Neigh   | 6.6815     | 6.6815     | 6.6815     |   0.0 | 45.48
+Comm    | 0.55477    | 0.55477    | 0.55477    |   0.0 |  3.78
+Output  | 0.0028885  | 0.0028885  | 0.0028885  |   0.0 |  0.02
+Modify  | 4.3341     | 4.3341     | 4.3341     |   0.0 | 29.50
+Other   |            | 0.07136    |            |       |  0.49
+
+Nlocal:            180 ave         180 max         180 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           1510 ave        1510 max        1510 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          13729 ave       13729 max       13729 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 13729
+Ave neighs/atom = 76.272222
+Ave special neighs/atom = 0
+Neighbor list builds = 10000
+Dangerous builds not checked
+Total wall time: 0:00:14

examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.1

@@ -0,0 +1,197 @@
+LAMMPS (8 Feb 2023)
+Processor partition = 1
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+variable ibead uloop 32 pad
+variable out_freq string 100
+variable job_name string H2
+
+units      real
+atom_style full
+pair_style table linear 10000
+
+neighbor 2.0 bin
+neigh_modify every 1 delay 0 check no
+
+read_data H2.data
+Reading data file ...
+  orthogonal box = (0 0 0) to (19.71219 19.71219 19.71219)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  180 atoms
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     0 = max # of 1-2 neighbors
+     0 = max # of 1-3 neighbors
+     0 = max # of 1-4 neighbors
+     1 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
+  read_data CPU = 0.003 seconds
+
+pair_coeff 1 * pair.table PAIR_H2
+WARNING: 5852 of 18000 force values in table PAIR_H2 are inconsistent with -dE/dr.
+WARNING:  Should only be flagged at inflection points (src/pair_table.cpp:466)
+
+timestep        0.001
+
+velocity all create 1.0 1985 rot yes dist gaussian
+
+fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 25.0 nhc 4
+
+thermo_style    custom step temp pe etotal pzz f_1[1] f_1[2] f_1[3]
+thermo_modify   colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial
+thermo          ${out_freq}
+thermo          100
+
+#dump dcd all dcd ${out_freq} ${job_name}_${ibead}.dcd
+
+#restart ${out_freq} ${job_name}_${ibead}.restart1 ${job_name}_${ibead}.restart2
+
+run 10000
+WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 11.55117
+  ghost atom cutoff = 11.55117
+  binsize = 5.775585, bins = 4 4 4
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair table, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 11.97 | 11.97 | 11.97 Mbytes
+   Step          Temp          PotEng         TotEng          Pzz          espring         T_ring         virial    
+         0   1             -50.292986     -49.759421      16.18218       0              0              4.331435e-14 
+       100   1.0008585     -50.292908     -49.758885      16.189586      7.3078196e-06  4.6642574     -0.013945396  
+       200   1.0034473     -50.292787     -49.757382      16.20341       2.9015288e-05  4.6763219     -0.027851725  
+       300   1.0078065     -50.292593     -49.754863      16.225711      6.4500006e-05  4.6966366     -0.041662754  
+       400   1.0140035     -50.29233      -49.751293      16.257176      0.00011280318  4.7255165     -0.055352542  
+       500   1.022135      -50.292004     -49.746629      16.297097      0.000172727    4.7634112     -0.068879202  
+       600   1.0323282     -50.291621     -49.740807      16.346105      0.00024293886  4.810914      -0.082221014  
+       700   1.044744      -50.291188     -49.733749      16.404167      0.00032206529  4.8687751     -0.095360512  
+       800   1.0595808     -50.290712     -49.725357      16.471712      0.00040876559  4.9379182     -0.10826526   
+       900   1.0770788     -50.290199     -49.715507      16.549069      0.00050178229  5.0194635     -0.1209272    
+      1000   1.0975268     -50.289655     -49.704053      16.636751      0.00059997025  5.1147563     -0.13335203   
+      1100   1.1212697     -50.289087     -49.690817      16.735749      0.00070230922  5.2254045     -0.14552504   
+      1200   1.1487191     -50.288499     -49.675582      16.846901      0.00080790454  5.3533259     -0.15745048   
+      1300   1.1803661     -50.287894     -49.658092      16.971484      0.00091598038  5.5008089     -0.16912662   
+      1400   1.2167975     -50.287272     -49.638032      17.111786      0.001025869    5.6705884     -0.18056175   
+      1500   1.2587169     -50.286644     -49.615037      17.26922       0.0011369979   5.8659438     -0.19176702   
+      1600   1.3069713     -50.286008     -49.588654      17.446637      0.0012488773   6.0908216     -0.20274823   
+      1700   1.3625842     -50.285365     -49.558338      17.646978      0.0013610874   6.349992      -0.21351296   
+      1800   1.4267987     -50.284719     -49.523429      17.874056      0.0014732674   6.6492481     -0.2240754    
+      1900   1.5011316     -50.284073     -49.483122      18.132347      0.0015851058   6.9956586     -0.23443788   
+      2000   1.5874426     -50.283426     -49.436422      18.428012      0.0016963317   7.3978897     -0.24461477   
+      2100   1.6880217     -50.282783     -49.382113      18.767914      0.0018067084   7.866614      -0.25461336   
+      2200   1.805701      -50.282144     -49.318685      19.160875      0.0019160281   8.4150298     -0.26443254   
+      2300   1.9439951     -50.281509     -49.244262      19.617751      0.0020241086   9.0595157     -0.27408815   
+      2400   2.1072772     -50.280879     -49.15651       20.152728      0.0021307926   9.8204522     -0.28357876   
+      2500   2.3009976     -50.28026      -49.052528      20.78256       0.0022359485   10.723239     -0.29290505   
+      2600   2.5319494     -50.279651     -48.928691      21.528586      0.0023394759   11.799534     -0.30206821   
+      2700   2.8085834     -50.279048     -48.780486      22.417919      0.0024413142   13.088719     -0.31106836   
+      2800   3.1413661     -50.278457     -48.602334      23.483643      0.0025414581   14.639572     -0.31990395   
+      2900   3.5431594     -50.277876     -48.38737       24.766603      0.0026399801   16.512032     -0.32855403   
+      3000   4.029577      -50.277305     -48.127264      26.316279      0.0027370628   18.778862     -0.33702346   
+      3100   4.6192292     -50.276739     -47.81208       28.192254      0.0028330445   21.526793     -0.3452905    
+      3200   5.333716      -50.276174     -47.43029       30.464107      0.0029284791   24.856485     -0.35332773   
+      3300   6.1971481     -50.275605     -46.969024      33.208128      0.0030242128   28.8803       -0.36114465   
+      3400   7.2349012     -50.27502      -46.41473       36.506582      0.0031214781   33.716495     -0.36868512   
+      3500   8.4712457     -50.274401     -45.754441      40.437918      0.0032219998   39.478178     -0.37595678   
+      3600   9.9255066     -50.273728     -44.977825      45.065017      0.0033281047   46.255407     -0.38292345   
+      3700   11.606561     -50.27297      -44.080116      50.41841       0.0034428151   54.089554     -0.38955061   
+      3800   13.505865     -50.272095     -43.065838      56.472981      0.0035698989   62.940797     -0.39583139   
+      3900   15.589837     -50.271059     -41.952868      63.125206      0.0037138374   72.652639     -0.40173444   
+      4000   17.793286     -50.26982      -40.775945      70.171007      0.0038796665   82.921278     -0.40724146   
+      4100   20.016352     -50.26833      -39.588305      77.297059      0.0040726574   93.281337     -0.350557     
+      4200   22.127692     -50.266548     -38.459986      84.091411      0.0042978175   103.12072     -0.42427987   
+      4300   23.975875     -50.264442     -37.471754      90.07826       0.0045592402   111.73373     -0.44332019   
+      4400   25.408871     -50.262001     -36.704717      94.780152      0.0048593802   118.41186     -0.4712594    
+      4500   26.298516     -50.259233     -36.227265      97.796601      0.0051983826   122.55783     -0.48751932   
+      4600   26.564146     -50.256176     -36.082477      98.874143      0.0055736202   123.79574     -0.50751557   
+      4700   26.188683     -50.252888     -36.279523      97.96053       0.0059795748   122.04598     -0.53463961   
+      4800   25.22218      -50.249455     -36.791783      95.211762      0.0064081371   117.54183     -0.56057187   
+      4900   23.771743     -50.245971     -37.562201      90.960801      0.0068493041   110.78242     -0.58649549   
+      5000   21.981009     -50.242542     -38.514245      85.651619      0.0072921623   102.43714     -0.58569676   
+      5100   20.005118     -50.239262     -39.565231      79.762203      0.0077259803   93.228984     -0.58814947   
+      5200   17.987555     -50.236217     -40.638687      73.732022      0.0081412203   83.826622     -0.64456631   
+      5300   16.043551     -50.23346      -41.673183      67.91308       0.0085303062   74.767062     -0.66253179   
+      5400   14.252123     -50.231042     -42.626609      62.542995      0.0088880521   66.418547     -0.67647833   
+      5500   12.656267     -50.228973     -43.476032      57.750687      0.0092117291   58.981452     -0.69035428   
+      5600   11.269006     -50.227253     -44.214506      53.573237      0.0095008225   52.516458     -0.70182381   
+      5700   10.082247     -50.225863     -44.846329      49.983875      0.0097565822   46.985857     -0.71107461   
+      5800   9.075711      -50.224777     -45.382295      46.920816      0.0099814848   42.295142     -0.72796918   
+      5900   8.2241323     -50.223954     -45.835845      44.308503      0.010178713    38.326566     -0.7341011    
+      6000   7.5020778     -50.223364     -46.220518      42.071534      0.010351726    34.961607     -0.73860614   
+      6100   6.8865776     -50.222972     -46.548535      40.142111      0.010503944    32.093218     -0.74169302   
+      6200   6.3581625     -50.222743     -46.83025       38.464555      0.010638555    29.630669     -0.74355815   
+      6300   5.9009471     -50.222651     -47.074112      36.993223      0.010758413    27.499927     -0.72351831   
+      6400   5.5022478     -50.222668     -47.286861      35.692229      0.010866003    25.641886     -0.72491142   
+      6500   5.1520445     -50.222775     -47.473825      34.533075      0.010963451    24.009849     -0.72550196   
+      6600   4.842444      -50.222956     -47.639197      33.493966      0.011052555    22.567032     -0.72539576   
+      6700   4.5672154     -50.223194     -47.786287      32.557859      0.011134828    21.284396     -0.72468094   
+      6800   4.3214112     -50.22348      -47.917726      31.710288      0.011211542    20.138885     -0.69977477   
+      6900   4.1010719     -50.223805     -48.035616      30.941022      0.011283771    19.112047     -0.6977173    
+      7000   3.9029992     -50.224161     -48.141657      30.240625      0.011352422    18.188977     -0.69521625   
+      7100   3.7245829     -50.22454      -48.237233      29.602229      0.011418274    17.357512     -0.69232721   
+      7200   3.5636708     -50.224941     -48.323491      29.019374      0.011482       16.60762      -0.68909561   
+      7300   3.4184697     -50.225359     -48.401383      28.487117      0.011544187    15.930946     -0.68553322   
+      7400   3.2874703     -50.225791     -48.471712      28.00136       0.011605358    15.320455     -0.68167743   
+      7500   3.1693898     -50.226236     -48.53516       27.5579        0.01166598     14.77017      -0.67389187   
+      7600   3.0631284     -50.226689     -48.592311      27.15399       0.011726479    14.274964     -0.66987688   
+      7700   2.9677349     -50.227151     -48.643671      26.786563      0.011787244    13.830406     -0.66561073   
+      7800   2.8823804     -50.227616     -48.689679      26.453373      0.011848631    13.432632     -0.66110134   
+      7900   2.8063371     -50.228091     -48.730728      26.151709      0.011910973    13.078251     -0.65637083   
+      8000   2.7389612     -50.228567     -48.767153      25.879876      0.011974573    12.764262     -0.65142182   
+      8100   2.6796793     -50.229048     -48.799265      25.636155      0.01203971     12.487993     -0.64626697   
+      8200   2.6279769     -50.229528     -48.827332      25.418653      0.012106636    12.247046     -0.64092634   
+      8300   2.583388      -50.230009     -48.851603      25.225967      0.012175578    12.039251     -0.63576886   
+      8400   2.5454874     -50.230488     -48.872305      25.056681      0.012246734    11.862624     -0.63004687   
+      8500   2.5138825     -50.230965     -48.889645      24.909342      0.012320275    11.715337     -0.62413585   
+      8600   2.4882074     -50.231439     -48.903818      24.782526      0.012396346    11.595685     -0.65229004   
+      8700   2.468117      -50.231904     -48.915003      24.674923      0.012475068    11.502059     -0.64624002   
+      8800   2.4532823     -50.232364     -48.923378      24.585268      0.012556541    11.432925     -0.6399876    
+      8900   2.4433865     -50.232811     -48.929106      24.512562      0.012640854    11.386808     -0.63354      
+      9000   2.4381226     -50.233249     -48.932352      24.45498       0.012728083    11.362277     -0.62690844   
+      9100   2.4371917     -50.233668     -48.933268      24.411953      0.012818306    11.357939     -0.62009589   
+      9200   2.4403031     -50.234074     -48.932014      24.381442      0.012911605    11.372438     -0.61311776   
+      9300   2.4471754     -50.234458     -48.928731      24.362769      0.013008072    11.404465     -0.60599097   
+      9400   2.4575396     -50.234822     -48.923565      24.354135      0.013107819    11.452765     -0.60061336   
+      9500   2.4711435     -50.235157     -48.916642      24.354998      0.013210974    11.516163     -0.59323525   
+      9600   2.4877569     -50.235465     -48.908085      24.363855      0.013317688    11.593585     -0.58576008   
+      9700   2.5071778     -50.235743     -48.898         24.380012      0.013428136    11.684092     -0.57821051   
+      9800   2.5292388     -50.235983     -48.886469      24.402788      0.013542514    11.786902     -0.57061067   
+      9900   2.5538131     -50.236185     -48.873559      24.431609      0.013661041    11.901424     -0.56299206   
+     10000   2.5808184     -50.236346     -48.859312      24.466316      0.013783954    12.027276     -0.55538687   
+Loop time of 14.691 on 1 procs for 10000 steps with 180 atoms
+
+Performance: 0.059 ns/day, 408.083 hours/ns, 680.690 timesteps/s, 122.524 katom-step/s
+98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.8924     | 2.8924     | 2.8924     |   0.0 | 19.69
+Bond    | 0.00092288 | 0.00092288 | 0.00092288 |   0.0 |  0.01
+Neigh   | 6.5718     | 6.5718     | 6.5718     |   0.0 | 44.73
+Comm    | 0.55162    | 0.55162    | 0.55162    |   0.0 |  3.75
+Output  | 0.0029431  | 0.0029431  | 0.0029431  |   0.0 |  0.02
+Modify  | 4.6104     | 4.6104     | 4.6104     |   0.0 | 31.38
+Other   |            | 0.06102    |            |       |  0.42
+
+Nlocal:            180 ave         180 max         180 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           1510 ave        1510 max        1510 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          13680 ave       13680 max       13680 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 13680
+Ave neighs/atom = 76
+Ave special neighs/atom = 0
+Neighbor list builds = 10000
+Dangerous builds not checked
+Total wall time: 0:00:14

examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.2

@@ -0,0 +1,197 @@
+LAMMPS (8 Feb 2023)
+Processor partition = 2
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+variable ibead uloop 32 pad
+variable out_freq string 100
+variable job_name string H2
+
+units      real
+atom_style full
+pair_style table linear 10000
+
+neighbor 2.0 bin
+neigh_modify every 1 delay 0 check no
+
+read_data H2.data
+Reading data file ...
+  orthogonal box = (0 0 0) to (19.71219 19.71219 19.71219)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  180 atoms
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     0 = max # of 1-2 neighbors
+     0 = max # of 1-3 neighbors
+     0 = max # of 1-4 neighbors
+     1 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
+  read_data CPU = 0.003 seconds
+
+pair_coeff 1 * pair.table PAIR_H2
+WARNING: 5852 of 18000 force values in table PAIR_H2 are inconsistent with -dE/dr.
+WARNING:  Should only be flagged at inflection points (src/pair_table.cpp:466)
+
+timestep        0.001
+
+velocity all create 1.0 1985 rot yes dist gaussian
+
+fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 25.0 nhc 4
+
+thermo_style    custom step temp pe etotal pzz f_1[1] f_1[2] f_1[3]
+thermo_modify   colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial
+thermo          ${out_freq}
+thermo          100
+
+#dump dcd all dcd ${out_freq} ${job_name}_${ibead}.dcd
+
+#restart ${out_freq} ${job_name}_${ibead}.restart1 ${job_name}_${ibead}.restart2
+
+run 10000
+WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 11.55117
+  ghost atom cutoff = 11.55117
+  binsize = 5.775585, bins = 4 4 4
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair table, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 11.97 | 11.97 | 11.97 Mbytes
+   Step          Temp          PotEng         TotEng          Pzz          espring         T_ring         virial    
+         0   1             -50.292986     -49.759421      16.18218       0              0              4.331435e-14 
+       100   1.0008585     -50.292972     -49.758949      16.185544      6.2619058e-07  4.6642574     -0.0025876701 
+       200   1.0034473     -50.292959     -49.757555      16.193637      2.4778684e-06  4.6763219     -0.0051513312 
+       300   1.0078065     -50.292946     -49.755216      16.20654       5.4785827e-06  4.6966366     -0.0076677455 
+       400   1.0140035     -50.292935     -49.751898      16.224472      9.5136721e-06  4.7255165     -0.010116117  
+       500   1.022135      -50.292924     -49.747548      16.247769      1.4445387e-05  4.7634112     -0.012478816  
+       600   1.0323281     -50.292913     -49.742099      16.276857      2.0128019e-05  4.810914      -0.014741354  
+       700   1.044744      -50.292903     -49.735464      16.312269      2.6420278e-05  4.868775      -0.01689316   
+       800   1.0595807     -50.292893     -49.727538      16.354636      3.3193675e-05  4.9379181     -0.018925599  
+       900   1.0770788     -50.292883     -49.718191      16.404759      4.0337059e-05  5.0194633     -0.020834008  
+      1000   1.0975267     -50.292873     -49.707271      16.463535      4.7758112e-05  5.114756      -0.022615739  
+      1100   1.1212696     -50.292864     -49.694594      16.532005      5.5382858e-05  5.2254042     -0.024272115  
+      1200   1.1487191     -50.292855     -49.679939      16.611504      6.3154057e-05  5.3533255     -0.025805429  
+      1300   1.180366      -50.292847     -49.663045      16.703525      7.1029151e-05  5.5008084     -0.027221135  
+      1400   1.2167974     -50.292839     -49.643599      16.809904      7.8978147e-05  5.6705878     -0.028525093  
+      1500   1.2587168     -50.292831     -49.621224      16.932872      8.6981686e-05  5.8659431     -0.029723588  
+      1600   1.3069711     -50.292824     -49.59547       17.075101      9.5029394e-05  6.0908207     -0.030823313  
+      1700   1.362584      -50.292817     -49.56579       17.239763      0.00010311856  6.3499909     -0.031831844  
+      1800   1.4267984     -50.29281      -49.53152       17.430752      0.00011125314  6.6492468     -0.032756757  
+      1900   1.5011313     -50.292803     -49.491852      17.652797      0.00011944307  6.995657      -0.033606551  
+      2000   1.5874422     -50.292796     -49.445792      17.911722      0.00012770381  7.3978879     -0.034390022  
+      2100   1.6880212     -50.292789     -49.39212       18.214723      0.00013605623  7.866612      -0.035116463  
+      2200   1.8057005     -50.292782     -49.329324      18.570726      0.00014452669  8.4150275     -0.035795677  
+      2300   1.9439945     -50.292774     -49.255527      18.990774      0.00015314733  9.0595131     -0.036438481  
+      2400   2.1072765     -50.292765     -49.168396      19.488686      0.00016195668  9.8204493     -0.037057048  
+      2500   2.3009969     -50.292755     -49.065024      20.081627      0.00017100046  10.723236     -0.037663926  
+      2600   2.5319487     -50.292742     -48.941783      20.791154      0.00018033268  11.799531     -0.038274916  
+      2700   2.8085828     -50.292725     -48.794164      21.644055      0.00019001711  13.088716     -0.038907942  
+      2800   3.1413656     -50.292704     -48.616581      22.673549      0.00020012896  14.63957      -0.039579122  
+      2900   3.5431592     -50.292679     -48.402173      23.920341      0.00021075711  16.512031     -0.040310879  
+      3000   4.0295773     -50.292645     -48.142604      25.434299      0.00022200654  18.778864     -0.041129941  
+      3100   4.6192303     -50.292603     -47.827943      27.274622      0.00023400135  21.526798     -0.042063049  
+      3200   5.3337183     -50.292548     -47.446663      29.510189      0.00024688797  24.856495     -0.043138944  
+      3300   6.1971521     -50.292476     -46.985893      32.218076      0.00026083874  28.880319     -0.044388363  
+      3400   7.2349077     -50.292383     -46.432089      35.479408      0.00027605543  33.716526     -0.04584988   
+      3500   8.4712558     -50.292263     -45.772298      39.371841      0.00029277252  39.478225     -0.04755723   
+      3600   9.9255215     -50.292106     -44.996195      43.95768       0.00031125948  46.255476     -0.04955234   
+      3700   11.606583     -50.291907     -44.099041      49.265647      0.00033182131  54.089653     -0.051868152  
+      3800   13.505895     -50.291653     -43.08538       55.269674      0.00035479603  62.940934     -0.060893692  
+      3900   15.589876     -50.291332     -41.973119      61.864426      0.00038054772  72.652823     -0.064129637  
+      4000   17.793337     -50.290932     -40.79703       68.843904      0.00040945342  82.921517     -0.070448746  
+      4100   20.016417     -50.290444     -39.610385      75.893194      0.0004418827   93.281639     -0.087116518  
+      4200   22.127771     -50.289857     -38.483253      82.59793       0.00047816979  103.12109     -0.097527157  
+      4300   23.975968     -50.289169     -37.496432      88.481352      0.00051857989  111.73416     -0.10722194   
+      4400   25.408977     -50.288385     -36.731045      93.065749      0.00056327427  118.41235     -0.11892611   
+      4500   26.298632     -50.287506     -36.255477      95.950674      0.0006122807   122.55837     -0.1303584    
+      4600   26.564268     -50.286547     -36.112784      96.88563       0.00066547749  123.79631     -0.14166752   
+      4700   26.188807     -50.285529     -36.312099      95.820823      0.00072259756  122.04656     -0.15261419   
+      4800   25.222299     -50.284475     -36.826739      92.916226      0.00078325554  117.54238     -0.16209083   
+      4900   23.771855     -50.283413     -37.599583      88.509238      0.00084699472  110.78294     -0.17260047   
+      5000   21.98111      -50.282357     -38.554006      83.049726      0.00091334478  102.43761     -0.18258656   
+      5100   20.005206     -50.281326     -39.607248      77.020285      0.0009818775   93.229392     -0.17186696   
+      5200   17.987631     -50.28033      -40.68276       70.86497       0.0010522474   83.826973     -0.18260146   
+      5300   16.043616     -50.279377     -41.719065      64.938011      0.0011242079   74.767366     -0.18655435   
+      5400   14.252181     -50.278457     -42.673992      59.48099       0.0011976018   66.41882      -0.20222138   
+      5500   12.656323     -50.277568     -43.524597      54.622777      0.0012723319   58.981714     -0.21168712   
+      5600   11.269064     -50.276696     -44.263917      50.401002      0.0013483229   52.516731     -0.20187998   
+      5700   10.082312     -50.275828     -44.896259      46.788408      0.0014254889   46.986161     -0.22324171   
+      5800   9.0757866     -50.274951     -45.432429      43.722025      0.0015037137   42.295494     -0.23860695   
+      5900   8.2242212     -50.274058     -45.885902      41.123761      0.0015828465   38.326981     -0.25414759   
+      6000   7.5021821     -50.273138     -46.270236      38.916656      0.0016627103   34.962093     -0.26976048   
+      6100   6.8866987     -50.272182     -46.597681      37.031655      0.0017431162   32.093783     -0.28539248   
+      6200   6.3583012     -50.27119      -46.878623      35.410368      0.0018238791   29.631315     -0.30095674   
+      6300   5.9011035     -50.270159     -47.121537      34.005676      0.0019048302   27.500656     -0.31640935   
+      6400   5.502422      -50.269086     -47.333186      32.779933      0.0019858256   25.642698     -0.33171137   
+      6500   5.1522361     -50.267972     -47.518919      31.703747      0.0020667509   24.010742     -0.34682514   
+      6600   4.8426527     -50.266817     -47.682947      30.753955      0.0021475225   22.568004     -0.36173006   
+      6700   4.5674405     -50.265625     -47.828599      29.911814      0.0022280866   21.285445     -0.37640709   
+      6800   4.3216522     -50.264395     -47.958513      29.163452      0.0023084174   20.140008     -0.39085666   
+      6900   4.1013282     -50.26313      -48.074805      28.496518      0.0023885139   19.113242     -0.40506248   
+      7000   3.9032702     -50.261831     -48.179183      27.90194       0.0024683969   18.19024      -0.41901469   
+      7100   3.724868      -50.2605       -48.273041      27.371896      0.0025481062   17.35884      -0.43272933   
+      7200   3.5639695     -50.259138     -48.357529      26.89966       0.0026276974   16.609012     -0.44620638   
+      7300   3.4187816     -50.257743     -48.433601      26.480439      0.0027072396   15.932399     -0.45945212   
+      7400   3.2877948     -50.256318     -48.502066      26.109145      0.0027868133   15.321967     -0.47246434   
+      7500   3.1697267     -50.254865     -48.56361       25.781971      0.0028665077   14.77174      -0.48526006   
+      7600   3.0634774     -50.25338      -48.618816      25.495767      0.0029464195   14.276591     -0.49784679   
+      7700   2.9680959     -50.251868     -48.668196      25.247434      0.0030266508   13.832088     -0.51022378   
+      7800   2.8827533     -50.250324     -48.712188      25.034584      0.0031073072   13.43437      -0.52242006   
+      7900   2.8067218     -50.248752     -48.751183      24.854648      0.0031884966   13.080044     -0.53441576   
+      8000   2.739358      -50.247146     -48.78552       24.705902      0.0032703269   12.766111     -0.54625728   
+      8100   2.6800884     -50.245512     -48.815511      24.586269      0.003352905    12.4899       -0.55792685   
+      8200   2.6283988     -50.243847     -48.841426      24.493934      0.0034363346   12.249013     -0.56944906   
+      8300   2.5838233     -50.242148     -48.86351       24.42802       0.0035207151   12.041279     -0.58082697   
+      8400   2.5459368     -50.240416     -48.881994      24.386467      0.0036061405   11.864719     -0.59207404   
+      8500   2.5143471     -50.23866      -48.897093      24.367425      0.0036926982   11.717503     -0.6031939    
+      8600   2.4886884     -50.236867     -48.90899       24.370737      0.0037804687   11.597926     -0.61420631   
+      8700   2.4686158     -50.235045     -48.917878      24.393872      0.003869526    11.504383     -0.62511248   
+      8800   2.4538005     -50.233192     -48.92393       24.436221      0.0039599381   11.43534      -0.63592614   
+      8900   2.4439261     -50.231311     -48.927318      24.495987      0.0040517678   11.389323     -0.64665221   
+      9000   2.4386859     -50.229399     -48.928202      24.571919      0.0041450744   11.364902     -0.65730127   
+      9100   2.4377812     -50.227462     -48.926747      24.662499      0.0042399143   11.360686     -0.66787619   
+      9200   2.4409216     -50.225498     -48.923108      24.766278      0.0043363422   11.375321     -0.67839903   
+      9300   2.447826      -50.223507     -48.917432      24.882071      0.0044344105   11.407497     -0.68886647   
+      9400   2.4582258     -50.22149      -48.909866      25.008577      0.0045341695   11.455963     -0.69927895   
+      9500   2.471869      -50.219451     -48.900548      25.143849      0.0046356651   11.519544     -0.70966102   
+      9600   2.4885255     -50.217386     -48.889596      25.286999      0.004738938    11.597167     -0.6940583    
+      9700   2.5079938     -50.215302     -48.877125      25.436871      0.0048440213   11.687895     -0.70437543   
+      9800   2.5301066     -50.213198     -48.863222      25.59205       0.0049509399   11.790946     -0.71464807   
+      9900   2.5547371     -50.211072     -48.847954      25.752316      0.0050597095   11.90573      -0.72487926   
+     10000   2.5818031     -50.208928     -48.831368      25.916904      0.0051703368   12.031865     -0.73506701   
+Loop time of 14.691 on 1 procs for 10000 steps with 180 atoms
+
+Performance: 0.059 ns/day, 408.083 hours/ns, 680.690 timesteps/s, 122.524 katom-step/s
+96.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.9104     | 2.9104     | 2.9104     |   0.0 | 19.81
+Bond    | 0.00098079 | 0.00098079 | 0.00098079 |   0.0 |  0.01
+Neigh   | 6.6139     | 6.6139     | 6.6139     |   0.0 | 45.02
+Comm    | 0.55394    | 0.55394    | 0.55394    |   0.0 |  3.77
+Output  | 0.0030074  | 0.0030074  | 0.0030074  |   0.0 |  0.02
+Modify  | 4.5374     | 4.5374     | 4.5374     |   0.0 | 30.89
+Other   |            | 0.07132    |            |       |  0.49
+
+Nlocal:            180 ave         180 max         180 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           1510 ave        1510 max        1510 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          13680 ave       13680 max       13680 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 13680
+Ave neighs/atom = 76
+Ave special neighs/atom = 0
+Neighbor list builds = 10000
+Dangerous builds not checked
+Total wall time: 0:00:14

examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.3

@@ -0,0 +1,197 @@
+LAMMPS (8 Feb 2023)
+Processor partition = 3
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+variable ibead uloop 32 pad
+variable out_freq string 100
+variable job_name string H2
+
+units      real
+atom_style full
+pair_style table linear 10000
+
+neighbor 2.0 bin
+neigh_modify every 1 delay 0 check no
+
+read_data H2.data
+Reading data file ...
+  orthogonal box = (0 0 0) to (19.71219 19.71219 19.71219)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  180 atoms
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     0 = max # of 1-2 neighbors
+     0 = max # of 1-3 neighbors
+     0 = max # of 1-4 neighbors
+     1 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
+  read_data CPU = 0.003 seconds
+
+pair_coeff 1 * pair.table PAIR_H2
+WARNING: 5852 of 18000 force values in table PAIR_H2 are inconsistent with -dE/dr.
+WARNING:  Should only be flagged at inflection points (src/pair_table.cpp:466)
+
+timestep        0.001
+
+velocity all create 1.0 1985 rot yes dist gaussian
+
+fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 25.0 nhc 4
+
+thermo_style    custom step temp pe etotal pzz f_1[1] f_1[2] f_1[3]
+thermo_modify   colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial
+thermo          ${out_freq}
+thermo          100
+
+#dump dcd all dcd ${out_freq} ${job_name}_${ibead}.dcd
+
+#restart ${out_freq} ${job_name}_${ibead}.restart1 ${job_name}_${ibead}.restart2
+
+run 10000
+WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 11.55117
+  ghost atom cutoff = 11.55117
+  binsize = 5.775585, bins = 4 4 4
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair table, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 11.97 | 11.97 | 11.97 Mbytes
+   Step          Temp          PotEng         TotEng          Pzz          espring         T_ring         virial    
+         0   1             -50.292986     -49.759421      16.18218       0              0              4.331435e-14 
+       100   0.99799183    -50.292972     -49.760479      16.176371      6.2763683e-07  15.879159     -0.0023935093 
+       200   0.99208279    -50.292959     -49.763618      16.157336      2.500618e-06   15.785139     -0.0047805057 
+       300   0.98260503    -50.292946     -49.768662      16.126279      5.5906177e-06  15.634338     -0.0071546335 
+       400   0.97006821    -50.292934     -49.775339      16.085102      9.8548762e-06  15.434863     -0.0095106986 
+       500   0.955104      -50.292922     -49.783311      16.036202      1.5241599e-05  15.196766     -0.011844212  
+       600   0.93840578    -50.292908     -49.792208      15.982141      2.1695575e-05  14.931079     -0.014152859  
+       700   0.92067359    -50.292894     -49.801655      15.925466      2.9163075e-05  14.64894      -0.016435757  
+       800   0.90257158    -50.292879     -49.811298      15.868564      3.7595562e-05  14.360917     -0.018694156  
+       900   0.88470062    -50.292862     -49.820817      15.813472      4.6952156e-05  14.07657      -0.020928907  
+      1000   0.8675856     -50.292845     -49.829932      15.761951      5.7201072e-05  13.804251     -0.02314186   
+      1100   0.85167476    -50.292826     -49.838402      15.715517      6.8320318e-05  13.551092     -0.025333843  
+      1200   0.83734746    -50.292806     -49.846027      15.675218      8.0297954e-05  13.323129     -0.027508552  
+      1300   0.8249274     -50.292785     -49.852632      15.642038      9.3132154e-05  13.125512     -0.0296698    
+      1400   0.81469844    -50.292762     -49.858068      15.616792      0.00010683122  12.962757     -0.031821941  
+      1500   0.80692178    -50.292739     -49.862194      15.600226      0.00012141373  12.839022     -0.033969494  
+      1600   0.80185336    -50.292715     -49.864874      15.593117      0.0001369088   12.758378     -0.03611606   
+      1700   0.79976156    -50.29269      -49.865965      15.596227      0.00015335664  12.725095     -0.038264652  
+      1800   0.80094541    -50.292664     -49.865307      15.610404      0.00017080942  12.743931     -0.040416801  
+      1900   0.80575383    -50.292637     -49.862715      15.636702      0.00018933238  12.820439     -0.042573524  
+      2000   0.81460711    -50.292611     -49.857965      15.67644       0.00020900552  12.961304     -0.044736822  
+      2100   0.82802133    -50.292583     -49.85078       15.731301      0.0002299256   13.174739     -0.046906382  
+      2200   0.84663738    -50.292556     -49.84082       15.80341       0.00025220879  13.470941     -0.049081478  
+      2300   0.87125571    -50.292527     -49.827656      15.895377      0.00027599404  13.862646     -0.051261652  
+      2400   0.90287869    -50.292499     -49.810754      16.010541      0.00030144708  14.365803     -0.053443791  
+      2500   0.94276179    -50.29247      -49.789446      16.15309       0.00032876555  15.000388     -0.055625674  
+      2600   0.99247509    -50.292441     -49.762891      16.328426      0.00035818508  15.791381     -0.05780423   
+      2700   1.0539754     -50.292412     -49.730048      16.543118      0.00038998665  16.76992      -0.059974442  
+      2800   1.1296876     -50.292383     -49.689621      16.805367      0.00042450539  17.974586     -0.062128128  
+      2900   1.2225906     -50.292352     -49.640021      17.125302      0.00046214072  19.452774     -0.064255792  
+      3000   1.3362969     -50.292321     -49.57932       17.515126      0.000503368    21.261968     -0.066348705  
+      3100   1.4751081     -50.292289     -49.505223      17.989435      0.0005487512   23.47061      -0.068394944  
+      3200   1.6440125     -50.292255     -49.415068      18.56525       0.00059895625  26.158066     -0.070379528  
+      3300   1.8485766     -50.292217     -49.305881      19.26156       0.00065476359  29.412908     -0.0722905    
+      3400   2.0946636     -50.292172     -49.174533      20.098518      0.0007170785   33.328425     -0.070298499  
+      3500   2.3878963     -50.292118     -49.01802       21.095116      0.00078693603  37.994084     -0.072718799  
+      3600   2.7327825     -50.29205      -48.833933      22.267046      0.00086549715  43.481606     -0.071117313  
+      3700   3.1314509     -50.291962     -48.621129      23.621508      0.00095403112  49.824863     -0.073902505  
+      3800   3.5820285     -50.29185      -48.380605      25.151938      0.0010538788   56.994053     -0.082019029  
+      3900   4.0768347     -50.291704     -48.116448      26.832847      0.0011663922   64.86697      -0.093365693  
+      4000   4.6007622     -50.291519     -47.836714      28.612446      0.0012928467   73.203239     -0.10732489   
+      4100   5.1304133     -50.29129      -47.553881      30.411364      0.0014343275   81.630577     -0.1197723    
+      4200   5.6346502     -50.291011     -47.284558      32.123915      0.0015915962   89.653545     -0.13080997   
+      4300   6.0770777     -50.290676     -47.04816       33.627475      0.0017649532   96.693059     -0.14165463   
+      4400   6.4205234     -50.29029      -46.864523      34.796349      0.0019541156   102.15766     -0.15242678   
+      4500   6.6328782     -50.28986      -46.750789      35.522716      0.0021581361   105.53646     -0.16280564   
+      4600   6.692974      -50.289399     -46.718262      35.736356      0.0023753855   106.49265     -0.17244062   
+      4700   6.5948627     -50.28892      -46.770133      35.418562      0.0026036121   104.93159     -0.18097864   
+      4800   6.3491738     -50.288443     -46.900746      34.606797      0.0028400768   101.02241     -0.18808564   
+      4900   5.981108      -50.287983     -47.096673      33.387033      0.0030817487   95.166073     -0.19348598   
+      5000   5.5256727     -50.287549     -47.339243      31.878041      0.0033255323   87.919593     -0.19697013   
+      5100   5.0215378     -50.287155     -47.607839      30.209726      0.0035684934   79.898246     -0.19841014   
+      5200   4.5051017     -50.286803     -47.883038      28.504102      0.0038080527   71.681174     -0.19776394   
+      5300   4.0060458     -50.286489     -48.149003      26.860164      0.0040421233   63.74064      -0.19507702   
+      5400   3.5450327     -50.286205     -48.394699      25.34642       0.0042691817   56.405409     -0.17980245   
+      5500   3.1335349     -50.28594      -48.613996      23.999815      0.0044882701   49.858022     -0.17499889   
+      5600   2.7752591     -50.28568      -48.804899      22.832197      0.0046989433   44.157456     -0.1804676    
+      5700   2.468384      -50.285415     -48.968371      21.836436      0.0049011768   39.274732     -0.17203381   
+      5800   2.2078676     -50.285131     -49.10709       20.994608      0.0050952576   35.129626     -0.17967923   
+      5900   1.9873283     -50.284819     -49.22445       20.285865      0.0052816779   31.620602     -0.18651596   
+      6000   1.8003086     -50.284474     -49.323892      19.687668      0.0054610429   28.64491      -0.19262321   
+      6100   1.640963      -50.284092     -49.408531      19.181029      0.0056340011   26.109545     -0.1982684    
+      6200   1.50433       -50.283675     -49.481017      18.749125      0.0058011964   23.935562     -0.19911595   
+      6300   1.3863531     -50.283219     -49.543509      18.379087      0.0059632392   22.058419     -0.20020649   
+      6400   1.2837837     -50.28273      -49.597748      18.059898      0.0061206908   20.426426     -0.20439271   
+      6500   1.1940433     -50.282206     -49.645106      17.783505      0.0062740588   18.998556     -0.19989782   
+      6600   1.1150882     -50.281655     -49.686683      17.543117      0.0064237975   17.742293     -0.20427813   
+      6700   1.0452925     -50.281076     -49.723345      17.333683      0.0065703119   16.631765     -0.20875566   
+      6800   0.98335363    -50.28048      -49.755796      17.150648      0.0067139628   15.646249     -0.21165511   
+      6900   0.92821916    -50.279858     -49.784593      16.991122      0.0068550735   14.768998     -0.21447191   
+      7000   0.87903062    -50.279219     -49.810199      16.85215       0.0069939349   13.986354     -0.21690274   
+      7100   0.83508106    -50.27857      -49.833         16.730809      0.0071308114   13.287068     -0.21879935   
+      7200   0.79578318    -50.277905     -49.853302      16.625931      0.007265945    12.661795     -0.24086146   
+      7300   0.76064516    -50.277227     -49.871373      16.535639      0.0073995599   12.10271      -0.24389998   
+      7400   0.72925259    -50.27654      -49.887437      16.458538      0.0075318653   11.603219     -0.24724178   
+      7500   0.70125479    -50.275848     -49.901683      16.39318       0.0076630586   11.157743     -0.24974257   
+      7600   0.67635448    -50.275145     -49.914266      16.338958      0.0077933274   10.761551     -0.26938357   
+      7700   0.65430014    -50.274434     -49.925322      16.294582      0.0079228516   10.410642     -0.27182741   
+      7800   0.63488023    -50.273717     -49.934967      16.259573      0.0080518043   10.10165      -0.27327965   
+      7900   0.61791898    -50.272993     -49.943293      16.233056      0.0081803536   9.8317776     -0.23270163   
+      8000   0.60327334    -50.272261     -49.950375      16.214226      0.0083086629   9.5987492     -0.21174158   
+      8100   0.59083054    -50.271521     -49.956274      16.203107      0.008436892    9.4007703     -0.20591477   
+      8200   0.580506      -50.270774     -49.961036      16.198733      0.0085651973   9.2364955     -0.20633623   
+      8300   0.57224102    -50.270016     -49.964688      16.201153      0.0086937323   9.1049904     -0.21200577   
+      8400   0.56599941    -50.26925      -49.967252      16.209734      0.0088226478   9.0056795     -0.21499276   
+      8500   0.56176264    -50.268474     -49.968737      16.224404      0.0089520921   8.9382678     -0.22565885   
+      8600   0.55952259    -50.267687     -49.969145      16.244765      0.0090822109   8.9026261     -0.23453558   
+      8700   0.55927158    -50.26689      -49.968482      16.270388      0.0092131476   8.8986323     -0.23126478   
+      8800   0.56098987    -50.266078     -49.966754      16.301455      0.009345043    8.9259722     -0.23759225   
+      8900   0.56463156    -50.265253     -49.963985      16.338219      0.0094780352   8.9839155     -0.25830691   
+      9000   0.57011105    -50.264414     -49.960222      16.379852      0.0096122592   9.0711003     -0.24455142   
+      9100   0.57729304    -50.263559     -49.955536      16.42695       0.0097478463   9.1853737     -0.25035816   
+      9200   0.5859895     -50.262689     -49.950026      16.479216      0.0098849239   9.3237441     -0.2560083    
+      9300   0.59596674    -50.261803     -49.943816      16.536984      0.010023615    9.482493      -0.26141076   
+      9400   0.60696386    -50.2609       -49.937045      16.600194      0.010164037    9.6574694     -0.26654733   
+      9500   0.61872142    -50.259982     -49.929854      16.669166      0.010306303    9.8445453     -0.2741745    
+      9600   0.63101587    -50.259043     -49.922355      16.744325      0.010450522    10.040164     -0.27940426   
+      9700   0.64369292    -50.258089     -49.914637      16.82549       0.010596798    10.24187      -0.28435931   
+      9800   0.65669202    -50.257118     -49.906731      16.913131      0.010745233    10.4487       -0.28904477   
+      9900   0.67005575    -50.256133     -49.898615      17.007446      0.01089593     10.661331     -0.29344272   
+     10000   0.68392108    -50.25513      -49.890213      17.108905      0.011048996    10.881944     -0.29755711   
+Loop time of 14.691 on 1 procs for 10000 steps with 180 atoms
+
+Performance: 0.059 ns/day, 408.083 hours/ns, 680.690 timesteps/s, 122.524 katom-step/s
+98.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.8325     | 2.8325     | 2.8325     |   0.0 | 19.28
+Bond    | 0.0010203  | 0.0010203  | 0.0010203  |   0.0 |  0.01
+Neigh   | 6.5808     | 6.5808     | 6.5808     |   0.0 | 44.80
+Comm    | 0.55003    | 0.55003    | 0.55003    |   0.0 |  3.74
+Output  | 0.0030145  | 0.0030145  | 0.0030145  |   0.0 |  0.02
+Modify  | 4.6599     | 4.6599     | 4.6599     |   0.0 | 31.72
+Other   |            | 0.06363    |            |       |  0.43
+
+Nlocal:            180 ave         180 max         180 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           1510 ave        1510 max        1510 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          13680 ave       13680 max       13680 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 13680
+Ave neighs/atom = 76
+Ave special neighs/atom = 0
+Neighbor list builds = 10000
+Dangerous builds not checked
+Total wall time: 0:00:14

examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.4

@@ -0,0 +1,197 @@
+LAMMPS (8 Feb 2023)
+Processor partition = 4
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+variable ibead uloop 32 pad
+variable out_freq string 100
+variable job_name string H2
+
+units      real
+atom_style full
+pair_style table linear 10000
+
+neighbor 2.0 bin
+neigh_modify every 1 delay 0 check no
+
+read_data H2.data
+Reading data file ...
+  orthogonal box = (0 0 0) to (19.71219 19.71219 19.71219)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  180 atoms
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     0 = max # of 1-2 neighbors
+     0 = max # of 1-3 neighbors
+     0 = max # of 1-4 neighbors
+     1 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
+  read_data CPU = 0.003 seconds
+
+pair_coeff 1 * pair.table PAIR_H2
+WARNING: 5852 of 18000 force values in table PAIR_H2 are inconsistent with -dE/dr.
+WARNING:  Should only be flagged at inflection points (src/pair_table.cpp:466)
+
+timestep        0.001
+
+velocity all create 1.0 1985 rot yes dist gaussian
+
+fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 25.0 nhc 4
+
+thermo_style    custom step temp pe etotal pzz f_1[1] f_1[2] f_1[3]
+thermo_modify   colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial
+thermo          ${out_freq}
+thermo          100
+
+#dump dcd all dcd ${out_freq} ${job_name}_${ibead}.dcd
+
+#restart ${out_freq} ${job_name}_${ibead}.restart1 ${job_name}_${ibead}.restart2
+
+run 10000
+WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 11.55117
+  ghost atom cutoff = 11.55117
+  binsize = 5.775585, bins = 4 4 4
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair table, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 11.97 | 11.97 | 11.97 Mbytes
+   Step          Temp          PotEng         TotEng          Pzz          espring         T_ring         virial    
+         0   1             -50.292986     -49.759421      16.18218       0              0              4.331435e-14 
+       100   0.99799183    -50.292972     -49.760479      16.17637       1.1826193e-13  15.879159     -0.0025913805 
+       200   0.99208279    -50.292959     -49.763618      16.157337      7.489305e-12   15.785139     -0.0051808234 
+       300   0.98260503    -50.292946     -49.768662      16.126285      8.3895453e-11  15.634338     -0.0077662384 
+       400   0.97006821    -50.292933     -49.775339      16.085117      4.6129385e-10  15.434863     -0.010346287  
+       500   0.955104      -50.292921     -49.783311      16.036242      1.7157587e-09  15.196766     -0.012920943  
+       600   0.93840577    -50.292907     -49.792206      15.982224      4.9828406e-09  14.931079     -0.015491155  
+       700   0.92067358    -50.292891     -49.801652      15.925608      1.2201305e-08  14.64894      -0.018055916  
+       800   0.90257157    -50.292875     -49.811294      15.868782      2.6375763e-08  14.360917     -0.020616424  
+       900   0.88470061    -50.292856     -49.820811      15.813794      5.1849593e-08  14.07657      -0.02317448   
+      1000   0.86758559    -50.292836     -49.829923      15.762447      9.4579685e-08  13.804251     -0.025732882  
+      1100   0.85167475    -50.292814     -49.83839       15.716171      1.6240678e-07  13.551092     -0.028294045  
+      1200   0.83734745    -50.29279      -49.846011      15.676049      2.6532099e-07  13.323128     -0.030863385  
+      1300   0.82492738    -50.292764     -49.852612      15.643102      4.1573034e-07  13.125511     -0.033446749  
+      1400   0.81469842    -50.292737     -49.858042      15.618114      6.287493e-07   12.962757     -0.036050518  
+      1500   0.80692176    -50.292706     -49.862161      15.601972      9.2253166e-07  12.839022     -0.038681006  
+      1600   0.80185333    -50.292674     -49.864833      15.595319      1.3186783e-06  12.758377     -0.041346087  
+      1700   0.79976154    -50.292639     -49.865914      15.598922      1.8427553e-06  12.725095     -0.044055451  
+      1800   0.80094538    -50.2926       -49.865244      15.613674      2.524964e-06   12.743931     -0.046819731  
+      1900   0.80575381    -50.292559     -49.862637      15.640669      3.4010112e-06  12.820438     -0.049651934  
+      2000   0.81460709    -50.292514     -49.857868      15.681364      4.5132409e-06  12.961304     -0.052564979  
+      2100   0.82802133    -50.292465     -49.850661      15.73743       5.9121027e-06  13.174739     -0.055577058  
+      2200   0.84663739    -50.29241      -49.840674      15.810925      7.658054e-06   13.470942     -0.058707326  
+      2300   0.87125574    -50.292349     -49.827477      15.904535      9.82402e-06    13.862647     -0.061977077  
+      2400   0.90287875    -50.29228      -49.810536      16.021749      1.2498571e-05  14.365804     -0.065412927  
+      2500   0.94276188    -50.292203     -49.789178      16.16688       1.5790021e-05  15.000389     -0.069043572  
+      2600   0.99247524    -50.292117     -49.762567      16.345151      1.9831692e-05  15.791384     -0.072902664  
+      2700   1.0539756     -50.292019     -49.729655      16.56334       2.4788664e-05  16.769923     -0.077026939  
+      2800   1.1296879     -50.291903     -49.689141      16.830177      3.0866362e-05  17.97459      -0.081462018  
+      2900   1.222591      -50.29177      -49.639438      17.155398      3.8321389e-05  19.45278      -0.086262136  
+      3000   1.3362974     -50.291614     -49.578613      17.551553      4.7474995e-05  21.261976     -0.091484095  
+      3100   1.4751088     -50.291433     -49.504367      18.033555      5.872952e-05   23.47062      -0.097184337  
+      3200   1.6440134     -50.291218     -49.41403       18.618802      7.2587889e-05  26.158079     -0.10344427   
+      3300   1.8485776     -50.290963     -49.304627      19.3265        8.9675809e-05  29.412924     -0.11033444   
+      3400   2.0946648     -50.290659     -49.17302       20.177003      0.00011076549  33.328444     -0.11794183   
+      3500   2.3878978     -50.290296     -49.016197      21.189599      0.00013679846  37.994106     -0.12634541   
+      3600   2.7327842     -50.289862     -48.831744      22.380493      0.0001689033   43.481633     -0.13563052   
+      3700   3.1314527     -50.289342     -48.618508      23.757417      0.00020840179  49.824892     -0.1458703    
+      3800   3.5820304     -50.288721     -48.377475      25.31432       0.00025679499  56.994084     -0.15714078   
+      3900   4.0768367     -50.287983     -48.112726      27.026228      0.0003157187   64.867001     -0.1694959    
+      4000   4.6007641     -50.287108     -47.832302      28.841926      0.0003868587   73.203268     -0.18296156   
+      4100   5.1304148     -50.286087     -47.548677      30.682328      0.00047181946  81.6306       -0.19756083   
+      4200   5.6346511     -50.284903     -47.278451      32.442736      0.00057194846  89.653559     -0.21328268   
+      4300   6.0770778     -50.283545     -47.041029      33.999964      0.00068813116  96.69306      -0.23008376   
+      4400   6.4205225     -50.282013     -46.856246      35.229403      0.00082058594  102.15765     -0.24791296   
+      4500   6.6328762     -50.280301     -46.74123       36.023883      0.0009687004   105.53643     -0.26668503   
+      4600   6.6929711     -50.278423     -46.707288      36.312847      0.0011309529   106.49261     -0.28630381   
+      4700   6.5948589     -50.27639      -46.757604      36.078132      0.0013049526   104.93153     -0.3066628    
+      4800   6.3491697     -50.274211     -46.886517      35.357678      0.0014876083   101.02235     -0.32764627   
+      4900   5.9811042     -50.271915     -47.080607      34.23668       0.0016754063   95.166014     -0.34912704   
+      5000   5.5256699     -50.269516     -47.321212      32.833829      0.001864752    87.919547     -0.37098454   
+      5100   5.0215364     -50.267032     -47.587716      31.279327      0.002052314    79.898224     -0.39310129   
+      5200   4.5051023     -50.264473     -47.860708      29.694368      0.0022353117   71.681183     -0.41536062   
+      5300   4.0060486     -50.261854     -48.124367      28.177158      0.0024117009   63.740684     -0.43765657   
+      5400   3.5450378     -50.259179     -48.367671      26.795368      0.0025802379   56.405491     -0.45989585   
+      5500   3.1335423     -50.256452     -48.584504      25.585853      0.0027404289   49.858139     -0.48198401   
+      5600   2.7752685     -50.253675     -48.772889      24.559285      0.0028923937   44.157606     -0.50383681   
+      5700   2.4683952     -50.250848     -48.933799      23.707506      0.0030366865   39.27491      -0.52540813   
+      5800   2.2078802     -50.247975     -49.069927      23.012724      0.0031741148   35.129826     -0.54664422   
+      5900   1.987342      -50.245052     -49.184676      22.453088      0.0033055867   31.62082      -0.56749825   
+      6000   1.8003231     -50.242086     -49.281496      22.005599      0.0034320005   28.645141     -0.5879444    
+      6100   1.6409782     -50.239078     -49.363509      21.650929      0.0035541789   26.109787     -0.6079799    
+      6200   1.5043457     -50.236031     -49.433365      21.372354      0.0036728367   23.935811     -0.62757526   
+      6300   1.3863692     -50.23295      -49.493232      21.15608       0.0037885737   22.058674     -0.64672985   
+      6400   1.2838        -50.229836     -49.544845      20.99171       0.0039018814   20.426685     -0.66545129   
+      6500   1.1940599     -50.2267       -49.589591      20.870492      0.0040131566   18.998819     -0.68374953   
+      6600   1.115105      -50.223537     -49.628556      20.785791      0.0041227168   17.742559     -0.70162987   
+      6700   1.0453095     -50.220351     -49.66261       20.732525      0.0042308155   16.632035     -0.7190951    
+      6800   0.98337083    -50.217149     -49.692456      20.706334      0.0043376557   15.646523     -0.73616716   
+      6900   0.92823665    -50.213933     -49.718658      20.703509      0.0044434008   14.769276     -0.75286641   
+      7000   0.87904844    -50.210704     -49.741675      20.721268      0.0045481845   13.986637     -0.7692006    
+      7100   0.83509929    -50.207463     -49.761883      20.757758      0.0046521178   13.287358     -0.78517926   
+      7200   0.79580187    -50.204208     -49.779596      20.810709      0.0047552948   12.662092     -0.80082697   
+      7300   0.76066442    -50.200945     -49.795082      20.878241      0.0048577976   12.103016     -0.8161606    
+      7400   0.72927251    -50.197671     -49.808557      20.959362      0.0049596993   11.603536     -0.83120088   
+      7500   0.70127548    -50.194387     -49.820211      21.052437      0.0050610673   11.158072     -0.84595004   
+      7600   0.67637608    -50.191091     -49.830201      21.156826      0.005161965    10.761895     -0.86043159   
+      7700   0.65432278    -50.187783     -49.838659      21.271416      0.0052624536   10.411002     -0.87466503   
+      7800   0.63490405    -50.184459     -49.845696      21.395737      0.0053625933   10.102029     -0.88866261   
+      7900   0.61794415    -50.181125     -49.851412      21.52846       0.0054624448   9.8321781     -0.90243744   
+      8000   0.60330004    -50.177777     -49.855877      21.669443      0.0055620701   9.599174      -0.91600112   
+      8100   0.59085898    -50.174411     -49.859149      21.81797       0.0056615336   9.4012229     -0.92936588   
+      8200   0.58053641    -50.171025     -49.861271      21.974141      0.0057609033   9.2369793     -0.94255403   
+      8300   0.57227364    -50.16762      -49.862274      22.13688       0.0058602524   9.1055094     -0.95557385   
+      8400   0.5660345     -50.164193     -49.862177      22.306138      0.0059596607   9.0062378     -0.9684373    
+      8500   0.56180048    -50.160744     -49.860987      22.48185       0.0060592167   8.9388698     -0.98115048   
+      8600   0.55956345    -50.15727      -49.858706      22.663291      0.0061590199   8.9032763     -0.9937296    
+      8700   0.55931575    -50.15377      -49.855339      22.850832      0.0062591826   8.899335      -1.0061868    
+      8800   0.56103758    -50.150241     -49.850891      23.043918      0.006359832    8.9267313     -1.0185265    
+      8900   0.564683      -50.146681     -49.845386      23.242887      0.0064611118   8.984734      -1.0307694    
+      9000   0.57016633    -50.143095     -49.838874      23.44706       0.0065631821   9.0719798     -1.0429186    
+      9100   0.57735215    -50.139473     -49.831418      23.657034      0.0066662188   9.1863142     -1.0549883    
+      9200   0.58605231    -50.13582      -49.823123      23.872662      0.0067704103   9.3247434     -1.0669874    
+      9300   0.59603298    -50.132131     -49.814109      24.094175      0.0068759533   9.483547      -1.078929     
+      9400   0.60703315    -50.128412     -49.80452       24.321354      0.0069830466   9.6585719     -1.0908215    
+      9500   0.61879332    -50.124656     -49.79449       24.554693      0.0070918841   9.8456893     -1.1026826    
+      9600   0.63108995    -50.120866     -49.784139      24.794372      0.0072026473   10.041342     -1.1145246    
+      9700   0.64376884    -50.117043     -49.773551      25.040354      0.0073154993   10.243078     -1.1263585    
+      9800   0.6567696     -50.113185     -49.762755      25.293643      0.00743058     10.449934     -1.1381891    
+      9900   0.67013503    -50.109296     -49.751736      25.553866      0.0075480045   10.662593     -1.150037     
+     10000   0.68400233    -50.105373     -49.740413      25.821695      0.007667864    10.883237     -1.1619081    
+Loop time of 14.691 on 1 procs for 10000 steps with 180 atoms
+
+Performance: 0.059 ns/day, 408.083 hours/ns, 680.690 timesteps/s, 122.524 katom-step/s
+96.6% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.9541     | 2.9541     | 2.9541     |   0.0 | 20.11
+Bond    | 0.00096595 | 0.00096595 | 0.00096595 |   0.0 |  0.01
+Neigh   | 6.6965     | 6.6965     | 6.6965     |   0.0 | 45.58
+Comm    | 0.55386    | 0.55386    | 0.55386    |   0.0 |  3.77
+Output  | 0.0030352  | 0.0030352  | 0.0030352  |   0.0 |  0.02
+Modify  | 4.4131     | 4.4131     | 4.4131     |   0.0 | 30.04
+Other   |            | 0.06945    |            |       |  0.47
+
+Nlocal:            180 ave         180 max         180 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           1510 ave        1510 max        1510 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          13680 ave       13680 max       13680 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 13680
+Ave neighs/atom = 76
+Ave special neighs/atom = 0
+Neighbor list builds = 10000
+Dangerous builds not checked
+Total wall time: 0:00:14

examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.5

@@ -0,0 +1,197 @@
+LAMMPS (8 Feb 2023)
+Processor partition = 5
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+variable ibead uloop 32 pad
+variable out_freq string 100
+variable job_name string H2
+
+units      real
+atom_style full
+pair_style table linear 10000
+
+neighbor 2.0 bin
+neigh_modify every 1 delay 0 check no
+
+read_data H2.data
+Reading data file ...
+  orthogonal box = (0 0 0) to (19.71219 19.71219 19.71219)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  180 atoms
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     0 = max # of 1-2 neighbors
+     0 = max # of 1-3 neighbors
+     0 = max # of 1-4 neighbors
+     1 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
+  read_data CPU = 0.003 seconds
+
+pair_coeff 1 * pair.table PAIR_H2
+WARNING: 5852 of 18000 force values in table PAIR_H2 are inconsistent with -dE/dr.
+WARNING:  Should only be flagged at inflection points (src/pair_table.cpp:466)
+
+timestep        0.001
+
+velocity all create 1.0 1985 rot yes dist gaussian
+
+fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 25.0 nhc 4
+
+thermo_style    custom step temp pe etotal pzz f_1[1] f_1[2] f_1[3]
+thermo_modify   colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial
+thermo          ${out_freq}
+thermo          100
+
+#dump dcd all dcd ${out_freq} ${job_name}_${ibead}.dcd
+
+#restart ${out_freq} ${job_name}_${ibead}.restart1 ${job_name}_${ibead}.restart2
+
+run 10000
+WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 11.55117
+  ghost atom cutoff = 11.55117
+  binsize = 5.775585, bins = 4 4 4
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair table, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 11.97 | 11.97 | 11.97 Mbytes
+   Step          Temp          PotEng         TotEng          Pzz          espring         T_ring         virial    
+         0   1             -50.292986     -49.759421      16.18218       0              0              4.331435e-14 
+       100   0.9951423     -50.292972     -49.761999      16.167253      6.8948763e-13  27.030021     -0.0025924671 
+       200   0.98099313    -50.292959     -49.769535      16.12199       4.364663e-11   26.645702     -0.0051895017 
+       300   0.95873287    -50.292945     -49.781399      16.050646      4.8814317e-10  26.041069     -0.0077954546 
+       400   0.93006021    -50.292933     -49.796685      15.959334      2.6734695e-09  25.262263     -0.010415337  
+       500   0.89689329    -50.29292      -49.814369      15.854928      9.8711643e-09  24.361385     -0.013055676  
+       600   0.86110024    -50.292904     -49.833451      15.743908      2.8339559e-08  23.389175     -0.015723485  
+       700   0.82431428    -50.292887     -49.853062      15.63173       6.8290594e-08  22.389996     -0.018423373  
+       800   0.78784526    -50.292868     -49.872501      15.522613      1.4463127e-07  21.399426     -0.021164155  
+       900   0.7526687     -50.292845     -49.891248      15.419533      2.77427e-07    20.443961     -0.023953669  
+      1000   0.71946253    -50.29282      -49.90894       15.324327      4.9211825e-07  19.542016     -0.026800589  
+      1100   0.6886647     -50.29279      -49.925343      15.237994      8.1957891e-07  18.705487     -0.029714543  
+      1200   0.66053403    -50.292757     -49.940319      15.160974      1.2961277e-06  17.941403     -0.032707733  
+      1300   0.63520454    -50.292719     -49.953796      15.093459      1.963599e-06   17.253404     -0.035794247  
+      1400   0.61273022    -50.292676     -49.965745      15.035373      2.869563e-06   16.642957     -0.03898766   
+      1500   0.59312003    -50.292628     -49.976159      14.9866        4.0677665e-06  16.110306     -0.042305977  
+      1600   0.57636482    -50.292572     -49.985044      14.947135      5.6188557e-06  15.655201     -0.045764398  
+      1700   0.56245786    -50.292508     -49.992401      14.916846      7.5914412e-06  15.277461     -0.049383169  
+      1800   0.55141125    -50.292438     -49.998224      14.895701      1.0063569e-05  14.977413     -0.053180653  
+      1900   0.54326954    -50.292356     -50.002487      14.8841        1.3124682e-05  14.756269     -0.057185281  
+      2000   0.53812235    -50.292262     -50.005139      14.882365      1.6878177e-05  14.616461     -0.06142508   
+      2100   0.53611706    -50.292157     -50.006103      14.891003      2.1444699e-05  14.561993     -0.065932846  
+      2200   0.5374728     -50.292036     -50.005259      14.911208      2.6966349e-05  14.598818     -0.070740681  
+      2300   0.54249683    -50.291895     -50.002438      14.944078      3.3612057e-05  14.73528      -0.075893774  
+      2400   0.55160424    -50.291734     -49.997418      14.991434      4.1584413e-05  14.982655     -0.081441387  
+      2500   0.56534189    -50.291548     -49.989902      15.055565      5.1128356e-05  15.355797     -0.08743341   
+      2600   0.58441729    -50.291332     -49.979508      15.139015      6.2542191e-05  15.873922     -0.093934223  
+      2700   0.60973261    -50.291079     -49.965747      15.245349      7.6191529e-05  16.561536     -0.10101976   
+      2800   0.64242331    -50.290782     -49.948007      15.379156      9.2526793e-05  17.44948      -0.10876973   
+      2900   0.68389894    -50.290432     -49.925527      15.54557       0.00011210502  18.576039     -0.11728634   
+      3000   0.7358813     -50.29002      -49.89738       15.751474      0.00013561664  19.987983     -0.12666711   
+      3100   0.80043068    -50.289531     -49.862449      16.004894      0.00016391766  21.741271     -0.13702882   
+      3200   0.87994476    -50.288947     -49.819439      16.314811      0.00019806723  23.901029     -0.14852041   
+      3300   0.97710684    -50.288249     -49.766899      16.691936      0.00023936963  26.540142     -0.16126751   
+      3400   1.0947513     -50.287415     -49.703294      17.14741       0.00028941795  29.735596     -0.17542667   
+      3500   1.2356068     -50.286413     -49.627136      17.692223      0.00035013447  33.561511     -0.19115489   
+      3600   1.401879      -50.285209     -49.537215      18.336419      0.00042379924  38.077789     -0.20858771   
+      3700   1.5946465     -50.283764     -49.432917      19.085164      0.00051305445  43.313732     -0.22786881   
+      3800   1.8130867     -50.282042     -49.314643      19.93789       0.00062086813  49.246998     -0.24911566   
+      3900   2.0536114     -50.279989     -49.184254      20.885144      0.0007504384   55.780123     -0.27238956   
+      4000   2.3090877     -50.277563     -49.045514      21.903844      0.00090502091  62.71936      -0.29774099   
+      4100   2.5684074     -50.274725     -48.904312      22.957566      0.00108767     69.762993     -0.32513211   
+      4200   2.8167154     -50.271434     -48.768533      23.996177      0.0013008998   76.507527     -0.35448596   
+      4300   3.036538      -50.267666     -48.647475      24.959984      0.0015462956   82.478341     -0.38565277   
+      4400   3.2098498     -50.263408     -48.550744      25.787127      0.0018241308   87.185831     -0.41841744   
+      4500   3.3207993     -50.258668     -48.486806      26.421384      0.0021330655   90.199435     -0.45253018   
+      4600   3.3584953     -50.253474     -48.461498      26.823507      0.0024700053   91.223334     -0.48770345   
+      4700   3.3191098     -50.247864     -48.476903      26.979088      0.002830177    90.153547     -0.523627     
+      4800   3.2066723     -50.24189      -48.530922      26.900395      0.0032074389   87.099523     -0.55998518   
+      4900   3.032313      -50.235626     -48.61769       26.623396      0.0035947863   82.363581     -0.59650144   
+      5000   2.8121843     -50.229136     -48.728653      26.202501      0.0039849754   76.384452     -0.63291394   
+      5100   2.5646536     -50.222488     -48.854078      25.698898      0.0043711592   69.661033     -0.66900289   
+      5200   2.3074927     -50.215744     -48.984547      25.172075      0.0047474367   62.676038     -0.70458409   
+      5300   2.0556743     -50.208948     -49.112112      24.671889      0.0051092373   55.836155     -0.73953676   
+      5400   1.8201204     -50.202145     -49.230993      24.233676      0.0054535012   49.438049     -0.77374738   
+      5500   1.6074397     -50.195362     -49.337688      23.877579      0.0057786579   43.661222     -0.80716644   
+      5600   1.4204402     -50.188613     -49.430716      23.612103      0.0060844379   38.581947     -0.83975723   
+      5700   1.2590781     -50.181911     -49.510111      23.435375      0.0063715815   34.199035     -0.8715173    
+      5800   1.1215024     -50.175255     -49.576861      23.340009      0.0066415095   30.462209     -0.90243963   
+      5900   1.0049565     -50.168645     -49.632435      23.316226      0.0068960167   27.296594     -0.93254359   
+      6000   0.90642655    -50.162073     -49.678436      23.35333       0.0071370232   24.620327     -0.96187362   
+      6100   0.82303426    -50.15554      -49.716398      23.441044      0.0073664003   22.355228     -0.99044001   
+      6200   0.75222945    -50.149036     -49.747672      23.571168      0.0075858646   20.432031     -1.0182716    
+      6300   0.69185157    -50.142555     -49.773408      23.736184      0.0077969274   18.792049     -1.0454141    
+      6400   0.64011849    -50.1361       -49.794555      23.930273      0.0080008828   17.386876     -1.0718977    
+      6500   0.59558258    -50.129659     -49.811877      24.148617      0.0081988179   16.177194     -1.0977481    
+      6600   0.55707711    -50.123229     -49.825992      24.387764      0.0083916354   15.131309     -1.1230042    
+      6700   0.52366443    -50.11681      -49.837401      24.644278      0.0085800803   14.223755     -1.1476911    
+      6800   0.49459087    -50.110398     -49.846502      24.915585      0.0087647672   13.43406      -1.1718456    
+      6900   0.46924933    -50.103993     -49.853618      25.199975      0.0089462046   12.745734     -1.1954836    
+      7000   0.44714908    -50.09759      -49.859007      25.495663      0.0091248169   12.145448     -1.2186489    
+      7100   0.42789171    -50.09119      -49.862882      25.801204      0.0093009621   11.62238      -1.2413589    
+      7200   0.41115213    -50.084791     -49.865415      26.115435      0.0094749465   11.1677       -1.2636357    
+      7300   0.39666341    -50.078389     -49.866743      26.43778       0.0096470373   10.774158     -1.2855199    
+      7400   0.38420469    -50.071981     -49.866983      26.767492      0.0098174711   10.435755     -1.3070246    
+      7500   0.37359146    -50.065568     -49.866233      27.103933      0.0099864621   10.147478     -1.3281809    
+      7600   0.36466763    -50.059148     -49.864574      27.446285      0.010154207    9.9050896     -1.3490095    
+      7700   0.35729911    -50.052716     -49.862074      27.794551      0.010320892    9.7049462     -1.3695395    
+      7800   0.35136861    -50.046271     -49.858793      28.148371      0.010486691    9.5438621     -1.3897895    
+      7900   0.34677153    -50.039813     -49.854788      28.507205      0.010651775    9.4189963     -1.4097881    
+      8000   0.34341297    -50.033336     -49.850103      28.870887      0.010816309    9.3277714     -1.4295506    
+      8100   0.34120579    -50.026841     -49.844785      29.238802      0.010980456    9.2678199     -1.4491058    
+      8200   0.3400696     -50.020321     -49.838872      29.611242      0.011144377    9.2369587     -1.4684765    
+      8300   0.33993073    -50.013777     -49.832402      29.987651      0.011308235    9.2331869     -1.4876802    
+      8400   0.34072278    -50.007208     -49.82541       30.367811      0.011472193    9.2547003     -1.5067423    
+      8500   0.34238718    -50.000608     -49.817922      30.75172       0.011636417    9.2999089     -1.5256766    
+      8600   0.34487349    -49.993976     -49.809964      31.138912      0.011801076    9.3674418     -1.5445114    
+      8700   0.34813839    -49.987308     -49.801554      31.529558      0.011966343    9.4561231     -1.5632615    
+      8800   0.35214326    -49.980605     -49.792714      31.923412      0.012132398    9.5649031     -1.5819515    
+      8900   0.35684992    -49.973862     -49.783459      32.320438      0.012299427    9.6927453     -1.6005873    
+      9000   0.36221521    -49.967079     -49.773813      32.720589      0.012467623    9.8384771     -1.6191906    
+      9100   0.36818518    -49.96025      -49.763799      33.12412       0.012637186    10.000633     -1.6377754    
+      9200   0.3746904     -49.953378     -49.753456      33.530521      0.012808324    10.177328     -1.6563518    
+      9300   0.3816439     -49.946457     -49.742826      33.940033      0.01298125     10.366198     -1.6749285    
+      9400   0.3889426     -49.939487     -49.73196       34.352706      0.013156185    10.564445     -1.6935206    
+      9500   0.39647284    -49.932468     -49.720924      34.768109      0.01333335     10.768982     -1.712126     
+      9600   0.40411904    -49.925391     -49.709767      35.186397      0.013512971    10.976668     -1.7307508    
+      9700   0.41177414    -49.918266     -49.698558      35.606965      0.013695276    11.184595     -1.7493922    
+      9800   0.41934973    -49.911084     -49.687333      36.03058       0.013880493    11.390363     -1.7680484    
+      9900   0.42678411    -49.903846     -49.676129      36.456503      0.014068856    11.592295     -1.7867244    
+     10000   0.43404714    -49.896555     -49.664963      36.884919      0.014260602    11.789574     -1.8054063    
+Loop time of 14.691 on 1 procs for 10000 steps with 180 atoms
+
+Performance: 0.059 ns/day, 408.083 hours/ns, 680.690 timesteps/s, 122.524 katom-step/s
+98.3% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.9459     | 2.9459     | 2.9459     |   0.0 | 20.05
+Bond    | 0.0010983  | 0.0010983  | 0.0010983  |   0.0 |  0.01
+Neigh   | 6.4646     | 6.4646     | 6.4646     |   0.0 | 44.00
+Comm    | 0.54538    | 0.54538    | 0.54538    |   0.0 |  3.71
+Output  | 0.0030317  | 0.0030317  | 0.0030317  |   0.0 |  0.02
+Modify  | 4.662      | 4.662      | 4.662      |   0.0 | 31.73
+Other   |            | 0.06897    |            |       |  0.47
+
+Nlocal:            180 ave         180 max         180 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           1510 ave        1510 max        1510 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          13680 ave       13680 max       13680 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 13680
+Ave neighs/atom = 76
+Ave special neighs/atom = 0
+Neighbor list builds = 10000
+Dangerous builds not checked
+Total wall time: 0:00:14

examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.6

@@ -0,0 +1,197 @@
+LAMMPS (8 Feb 2023)
+Processor partition = 6
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+variable ibead uloop 32 pad
+variable out_freq string 100
+variable job_name string H2
+
+units      real
+atom_style full
+pair_style table linear 10000
+
+neighbor 2.0 bin
+neigh_modify every 1 delay 0 check no
+
+read_data H2.data
+Reading data file ...
+  orthogonal box = (0 0 0) to (19.71219 19.71219 19.71219)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  180 atoms
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     0 = max # of 1-2 neighbors
+     0 = max # of 1-3 neighbors
+     0 = max # of 1-4 neighbors
+     1 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
+  read_data CPU = 0.003 seconds
+
+pair_coeff 1 * pair.table PAIR_H2
+WARNING: 5852 of 18000 force values in table PAIR_H2 are inconsistent with -dE/dr.
+WARNING:  Should only be flagged at inflection points (src/pair_table.cpp:466)
+
+timestep        0.001
+
+velocity all create 1.0 1985 rot yes dist gaussian
+
+fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 25.0 nhc 4
+
+thermo_style    custom step temp pe etotal pzz f_1[1] f_1[2] f_1[3]
+thermo_modify   colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial
+thermo          ${out_freq}
+thermo          100
+
+#dump dcd all dcd ${out_freq} ${job_name}_${ibead}.dcd
+
+#restart ${out_freq} ${job_name}_${ibead}.restart1 ${job_name}_${ibead}.restart2
+
+run 10000
+WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 11.55117
+  ghost atom cutoff = 11.55117
+  binsize = 5.775585, bins = 4 4 4
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair table, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 11.97 | 11.97 | 11.97 Mbytes
+   Step          Temp          PotEng         TotEng          Pzz          espring         T_ring         virial    
+         0   1             -50.292986     -49.759421      16.18218       0              0              4.331435e-14 
+       100   0.9951423     -50.292972     -49.761999      16.167254      3.663073e-06   27.030021     -0.0025950927 
+       200   0.98099313    -50.292958     -49.769535      16.121999      1.4652294e-05  26.645702     -0.0052104718 
+       300   0.95873287    -50.292945     -49.781399      16.050672      3.2966429e-05  26.041069     -0.0078660339 
+       400   0.93006021    -50.292932     -49.796684      15.959387      5.8599875e-05  25.262263     -0.010582044  
+       500   0.89689329    -50.292917     -49.814366      15.855074      9.1539141e-05  24.361385     -0.013380753  
+       600   0.86110024    -50.292898     -49.833445      15.744205      0.00013176059  23.389175     -0.016282487  
+       700   0.82431428    -50.292877     -49.853052      15.632253      0.00017923062  22.389996     -0.019305323  
+       800   0.78784526    -50.29285      -49.872483      15.523595      0.00023390859  21.399426     -0.022473781  
+       900   0.7526687     -50.292816     -49.891219      15.421094      0.00029575217  20.443961     -0.025805439  
+      1000   0.71946253    -50.292776     -49.908896      15.326586      0.0003647244   19.542016     -0.029318877  
+      1100   0.6886647     -50.292726     -49.925279      15.241234      0.00044080156  18.705487     -0.033035613  
+      1200   0.66053404    -50.292668     -49.94023       15.165485      0.00052398138  17.941403     -0.036980816  
+      1300   0.63520455    -50.292595     -49.953672      15.099745      0.00061429107  17.253404     -0.041183239  
+      1400   0.61273022    -50.292511     -49.965579      15.043883      0.00071179519  16.642957     -0.045662316  
+      1500   0.59312004    -50.29241      -49.975942      14.99787       0.00081660341  16.110306     -0.050440479  
+      1600   0.57636482    -50.292289     -49.984761      14.961722      0.00092887845  15.655202     -0.055550832  
+      1700   0.56245787    -50.292149     -49.992041      14.935319      0.0010488445   15.277461     -0.061027295  
+      1800   0.55141126    -50.291984     -49.99777       14.919091      0.0011767964   14.977414     -0.066900795  
+      1900   0.54326956    -50.291792     -50.001923      14.913094      0.0013131107   14.756269     -0.073216193  
+      2000   0.53812238    -50.29157      -50.004447      14.917947      0.0014582582   14.616462     -0.080017237  
+      2100   0.53611709    -50.291312     -50.005259      14.934473      0.0016128191   14.561994     -0.087363239  
+      2200   0.53747284    -50.291009     -50.004233      14.964038      0.0017775021   14.598819     -0.095297839  
+      2300   0.54249688    -50.290657     -50.001199      15.008081      0.0019531669   14.735282     -0.10390758   
+      2400   0.5516043     -50.290246     -49.995929      15.068555      0.0021408527   14.982657     -0.11326027   
+      2500   0.56534197    -50.289766     -49.988119      15.147769      0.0023418123   15.355799     -0.12345646   
+      2600   0.58441738    -50.289207     -49.977382      15.249155      0.0025575544   15.873925     -0.13459188   
+      2700   0.60973272    -50.28855      -49.963218      15.376625      0.0027898943   16.561539     -0.14680402   
+      2800   0.64242344    -50.287778     -49.945003      15.535379      0.0030410156   17.449483     -0.16021499   
+      2900   0.68389909    -50.286869     -49.921964      15.731194      0.003313542    18.576043     -0.1749965    
+      3000   0.73588147    -50.28579      -49.893149      15.972304      0.0036106211   19.987987     -0.19131687   
+      3100   0.80043087    -50.284508     -49.857426      16.267625      0.0039360184   21.741276     -0.20938994   
+      3200   0.87994497    -50.282984     -49.813476      16.627323      0.0042942181   23.901035     -0.229419     
+      3300   0.97710707    -50.281162     -49.759812      17.064318      0.0046905236   26.540149     -0.25165651   
+      3400   1.0947515     -50.278979     -49.694858      17.591402      0.0051311469   29.735603     -0.27634359   
+      3500   1.2356071     -50.276358     -49.617081      18.222808      0.0056232657   33.561517     -0.30373125   
+      3600   1.4018792     -50.273211     -49.525217      18.97057       0.0061750242   38.077795     -0.33406344   
+      3700   1.5946467     -50.269438     -49.41859       19.844391      0.0067954397   43.313738     -0.36756248   
+      3800   1.8130868     -50.264926     -49.297526      20.847335      0.0074941739   49.247003     -0.4044001    
+      3900   2.0536116     -50.259558     -49.163823      21.972799      0.0082811282   55.780127     -0.44468343   
+      4000   2.3090877     -50.253214     -49.021165      23.203274      0.0091658295   62.719362     -0.48844585   
+      4100   2.5684074     -50.245778     -48.875365      24.50535       0.010156603    69.762993     -0.53559997   
+      4200   2.8167153     -50.237155     -48.734254      25.832794      0.011259571    76.507524     -0.58595872   
+      4300   3.0365377     -50.22728      -48.607089      27.128084      0.012477576    82.478334     -0.63920669   
+      4400   3.2098494     -50.216129     -48.503465      28.32938       0.013809186    87.18582      -0.69492156   
+      4500   3.3207987     -50.203729     -48.431867      29.380289      0.015247971    90.19942      -0.75258375   
+      4600   3.3584946     -50.190151     -48.398176      30.239405      0.016782256    91.223315     -0.81162394   
+      4700   3.319109      -50.175529     -48.404569      30.887433      0.01839546     90.153525     -0.87142276   
+      4800   3.2066714     -50.160034     -48.449067      31.329923      0.020067061    87.099499     -0.93139568   
+      4900   3.0323121     -50.14386      -48.525924      31.596801      0.021774071    82.363558     -0.99098372   
+      5000   2.8121835     -50.127216     -48.626733      31.734704      0.02349282     76.384432     -1.04971      
+      5100   2.5646531     -50.11031      -48.741901      31.798135      0.025200765    69.661019     -1.1071803    
+      5200   2.3074925     -50.093317     -48.86212       31.840218      0.026878076    62.676032     -1.16309      
+      5300   2.0556744     -50.076391     -48.979555      31.905031      0.028508785    55.836159     -1.217247     
+      5400   1.820121      -50.059654     -49.088501      32.023732      0.030081384    49.438064     -1.2695269    
+      5500   1.6074407     -50.04318      -49.185506      32.214415      0.031588873    43.661248     -1.319891     
+      5600   1.4204416     -50.02701      -49.269112      32.484092      0.033028319    38.581985     -1.3683615    
+      5700   1.2590798     -50.011162     -49.339361      32.830285      0.034400107    34.199083     -1.4149934    
+      5800   1.1215045     -49.995631     -49.397236      33.245821      0.035707041    30.462267     -1.4598878    
+      5900   1.0049589     -49.980399     -49.444188      33.721747      0.03695346     27.29666      -1.5031416    
+      6000   0.90642926    -49.965438     -49.4818        34.248321      0.038144494    24.620401     -1.5448741    
+      6100   0.82303723    -49.950718     -49.511574      34.817039      0.039285497    22.355309     -1.585191     
+      6200   0.75223267    -49.936211     -49.534846      35.419814      0.040381668    20.432118     -1.6242074    
+      6300   0.69185501    -49.921889     -49.552739      36.050843      0.041437835    18.792142     -1.6620216    
+      6400   0.64012215    -49.907725     -49.566179      36.704661      0.042458347    17.386976     -1.6987306    
+      6500   0.59558646    -49.893699     -49.575915      37.378286      0.04344705     16.177299     -1.7344148    
+      6600   0.55708121    -49.879794     -49.582555      38.067181      0.044407312    15.131421     -1.7691453    
+      6700   0.52366875    -49.865988     -49.586576      38.769884      0.045342063    14.223873     -1.8030059    
+      6800   0.49459542    -49.852276     -49.588377      39.48355       0.046253857    13.434184     -1.8360506    
+      6900   0.46925412    -49.838637     -49.58826       40.206955      0.047144922    12.745864     -1.8683386    
+      7000   0.44715411    -49.825066     -49.58648       40.938794      0.048017218    12.145585     -1.8999205    
+      7100   0.427897      -49.811553     -49.583243      41.677982      0.048872484    11.622524     -1.9308529    
+      7200   0.4111577     -49.798086     -49.578707      42.423605      0.049712274    11.167851     -1.9611851    
+      7300   0.39666926    -49.784662     -49.573013      43.175155      0.050538       10.774317     -1.9909515    
+      7400   0.38421083    -49.771272     -49.56627       43.931762      0.051350953    10.435921     -2.0202015    
+      7500   0.37359789    -49.757907     -49.558568      44.69348       0.052152332    10.147653     -2.0489622    
+      7600   0.36467436    -49.744563     -49.549985      45.459725      0.052943262    9.9052723     -2.0772881    
+      7700   0.35730613    -49.731235     -49.540589      46.229921      0.053724811    9.7051368     -2.1052027    
+      7800   0.3513759     -49.717911     -49.530429      47.004627      0.054498005    9.54406       -2.1327445    
+      7900   0.34677906    -49.704589     -49.51956       47.78318       0.055263836    9.419201      -2.1599468    
+      8000   0.34342073    -49.691262     -49.508025      48.565675      0.056023277    9.327982      -2.1868375    
+      8100   0.34121371    -49.677922     -49.495862      49.351802      0.056777286    9.2680351     -2.2134444    
+      8200   0.34007764    -49.664566     -49.483112      50.141603      0.057526819    9.2371771     -2.2397997    
+      8300   0.33993883    -49.651181     -49.469802      50.935241      0.05827283     9.2334067     -2.2659331    
+      8400   0.34073085    -49.637766     -49.455963      51.732654      0.059016284    9.2549196     -2.2918688    
+      8500   0.34239516    -49.62431      -49.441619      52.534019      0.059758157    9.3001256     -2.317626     
+      8600   0.3448813     -49.610812     -49.426796      53.338612      0.060499441    9.367654      -2.3432261    
+      8700   0.34814597    -49.597265     -49.411506      54.147073      0.061241149    9.4563288     -2.3686991    
+      8800   0.35215054    -49.583658     -49.395763      54.959512      0.061984314    9.5651009     -2.3940587    
+      8900   0.35685687    -49.569985     -49.379579      55.776434      0.062729991    9.692934      -2.419329     
+      9000   0.36222181    -49.556241     -49.362972      56.597626      0.063479254    9.8386562     -2.4445253    
+      9100   0.36819143    -49.54242      -49.345966      57.423306      0.064233198    10.000803     -2.469667     
+      9200   0.37469636    -49.528518     -49.328593      58.253634      0.064992931    10.17749      -2.4947681    
+      9300   0.38164964    -49.514521     -49.310886      59.088869      0.065759574    10.366354     -2.5198522    
+      9400   0.38894823    -49.500427     -49.292898      59.929378      0.066534253    10.564598     -2.5449285    
+      9500   0.3964785     -49.486229     -49.274681      60.775174      0.067318101    10.769135     -2.5700196    
+      9600   0.4041249     -49.471917     -49.25629       61.626259      0.068112253    10.976827     -2.5951326    
+      9700   0.41178035    -49.457494     -49.237782      62.482132      0.06891785     11.184764     -2.6202815    
+      9800   0.41935645    -49.44294      -49.219186      63.343831      0.069736042    11.390545     -2.6454805    
+      9900   0.42679147    -49.428257     -49.200536      64.211037      0.070567996    11.592495     -2.670741     
+     10000   0.43405521    -49.413432     -49.181835      65.08463       0.071414903    11.789793     -2.6960774    
+Loop time of 14.691 on 1 procs for 10000 steps with 180 atoms
+
+Performance: 0.059 ns/day, 408.083 hours/ns, 680.690 timesteps/s, 122.524 katom-step/s
+95.3% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 3.1084     | 3.1084     | 3.1084     |   0.0 | 21.16
+Bond    | 0.0010414  | 0.0010414  | 0.0010414  |   0.0 |  0.01
+Neigh   | 6.6306     | 6.6306     | 6.6306     |   0.0 | 45.13
+Comm    | 0.56093    | 0.56093    | 0.56093    |   0.0 |  3.82
+Output  | 0.002951   | 0.002951   | 0.002951   |   0.0 |  0.02
+Modify  | 4.3177     | 4.3177     | 4.3177     |   0.0 | 29.39
+Other   |            | 0.06942    |            |       |  0.47
+
+Nlocal:            180 ave         180 max         180 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           1510 ave        1510 max        1510 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          13680 ave       13680 max       13680 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 13680
+Ave neighs/atom = 76
+Ave special neighs/atom = 0
+Neighbor list builds = 10000
+Dangerous builds not checked
+Total wall time: 0:00:14

examples/PACKAGES/pimd/para-h2/log.25Feb23.scp.g++.8.7

@@ -0,0 +1,197 @@
+LAMMPS (8 Feb 2023)
+Processor partition = 7
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+variable ibead uloop 32 pad
+variable out_freq string 100
+variable job_name string H2
+
+units      real
+atom_style full
+pair_style table linear 10000
+
+neighbor 2.0 bin
+neigh_modify every 1 delay 0 check no
+
+read_data H2.data
+Reading data file ...
+  orthogonal box = (0 0 0) to (19.71219 19.71219 19.71219)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  180 atoms
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     0 = max # of 1-2 neighbors
+     0 = max # of 1-3 neighbors
+     0 = max # of 1-4 neighbors
+     1 = max # of special neighbors
+  special bonds CPU = 0.000 seconds
+  read_data CPU = 0.002 seconds
+
+pair_coeff 1 * pair.table PAIR_H2
+WARNING: 5852 of 18000 force values in table PAIR_H2 are inconsistent with -dE/dr.
+WARNING:  Should only be flagged at inflection points (src/pair_table.cpp:466)
+
+timestep        0.001
+
+velocity all create 1.0 1985 rot yes dist gaussian
+
+fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 25.0 nhc 4
+
+thermo_style    custom step temp pe etotal pzz f_1[1] f_1[2] f_1[3]
+thermo_modify   colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial
+thermo          ${out_freq}
+thermo          100
+
+#dump dcd all dcd ${out_freq} ${job_name}_${ibead}.dcd
+
+#restart ${out_freq} ${job_name}_${ibead}.restart1 ${job_name}_${ibead}.restart2
+
+run 10000
+WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
+Generated 0 of 0 mixed pair_coeff terms from geometric mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 0 steps, check = no
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 11.55117
+  ghost atom cutoff = 11.55117
+  binsize = 5.775585, bins = 4 4 4
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair table, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+Per MPI rank memory allocation (min/avg/max) = 11.97 | 11.97 | 11.97 Mbytes
+   Step          Temp          PotEng         TotEng          Pzz          espring         T_ring         virial    
+         0   1             -50.292986     -49.759421      16.18218       0              0              4.331435e-14 
+       100   0.99396717    -50.292908     -49.762562      16.16754       3.6546345e-06  31.630244     -0.01511026   
+       200   0.97647843    -50.292785     -49.77177       16.117482      1.4519126e-05  31.073714     -0.030258999  
+       300   0.94920978    -50.292584     -49.786119      16.040198      3.2307193e-05  30.205965     -0.045469889  
+       400   0.91451321    -50.292301     -49.804349      15.94486       5.6578376e-05  29.101843     -0.060775514  
+       500   0.87495051    -50.291935     -49.825092      15.839811      8.6783378e-05  27.84287      -0.07621024   
+       600   0.83290521    -50.291484     -49.847075      15.733867      0.00012231241  26.504895     -0.091795014  
+       700   0.79035049    -50.290943     -49.869239      15.633262      0.0001625386   25.150709     -0.10756384   
+       800   0.74877056    -50.29031      -49.890792      15.542706      0.00020685191  23.827543     -0.12353621   
+       900   0.70918842    -50.289582     -49.911184      15.465561      0.00025468227  22.567951     -0.13974782   
+      1000   0.67224667    -50.288756     -49.930069      15.403036      0.00030551305  21.392383     -0.15621567   
+      1100   0.63830199    -50.287828     -49.947252      15.356514      0.00035888685  20.312188     -0.17298512   
+      1200   0.60751172    -50.286791     -49.962644      15.325845      0.0004144061   19.332373     -0.19008041   
+      1300   0.57990404    -50.285641     -49.976225      15.311509      0.00047173031  18.453835     -0.20753645   
+      1400   0.5554312     -50.284374     -49.988015      15.313263      0.00053057146  17.675055     -0.22539174   
+      1500   0.53400813    -50.282975     -49.998047      15.33133       0.00059068877  16.993325     -0.24369544   
+      1600   0.51553984    -50.281444     -50.00637       15.365561      0.00065188331  16.405623     -0.26248285   
+      1700   0.49994085    -50.279767     -50.013016      15.416271      0.00071399304  15.909229     -0.28182209   
+      1800   0.48714931    -50.277932     -50.018006      15.48387       0.00077688833  15.502174     -0.30176215   
+      1900   0.47713797    -50.275928     -50.021344      15.569019      0.00084046832  15.183591     -0.32238808   
+      2000   0.46992375    -50.273735     -50.023         15.673314      0.00090465799  14.954018     -0.3437631    
+      2100   0.46557711    -50.271332     -50.022917      15.797801      0.00096940607  14.815698     -0.36598703   
+      2200   0.46423244    -50.2687       -50.021002      15.944553      0.0010346838   14.772908     -0.38915619   
+      2300   0.46610038    -50.26581      -50.017115      16.115839      0.0011004847   14.83235      -0.41338963   
+      2400   0.47148286    -50.262625     -50.011058      16.314677      0.0011668255   15.003632     -0.43882597   
+      2500   0.48079165    -50.259109     -50.002575      16.545079      0.0012337477   15.299859     -0.46562537   
+      2600   0.49457102    -50.255212     -49.991327      16.811386      0.0013013219   15.738349     -0.49395245   
+      2700   0.51352449    -50.250875     -49.976877      17.11979       0.0013696525   16.341491     -0.52401609   
+      2800   0.53854543    -50.246032     -49.958683      17.477089      0.0014388859   17.137712     -0.55604082   
+      2900   0.57074936    -50.240596     -49.936064      17.892199      0.0015092207   18.162513     -0.59030618   
+      3000   0.61150422    -50.234467     -49.90819       18.375616      0.001580922    19.459423     -0.62708735   
+      3100   0.66245096    -50.227523     -49.874062      18.939819      0.0016543394   21.080662     -0.66672955   
+      3200   0.72550205    -50.219616     -49.832514      19.60023       0.0017299293   23.087088     -0.70958417   
+      3300   0.80279929    -50.210579     -49.782233      20.37383       0.0018082826   25.546857     -0.75603924   
+      3400   0.89660476    -50.200203     -49.721806      21.28012       0.0018901552   28.531956     -0.80651501   
+      3500   1.0090938     -50.188252     -49.649835      22.340233      0.0019765002   32.111606     -0.86141363   
+      3600   1.1420183     -50.174459     -49.565118      23.57558       0.0020684981   36.34156      -0.92115194   
+      3700   1.2962221     -50.158518     -49.466899      25.006266      0.0021675754   41.248667     -0.98609175   
+      3800   1.4710194     -50.140107     -49.355223      26.648455      0.0022754045   46.811106     -1.0565325    
+      3900   1.6635051     -50.118886     -49.231298      28.511102      0.0023938687   52.936429     -1.1326688    
+      4000   1.8679372     -50.094526     -49.097861      30.592386      0.0025249809   59.441913     -1.214555     
+      4100   2.075405      -50.066723     -48.95936       32.878933      0.0026707445   66.044        -1.3020682    
+      4200   2.2740293     -50.035234     -48.821891      35.342354      0.0028329538   72.364666     -1.394874     
+      4300   2.449883      -49.999912     -48.69274       37.94169       0.0030129483   77.96072      -1.4924536    
+      4400   2.5886538     -49.960721     -48.579506      40.62924       0.0032113484   82.376716     -1.5940701    
+      4500   2.6778127     -49.917775     -48.488988      43.35421       0.0034278221   85.21395      -1.6987968    
+      4600   2.7088053     -49.871336     -48.426012      46.071925      0.0036609337   86.200203     -1.8055903    
+      4700   2.6786752     -49.821807     -48.39256       48.749456      0.0039081229   85.241397     -1.9133555    
+      4800   2.5906421     -49.769708     -48.387433      51.369043      0.0041658356   82.439989     -2.0209603    
+      4900   2.4534656     -49.71564      -48.406557      53.929171      0.0044297991   78.074727     -2.1273728    
+      5000   2.2797967     -49.660246     -48.443826      56.439389      0.0046953978   72.548196     -2.2316692    
+      5100   2.0839917     -49.60414      -48.492195      58.917167      0.0049580886   66.317246     -2.3330819    
+      5200   1.8799454     -49.547898     -48.544825      61.38072       0.0052137855   59.824039     -2.4310487    
+      5300   1.6794028     -49.492001     -48.59593       63.845702      0.0054591569   53.442329     -2.5251887    
+      5400   1.4910004     -49.436812     -48.641266      66.323664      0.0056917984   47.446947     -2.6153153    
+      5500   1.3200581     -49.382602     -48.678265      68.81759       0.0059102724   42.007182     -2.7013892    
+      5600   1.1689597     -49.32954      -48.705824      71.326608      0.0061140319   37.198896     -2.7834961    
+      5700   1.0378669     -49.277687     -48.723917      73.847293      0.0063032634   33.027232     -2.8618238    
+      5800   0.92551081    -49.227051     -48.733231      76.373912      0.0064786911   29.451811     -2.9366159    
+      5900   0.82988009    -49.177354     -48.734559      78.907054      0.0066413821   26.408629     -3.0079862    
+      6000   0.74872148    -49.128988     -48.729496      81.429069      0.0067925784   23.825981     -3.0765541    
+      6100   0.6798481     -49.081399     -48.718656      83.949013      0.0069335708   21.634277     -3.1425093    
+      6200   0.62129621    -49.034965     -48.703463      86.450184      0.0070656124   19.771026     -3.2059256    
+      6300   0.5713815     -48.989354     -48.684484      88.938306      0.0071898691   18.182629     -3.2671248    
+      6400   0.52869861    -48.944483     -48.662388      91.411964      0.0073073957   16.824365     -3.326325     
+      6500   0.49209369    -48.900284     -48.63772       93.869881      0.00741913     15.659515     -3.383704     
+      6600   0.4606278     -48.85645      -48.610675      96.319181      0.0075258972   14.6582       -3.4393879    
+      6700   0.4335401     -48.813153     -48.581831      98.754093      0.0076284202   13.796209     -3.4935699    
+      6800   0.41021495    -48.770575     -48.551698      101.16784      0.0077273325   13.053951     -3.546418     
+      6900   0.39015391    -48.728202     -48.520029      103.57385      0.0078231904   12.415565     -3.5980989    
+      7000   0.37295279    -48.686464     -48.487469      105.95986      0.0079164859   11.868187     -3.6485312    
+      7100   0.35828286    -48.645075     -48.453908      108.33347      0.008007657    11.401357     -3.6979091    
+      7200   0.34587564    -48.603786     -48.419239      110.70102      0.0080970974   11.006532     -3.7462688    
+      7300   0.33551045    -48.563011     -48.383994      113.05147      0.0081851643   10.676688     -3.7937749    
+      7400   0.32700405    -48.5225       -48.348023      115.39114      0.008272185    10.405996     -3.8404567    
+      7500   0.32020193    -48.481991     -48.311143      117.72756      0.0083584619   10.189537     -3.8863461    
+      7600   0.31497086    -48.441913     -48.273856      120.0495       0.008444277    10.023073     -3.9315862    
+      7700   0.31119256    -48.401778     -48.235736      122.37022      0.0085298943   9.9028389     -3.9761586    
+      7800   0.30875834    -48.362027     -48.197284      124.67777      0.0086155626   9.8253766     -4.020194     
+      7900   0.30756489    -48.322398     -48.158292      126.9798       0.0087015164   9.7873982     -4.0637137    
+      8000   0.30751134    -48.282865     -48.118788      129.27742      0.0087879767   9.7856943     -4.1067668    
+      8100   0.30849789    -48.243167     -48.078563      131.57737      0.0088751511   9.8170884     -4.1492332    
+      8200   0.31042593    -48.203515     -48.037882      133.87491      0.0089632335   9.8784428     -4.1915847    
+      8300   0.31319977    -48.163874     -47.996762      136.17056      0.0090524039   9.9667128     -4.2336145    
+      8400   0.3167294     -48.124228     -47.955232      138.46555      0.0091428273   10.079033     -4.2753558    
+      8500   0.32093339    -48.084773     -47.913534      140.75426      0.0092346543   10.212814     -4.3167737    
+      8600   0.32574097    -48.045251     -47.871447      143.04447      0.0093280205   10.365802     -4.3579897    
+      8700   0.33109202    -48.005633     -47.828974      145.33751      0.0094230472   10.536084     -4.3990428    
+      8800   0.33693414    -47.965895     -47.786118      147.63516      0.0095198428   10.721993     -4.4399711    
+      8900   0.34321684    -47.926004     -47.742875      149.9379       0.009618504    10.921922     -4.4808086    
+      9000   0.34988367    -47.885934     -47.699248      152.24678      0.0097191181   11.134076     -4.5215921    
+      9100   0.35686443    -47.845658     -47.655247      154.56358      0.0098217652   11.356219     -4.5623394    
+      9200   0.3640698     -47.805147     -47.610893      156.88915      0.0099265208   11.58551      -4.6030874    
+      9300   0.37139091    -47.764138     -47.565977      159.23099      0.010033457    11.818484     -4.6439479    
+      9400   0.37870543    -47.722844     -47.52078       161.5788       0.010142648    12.051248     -4.6846276    
+      9500   0.38588975    -47.68146      -47.475562      163.93728      0.010254165    12.279869     -4.7255143    
+      9600   0.39283543    -47.639735     -47.430132      166.30871      0.010368088    12.500896     -4.7664862    
+      9700   0.39946605    -47.597406     -47.384265      168.70114      0.010484497    12.711897     -4.8075181    
+      9800   0.40575037    -47.55491      -47.338416      171.10373      0.010603483    12.911878     -4.848721     
+      9900   0.41170816    -47.511756     -47.292083      173.53055      0.010725141    13.101469     -4.8900195    
+     10000   0.41740707    -47.468384     -47.245671      175.97095      0.010849577    13.282821     -4.9315123    
+Loop time of 14.691 on 1 procs for 10000 steps with 180 atoms
+
+Performance: 0.059 ns/day, 408.083 hours/ns, 680.690 timesteps/s, 122.524 katom-step/s
+97.9% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 2.9822     | 2.9822     | 2.9822     |   0.0 | 20.30
+Bond    | 0.00090722 | 0.00090722 | 0.00090722 |   0.0 |  0.01
+Neigh   | 6.5119     | 6.5119     | 6.5119     |   0.0 | 44.33
+Comm    | 0.55377    | 0.55377    | 0.55377    |   0.0 |  3.77
+Output  | 0.0024523  | 0.0024523  | 0.0024523  |   0.0 |  0.02
+Modify  | 4.5713     | 4.5713     | 4.5713     |   0.0 | 31.12
+Other   |            | 0.06845    |            |       |  0.47
+
+Nlocal:            180 ave         180 max         180 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:           1510 ave        1510 max        1510 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:          13712 ave       13712 max       13712 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 13712
+Ave neighs/atom = 76.177778
+Ave special neighs/atom = 0
+Neighbor list builds = 10000
+Dangerous builds not checked
+Total wall time: 0:00:14

examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8

@@ -0,0 +1,2 @@
+LAMMPS (8 Feb 2023)
+Running on 8 partitions of processors

examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.0

@@ -0,0 +1,148 @@
+LAMMPS (8 Feb 2023)
+Processor partition = 0
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+variable ibead uloop 8 pad
+
+units           real
+neigh_modify    delay 2 every 1
+
+atom_style      full
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+
+pair_style      lj/charmm/coul/long 11 12
+pair_modify     mix arithmetic
+kspace_style    pppm 1e-4
+
+read_data system.data
+Reading data file ...
+  orthogonal box = (-23.109 -22.733 -23.141) to (22.853 22.912 22.8)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  8674 atoms
+  reading velocities ...
+  8674 velocities
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  18 = max dihedrals/atom
+  scanning impropers ...
+  1 = max impropers/atom
+  reading bonds ...
+  5869 bonds
+  reading angles ...
+  3264 angles
+  reading dihedrals ...
+  708 dihedrals
+  reading impropers ...
+  38 impropers
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     4 = max # of 1-2 neighbors
+     9 = max # of 1-3 neighbors
+    17 = max # of 1-4 neighbors
+    21 = max # of special neighbors
+  special bonds CPU = 0.004 seconds
+  read_data CPU = 0.138 seconds
+#read_restart    system_${ibead}.rest1
+special_bonds   charmm
+
+fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 300.0 nhc 4 sp 2.0
+
+thermo          10
+thermo_style    custom step temp pe etotal f_1[1] f_1[2] f_1[3]
+thermo_modify   colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial
+timestep        0.08
+
+# restart         100 system_${ibead}.rest1 system_${ibead}.rest2
+
+group prot id <= 256
+256 atoms in group prot
+# dump 1 prot dcd 100 prot_${ibead}.dcd
+
+run             200
+WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
+  G vector (1/distance) = 0.22071363
+  grid = 20 20 20
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.024910591
+  estimated relative force accuracy = 7.5017505e-05
+  using double precision KISS FFT
+  3d grid and FFT values/proc = 15625 8000
+Generated 231 of 231 mixed pair_coeff terms from arithmetic mixing rule
+Fix pimd/nvt -P/(beta^2 * hbar^2) =       -2.9535019e+01 (kcal/mol/A^2)
+
+Neighbor list info ...
+  update: every = 1 steps, delay = 2 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 14
+  ghost atom cutoff = 14
+  binsize = 7, bins = 7 7 7
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/charmm/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+WARNING: Inconsistent image flags (src/domain.cpp:815)
+Per MPI rank memory allocation (min/avg/max) = 84.59 | 84.59 | 84.59 Mbytes
+   Step          Temp          PotEng         TotEng        espring         T_ring         virial    
+         0   306.20099     -26166.171     -18250.089      0              0             -676.31071    
+        10   131.27164     -24353.129     -20959.421      307.69774      131.25651     -622.84631    
+        20   173.87922     -20639.595     -16144.371      903.19698      173.85917     -146.32235    
+        30   174.36894     -14805.957     -10298.072      2123.5094      174.34883      1001.9707    
+        40   209.39721     -9107.42       -3693.9648      3643.8992      209.37307      2169.6179    
+        50   224.56543     -4755.7551      1049.8374      5433.6153      224.53954      3077.7538    
+        60   236.84365     -1848.0123      4275.0036      7420.6008      236.81634      3690.4423    
+        70   251.60145     -545.63452      5958.9084      9472.1666      251.57244      3930.8483    
+        80   259.97884     -310.2814       6410.8387      11592.586      259.94887      4052.0897    
+        90   266.56259     -619.03771      6272.2892      13763.979      266.53186      3895.0106    
+       100   277.74387     -1327.8055      5852.5862      15788.989      277.71185      3691.775     
+       110   278.73044     -1998.5         5207.397       17723.605      278.69831      2838.6857    
+       120   286.74106     -2688.0018      4724.9903      19437.173      286.70801      2354.3367    
+       130   284.45763     -3484.7277      3869.2319      20933.859      284.42484      2037.2135    
+       140   290.24681     -4412.7819      3090.8428      22113.049      290.21335      1802.8857    
+       150   294.32521     -5490.1829      2118.8788      23005.855      294.29127      1927.3626    
+       160   293.9109      -6586.1293      1012.2214      23597.9        293.87701      2198.3058    
+       170   290.52772     -7737.8309     -226.94392      23882.219      290.49423      2454.2765    
+       180   289.91516     -8766.2419     -1271.1912      23875.129      289.88174      2549.258     
+       190   292.57992     -9618.0848     -2054.1432      23580.482      292.54619      2605.4823    
+       200   295.4078      -10200.536     -2563.4865      23028.461      295.37374      2587.5531    
+Loop time of 35.3333 on 1 procs for 200 steps with 8674 atoms
+
+Performance: 0.039 ns/day, 613.425 hours/ns, 5.660 timesteps/s, 49.098 katom-step/s
+99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 27.689     | 27.689     | 27.689     |   0.0 | 78.37
+Bond    | 0.1312     | 0.1312     | 0.1312     |   0.0 |  0.37
+Kspace  | 2.4446     | 2.4446     | 2.4446     |   0.0 |  6.92
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.12014    | 0.12014    | 0.12014    |   0.0 |  0.34
+Output  | 0.0020193  | 0.0020193  | 0.0020193  |   0.0 |  0.01
+Modify  | 4.886      | 4.886      | 4.886      |   0.0 | 13.83
+Other   |            | 0.05992    |            |       |  0.17
+
+Nlocal:           8674 ave        8674 max        8674 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:          27366 ave       27366 max       27366 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    4.48585e+06 ave 4.48585e+06 max 4.48585e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 4485849
+Ave neighs/atom = 517.16036
+Ave special neighs/atom = 2.2573207
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:35

examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.1

@@ -0,0 +1,146 @@
+LAMMPS (8 Feb 2023)
+Processor partition = 1
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+variable ibead uloop 8 pad
+
+units           real
+neigh_modify    delay 2 every 1
+
+atom_style      full
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+
+pair_style      lj/charmm/coul/long 11 12
+pair_modify     mix arithmetic
+kspace_style    pppm 1e-4
+
+read_data system.data
+Reading data file ...
+  orthogonal box = (-23.109 -22.733 -23.141) to (22.853 22.912 22.8)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  8674 atoms
+  reading velocities ...
+  8674 velocities
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  18 = max dihedrals/atom
+  scanning impropers ...
+  1 = max impropers/atom
+  reading bonds ...
+  5869 bonds
+  reading angles ...
+  3264 angles
+  reading dihedrals ...
+  708 dihedrals
+  reading impropers ...
+  38 impropers
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     4 = max # of 1-2 neighbors
+     9 = max # of 1-3 neighbors
+    17 = max # of 1-4 neighbors
+    21 = max # of special neighbors
+  special bonds CPU = 0.004 seconds
+  read_data CPU = 0.139 seconds
+#read_restart    system_${ibead}.rest1
+special_bonds   charmm
+
+fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 300.0 nhc 4 sp 2.0
+
+thermo          10
+thermo_style    custom step temp pe etotal f_1[1] f_1[2] f_1[3]
+thermo_modify   colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial
+timestep        0.08
+
+# restart         100 system_${ibead}.rest1 system_${ibead}.rest2
+
+group prot id <= 256
+256 atoms in group prot
+# dump 1 prot dcd 100 prot_${ibead}.dcd
+
+run             200
+WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
+  G vector (1/distance) = 0.22071363
+  grid = 20 20 20
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.024910591
+  estimated relative force accuracy = 7.5017505e-05
+  using double precision KISS FFT
+  3d grid and FFT values/proc = 15625 8000
+Generated 231 of 231 mixed pair_coeff terms from arithmetic mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 2 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 14
+  ghost atom cutoff = 14
+  binsize = 7, bins = 7 7 7
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/charmm/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+WARNING: Inconsistent image flags (src/domain.cpp:815)
+Per MPI rank memory allocation (min/avg/max) = 84.59 | 84.59 | 84.59 Mbytes
+   Step          Temp          PotEng         TotEng        espring         T_ring         virial    
+         0   306.20099     -26166.171     -18250.089      0              0             -676.31071    
+        10   64.17217      -26206.83      -24547.814      19.798491      300.69483     -715.39964    
+        20   68.220475     -26516.716     -24753.042      40.042407      319.66418     -514.11207    
+        30   57.966715     -26566.219     -25067.631      92.36071       271.61761      32.199121    
+        40   49.627434     -26115.147     -24832.15       156.77313      232.54181      589.56751    
+        50   50.238512     -24830.72      -23531.926      251.81147      235.40517      1098.4708    
+        60   56.338925     -22753.456     -21296.951      361.53524      263.99019      1897.4199    
+        70   54.380851     -19964.7       -18558.815      512.1854       254.81514      2327.9231    
+        80   56.718808     -16822.195     -15355.868      692.48978      265.77022      2784.4839    
+        90   57.350586     -13726.44      -12243.78       926.0914       268.73058      3260.3863    
+       100   57.262365     -11280.793     -9800.4136      1186.0078      268.3172       3554.7754    
+       110   58.507688     -9681.3843     -8168.8105      1483.328       274.15247      3368.3688    
+       120   58.690757     -9008.7198     -7491.4132      1803.3617      275.01029      2974.5497    
+       130   58.623212     -9097.3273     -7581.7669      2143.6544      274.69379      2535.9822    
+       140   59.453502     -9689.6967     -8152.6711      2490.8635      278.58432      1947.3155    
+       150   59.231787     -10601.929     -9070.635       2837.9543      277.54542      1774.9432    
+       160   58.39319      -11413.85      -9904.2362      3183.3024      273.61596      1744.3579    
+       170   60.201493     -12074.462     -10518.099      3515.6508      282.08922      1744.1497    
+       180   59.592955     -12415.79      -10875.16       3827.6991      279.23776      1935.0884    
+       190   59.698333     -12625.161     -11081.806      4120.4275      279.73154      1962.5444    
+       200   59.87495      -12794.677     -11246.756      4387.202       280.55912      1854.7836    
+Loop time of 35.3334 on 1 procs for 200 steps with 8674 atoms
+
+Performance: 0.039 ns/day, 613.427 hours/ns, 5.660 timesteps/s, 49.098 katom-step/s
+97.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 27.948     | 27.948     | 27.948     |   0.0 | 79.10
+Bond    | 0.12842    | 0.12842    | 0.12842    |   0.0 |  0.36
+Kspace  | 2.4577     | 2.4577     | 2.4577     |   0.0 |  6.96
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.11986    | 0.11986    | 0.11986    |   0.0 |  0.34
+Output  | 0.0021166  | 0.0021166  | 0.0021166  |   0.0 |  0.01
+Modify  | 4.617      | 4.617      | 4.617      |   0.0 | 13.07
+Other   |            | 0.06042    |            |       |  0.17
+
+Nlocal:           8674 ave        8674 max        8674 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:          27366 ave       27366 max       27366 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    4.48585e+06 ave 4.48585e+06 max 4.48585e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 4485849
+Ave neighs/atom = 517.16036
+Ave special neighs/atom = 2.2573207
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:35

examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.2

@@ -0,0 +1,146 @@
+LAMMPS (8 Feb 2023)
+Processor partition = 2
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+variable ibead uloop 8 pad
+
+units           real
+neigh_modify    delay 2 every 1
+
+atom_style      full
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+
+pair_style      lj/charmm/coul/long 11 12
+pair_modify     mix arithmetic
+kspace_style    pppm 1e-4
+
+read_data system.data
+Reading data file ...
+  orthogonal box = (-23.109 -22.733 -23.141) to (22.853 22.912 22.8)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  8674 atoms
+  reading velocities ...
+  8674 velocities
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  18 = max dihedrals/atom
+  scanning impropers ...
+  1 = max impropers/atom
+  reading bonds ...
+  5869 bonds
+  reading angles ...
+  3264 angles
+  reading dihedrals ...
+  708 dihedrals
+  reading impropers ...
+  38 impropers
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     4 = max # of 1-2 neighbors
+     9 = max # of 1-3 neighbors
+    17 = max # of 1-4 neighbors
+    21 = max # of special neighbors
+  special bonds CPU = 0.004 seconds
+  read_data CPU = 0.139 seconds
+#read_restart    system_${ibead}.rest1
+special_bonds   charmm
+
+fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 300.0 nhc 4 sp 2.0
+
+thermo          10
+thermo_style    custom step temp pe etotal f_1[1] f_1[2] f_1[3]
+thermo_modify   colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial
+timestep        0.08
+
+# restart         100 system_${ibead}.rest1 system_${ibead}.rest2
+
+group prot id <= 256
+256 atoms in group prot
+# dump 1 prot dcd 100 prot_${ibead}.dcd
+
+run             200
+WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
+  G vector (1/distance) = 0.22071363
+  grid = 20 20 20
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.024910591
+  estimated relative force accuracy = 7.5017505e-05
+  using double precision KISS FFT
+  3d grid and FFT values/proc = 15625 8000
+Generated 231 of 231 mixed pair_coeff terms from arithmetic mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 2 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 14
+  ghost atom cutoff = 14
+  binsize = 7, bins = 7 7 7
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/charmm/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+WARNING: Inconsistent image flags (src/domain.cpp:815)
+Per MPI rank memory allocation (min/avg/max) = 84.59 | 84.59 | 84.59 Mbytes
+   Step          Temp          PotEng         TotEng        espring         T_ring         virial    
+         0   306.20099     -26166.171     -18250.089      0              0             -676.31071    
+        10   64.17182      -26152.123     -24493.117      2.6867435      300.69318     -871.30328    
+        20   68.223719     -26376.797     -24613.039      8.6943178      319.67938     -734.6258     
+        30   57.962426     -26437.775     -24939.297      20.196606      271.59751     -442.97527    
+        40   49.527052     -26345.74      -25065.339      36.486067      232.07145     -109.57718    
+        50   50.00573      -26013.669     -24720.893      64.828577      234.31441      90.23132     
+        60   56.176816     -25453.583     -24001.268      104.35099      263.23058      350.85294    
+        70   54.335616     -24764.408     -23359.692      168.84911      254.60318      370.58559    
+        80   56.386432     -24068.851     -22611.117      255.96556      264.21279      359.85013    
+        90   57.394261     -23487.859     -22004.071      377.57122      268.93523      350.57006    
+       100   56.595909     -23070.567     -21607.418      531.24569      265.19435      380.72648    
+       110   56.785626     -22692.803     -21224.749      716.4839       266.08332      119.53289    
+       120   57.068588     -22142.475     -20667.105      936.74977      267.4092       53.114976    
+       130   57.211273     -21289.908     -19810.849      1184.7712      268.0778       165.3536     
+       140   58.110208     -20136.125     -18633.827      1461.5509      272.28998      268.40059    
+       150   57.980844     -18752.784     -17253.831      1762.042       271.68381      732.81511    
+       160   58.120526     -17237.742     -15735.177      2083.496       272.33833      1353.819     
+       170   58.192327     -15808.132     -14303.711      2418.0799      272.67477      1963.8895    
+       180   59.169638     -14676.59      -13146.903      2755.6611      277.2542       2483.717     
+       190   60.190674     -13997.692     -12441.609      3096.3553      282.03852      2865.7644    
+       200   60.619191     -13706.35      -12139.188      3426.2396      284.04645      2830.1842    
+Loop time of 35.3333 on 1 procs for 200 steps with 8674 atoms
+
+Performance: 0.039 ns/day, 613.425 hours/ns, 5.660 timesteps/s, 49.098 katom-step/s
+99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 27.558     | 27.558     | 27.558     |   0.0 | 77.99
+Bond    | 0.1313     | 0.1313     | 0.1313     |   0.0 |  0.37
+Kspace  | 2.4344     | 2.4344     | 2.4344     |   0.0 |  6.89
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.11913    | 0.11913    | 0.11913    |   0.0 |  0.34
+Output  | 0.0022372  | 0.0022372  | 0.0022372  |   0.0 |  0.01
+Modify  | 5.0291     | 5.0291     | 5.0291     |   0.0 | 14.23
+Other   |            | 0.05932    |            |       |  0.17
+
+Nlocal:           8674 ave        8674 max        8674 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:          27366 ave       27366 max       27366 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    4.48585e+06 ave 4.48585e+06 max 4.48585e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 4485849
+Ave neighs/atom = 517.16036
+Ave special neighs/atom = 2.2573207
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:35

examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.3

@@ -0,0 +1,146 @@
+LAMMPS (8 Feb 2023)
+Processor partition = 3
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+variable ibead uloop 8 pad
+
+units           real
+neigh_modify    delay 2 every 1
+
+atom_style      full
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+
+pair_style      lj/charmm/coul/long 11 12
+pair_modify     mix arithmetic
+kspace_style    pppm 1e-4
+
+read_data system.data
+Reading data file ...
+  orthogonal box = (-23.109 -22.733 -23.141) to (22.853 22.912 22.8)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  8674 atoms
+  reading velocities ...
+  8674 velocities
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  18 = max dihedrals/atom
+  scanning impropers ...
+  1 = max impropers/atom
+  reading bonds ...
+  5869 bonds
+  reading angles ...
+  3264 angles
+  reading dihedrals ...
+  708 dihedrals
+  reading impropers ...
+  38 impropers
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     4 = max # of 1-2 neighbors
+     9 = max # of 1-3 neighbors
+    17 = max # of 1-4 neighbors
+    21 = max # of special neighbors
+  special bonds CPU = 0.015 seconds
+  read_data CPU = 0.153 seconds
+#read_restart    system_${ibead}.rest1
+special_bonds   charmm
+
+fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 300.0 nhc 4 sp 2.0
+
+thermo          10
+thermo_style    custom step temp pe etotal f_1[1] f_1[2] f_1[3]
+thermo_modify   colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial
+timestep        0.08
+
+# restart         100 system_${ibead}.rest1 system_${ibead}.rest2
+
+group prot id <= 256
+256 atoms in group prot
+# dump 1 prot dcd 100 prot_${ibead}.dcd
+
+run             200
+WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
+  G vector (1/distance) = 0.22071363
+  grid = 20 20 20
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.024910591
+  estimated relative force accuracy = 7.5017505e-05
+  using double precision KISS FFT
+  3d grid and FFT values/proc = 15625 8000
+Generated 231 of 231 mixed pair_coeff terms from arithmetic mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 2 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 14
+  ghost atom cutoff = 14
+  binsize = 7, bins = 7 7 7
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/charmm/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+WARNING: Inconsistent image flags (src/domain.cpp:815)
+Per MPI rank memory allocation (min/avg/max) = 84.59 | 84.59 | 84.59 Mbytes
+   Step          Temp          PotEng         TotEng        espring         T_ring         virial    
+         0   306.20099     -26166.171     -18250.089      0              0             -676.31071    
+        10   23.892089     -26194.747     -25577.075      6.0651132      382.22935     -806.80519    
+        20   27.051257     -26510.555     -25811.21       19.798054      432.77021     -722.7628     
+        30   27.053581     -26558.283     -25858.879      46.409761      432.8074      -314.77439    
+        40   19.1336       -26301.271     -25806.618      80.715535      306.1023       33.240778    
+        50   19.277021     -25564.199     -25065.839      122.0411       308.39678      420.32166    
+        60   20.762569     -24490.516     -23953.751      171.68786      332.16281      922.0134     
+        70   18.895283     -23277.775     -22789.283      228.13302      302.28967      1340.4892    
+        80   20.103678     -22119.758     -21600.026      293.69148      321.62176      1692.277     
+        90   18.733051     -21236.09      -20751.793      371.14173      299.69426      2111.5887    
+       100   18.287299     -20684.674     -20211.9        458.53118      292.56305      2434.0418    
+       110   18.012563     -20345.727     -19880.056      560.10663      288.16778      2560.064     
+       120   17.92092      -19998.225     -19534.923      676.3247       286.70167      2752.7643    
+       130   17.494577     -19524.549     -19072.269      808.35795      279.88096      3081.7784    
+       140   17.122298     -18815.761     -18373.106      957.14076      273.92518      3209.6451    
+       150   17.447826     -17981.659     -17530.588      1123.5613      279.13303      3627.9284    
+       160   17.6202       -17066.393     -16610.866      1310.1872      281.8907       4230.0427    
+       170   17.370561     -16269.055     -15819.981      1507.5411      277.89693      4602.925     
+       180   17.444401     -15692.511     -15241.529      1720.5033      279.07824      5000.4081    
+       190   17.587192     -15476.239     -15021.565      1938.8703      281.36263      5063.6159    
+       200   18.000638     -15470.948     -15005.586      2164.2187      287.977        4707.0585    
+Loop time of 35.3335 on 1 procs for 200 steps with 8674 atoms
+
+Performance: 0.039 ns/day, 613.428 hours/ns, 5.660 timesteps/s, 49.098 katom-step/s
+99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 27.094     | 27.094     | 27.094     |   0.0 | 76.68
+Bond    | 0.1276     | 0.1276     | 0.1276     |   0.0 |  0.36
+Kspace  | 2.3873     | 2.3873     | 2.3873     |   0.0 |  6.76
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.11312    | 0.11312    | 0.11312    |   0.0 |  0.32
+Output  | 0.0020657  | 0.0020657  | 0.0020657  |   0.0 |  0.01
+Modify  | 5.5507     | 5.5507     | 5.5507     |   0.0 | 15.71
+Other   |            | 0.05892    |            |       |  0.17
+
+Nlocal:           8674 ave        8674 max        8674 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:          27366 ave       27366 max       27366 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    4.48585e+06 ave 4.48585e+06 max 4.48585e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 4485849
+Ave neighs/atom = 517.16036
+Ave special neighs/atom = 2.2573207
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:35

examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.4

@@ -0,0 +1,146 @@
+LAMMPS (8 Feb 2023)
+Processor partition = 4
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+variable ibead uloop 8 pad
+
+units           real
+neigh_modify    delay 2 every 1
+
+atom_style      full
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+
+pair_style      lj/charmm/coul/long 11 12
+pair_modify     mix arithmetic
+kspace_style    pppm 1e-4
+
+read_data system.data
+Reading data file ...
+  orthogonal box = (-23.109 -22.733 -23.141) to (22.853 22.912 22.8)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  8674 atoms
+  reading velocities ...
+  8674 velocities
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  18 = max dihedrals/atom
+  scanning impropers ...
+  1 = max impropers/atom
+  reading bonds ...
+  5869 bonds
+  reading angles ...
+  3264 angles
+  reading dihedrals ...
+  708 dihedrals
+  reading impropers ...
+  38 impropers
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     4 = max # of 1-2 neighbors
+     9 = max # of 1-3 neighbors
+    17 = max # of 1-4 neighbors
+    21 = max # of special neighbors
+  special bonds CPU = 0.004 seconds
+  read_data CPU = 0.138 seconds
+#read_restart    system_${ibead}.rest1
+special_bonds   charmm
+
+fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 300.0 nhc 4 sp 2.0
+
+thermo          10
+thermo_style    custom step temp pe etotal f_1[1] f_1[2] f_1[3]
+thermo_modify   colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial
+timestep        0.08
+
+# restart         100 system_${ibead}.rest1 system_${ibead}.rest2
+
+group prot id <= 256
+256 atoms in group prot
+# dump 1 prot dcd 100 prot_${ibead}.dcd
+
+run             200
+WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
+  G vector (1/distance) = 0.22071363
+  grid = 20 20 20
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.024910591
+  estimated relative force accuracy = 7.5017505e-05
+  using double precision KISS FFT
+  3d grid and FFT values/proc = 15625 8000
+Generated 231 of 231 mixed pair_coeff terms from arithmetic mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 2 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 14
+  ghost atom cutoff = 14
+  binsize = 7, bins = 7 7 7
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/charmm/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+WARNING: Inconsistent image flags (src/domain.cpp:815)
+Per MPI rank memory allocation (min/avg/max) = 84.59 | 84.59 | 84.59 Mbytes
+   Step          Temp          PotEng         TotEng        espring         T_ring         virial    
+         0   306.20099     -26166.171     -18250.089      0              0             -676.31071    
+        10   23.892095     -26119.899     -25502.227      4.2771563      382.22944     -813.96512    
+        20   27.051103     -26287.602     -25588.262      15.607084      432.76775     -745.77933    
+        30   27.042026     -26290.973     -25591.867      35.550734      432.62253     -326.69805    
+        40   19.133546     -26173.654     -25679.002      70.11544       306.10144     -11.324153    
+        50   19.302675     -25883.61      -25384.586      121.68648      308.8072       290.09295    
+        60   20.704866     -25425.468     -24890.194      201.50535      331.23967      650.74045    
+        70   18.95281      -24809.575     -24319.596      321.84847      303.21         967.87686    
+        80   20.178541     -24115.258     -23593.591      491.86818      322.81943      1230.7506    
+        90   18.755289     -23448.841     -22963.969      726.07287      300.05003      1426.7932    
+       100   18.159265     -22868.418     -22398.954      1013.598       290.51475      1609.3405    
+       110   17.922985     -22283.38      -21820.025      1355.5366      286.7347       1483.5981    
+       120   17.617358     -21583.469     -21128.015      1747.6539      281.84524      1444.208     
+       130   17.233206     -20748.165     -20302.643      2173.0115      275.6995       1597.8139    
+       140   17.06066      -19726.034     -19284.972      2629.6918      272.9391       1704.3744    
+       150   17.004216     -18648.306     -18208.703      3099.2098      272.0361       2025.6026    
+       160   17.414218     -17588.638     -17138.435      3580.8838      278.59537      2747.2565    
+       170   17.295959     -16669.449     -16222.304      4058.5589      276.70344      3432.2976    
+       180   17.706054     -15991.367     -15533.62       4524.6837      283.26421      4008.5413    
+       190   17.649786     -15623.329     -15167.037      4968.3076      282.36402      4251.4209    
+       200   17.914982     -15484.434     -15021.286      5382.5961      286.60667      4187.5146    
+Loop time of 35.3335 on 1 procs for 200 steps with 8674 atoms
+
+Performance: 0.039 ns/day, 613.428 hours/ns, 5.660 timesteps/s, 49.098 katom-step/s
+98.1% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 27.644     | 27.644     | 27.644     |   0.0 | 78.24
+Bond    | 0.1292     | 0.1292     | 0.1292     |   0.0 |  0.37
+Kspace  | 2.4108     | 2.4108     | 2.4108     |   0.0 |  6.82
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.12913    | 0.12913    | 0.12913    |   0.0 |  0.37
+Output  | 0.0021704  | 0.0021704  | 0.0021704  |   0.0 |  0.01
+Modify  | 4.959      | 4.959      | 4.959      |   0.0 | 14.03
+Other   |            | 0.05951    |            |       |  0.17
+
+Nlocal:           8674 ave        8674 max        8674 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:          27366 ave       27366 max       27366 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    4.48585e+06 ave 4.48585e+06 max 4.48585e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 4485849
+Ave neighs/atom = 517.16036
+Ave special neighs/atom = 2.2573207
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:35

examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.5

@@ -0,0 +1,146 @@
+LAMMPS (8 Feb 2023)
+Processor partition = 5
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+variable ibead uloop 8 pad
+
+units           real
+neigh_modify    delay 2 every 1
+
+atom_style      full
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+
+pair_style      lj/charmm/coul/long 11 12
+pair_modify     mix arithmetic
+kspace_style    pppm 1e-4
+
+read_data system.data
+Reading data file ...
+  orthogonal box = (-23.109 -22.733 -23.141) to (22.853 22.912 22.8)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  8674 atoms
+  reading velocities ...
+  8674 velocities
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  18 = max dihedrals/atom
+  scanning impropers ...
+  1 = max impropers/atom
+  reading bonds ...
+  5869 bonds
+  reading angles ...
+  3264 angles
+  reading dihedrals ...
+  708 dihedrals
+  reading impropers ...
+  38 impropers
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     4 = max # of 1-2 neighbors
+     9 = max # of 1-3 neighbors
+    17 = max # of 1-4 neighbors
+    21 = max # of special neighbors
+  special bonds CPU = 0.004 seconds
+  read_data CPU = 0.139 seconds
+#read_restart    system_${ibead}.rest1
+special_bonds   charmm
+
+fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 300.0 nhc 4 sp 2.0
+
+thermo          10
+thermo_style    custom step temp pe etotal f_1[1] f_1[2] f_1[3]
+thermo_modify   colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial
+timestep        0.08
+
+# restart         100 system_${ibead}.rest1 system_${ibead}.rest2
+
+group prot id <= 256
+256 atoms in group prot
+# dump 1 prot dcd 100 prot_${ibead}.dcd
+
+run             200
+WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
+  G vector (1/distance) = 0.22071363
+  grid = 20 20 20
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.024910591
+  estimated relative force accuracy = 7.5017505e-05
+  using double precision KISS FFT
+  3d grid and FFT values/proc = 15625 8000
+Generated 231 of 231 mixed pair_coeff terms from arithmetic mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 2 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 14
+  ghost atom cutoff = 14
+  binsize = 7, bins = 7 7 7
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/charmm/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+WARNING: Inconsistent image flags (src/domain.cpp:815)
+Per MPI rank memory allocation (min/avg/max) = 84.59 | 84.59 | 84.59 Mbytes
+   Step          Temp          PotEng         TotEng        espring         T_ring         virial    
+         0   306.20099     -26166.171     -18250.089      0              0             -676.31071    
+        10   14.020019     -26051.605     -25689.152      7.3596437      382.89455     -789.8534     
+        20   15.752865     -25975.95      -25568.698      25.331469      430.21956     -594.00538    
+        30   17.181375     -25873.108     -25428.926      57.426817      469.23297     -181.78718    
+        40   11.772036     -25785.82      -25481.483      101.0172       321.50089      318.12089    
+        50   11.907234     -25813.038     -25505.205      157.46734      325.19321      630.72419    
+        60   12.407378     -25738.74      -25417.978      232.72881      338.85245      1042.2805    
+        70   11.569463     -25485.646     -25186.546      331.59654      315.9685       1219.4474    
+        80   12.423569     -25007.927     -24686.746      455.84829      339.29462      1585.4189    
+        90   11.222078     -24360.128     -24070.009      610.51406      306.48124      1770.0165    
+       100   10.746584     -23649.481     -23371.654      794.88729      293.49524      1751.0868    
+       110   10.688659     -22906.499     -22630.17       1011.4935      291.91326      1164.4167    
+       120   10.413653     -22131.25      -21862.03       1258.7802      284.40268      494.75639    
+       130   10.207431     -21354.621     -21090.733      1532.012       278.77066     -85.33744     
+       140   9.9484212     -20506.422     -20249.23       1833.2006      271.69695     -582.25635    
+       150   9.8592991     -19641.288     -19386.399      2150.5002      269.26298     -860.97106    
+       160   9.9476229     -18750.371     -18493.199      2484.32        271.67515     -781.67257    
+       170   9.9050652     -17855.648     -17599.576      2822.3305      270.51287     -564.01235    
+       180   9.9461836     -17049.565     -16792.431      3164.947       271.63584     -414.44888    
+       190   9.9650455     -16346.398     -16088.776      3500.8641      272.15097     -250.509      
+       200   10.114117     -15721.822     -15460.346      3824.3372      276.22219     -539.50977    
+Loop time of 35.3336 on 1 procs for 200 steps with 8674 atoms
+
+Performance: 0.039 ns/day, 613.431 hours/ns, 5.660 timesteps/s, 49.098 katom-step/s
+98.8% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 27.569     | 27.569     | 27.569     |   0.0 | 78.03
+Bond    | 0.13166    | 0.13166    | 0.13166    |   0.0 |  0.37
+Kspace  | 2.4398     | 2.4398     | 2.4398     |   0.0 |  6.91
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.12114    | 0.12114    | 0.12114    |   0.0 |  0.34
+Output  | 0.0022707  | 0.0022707  | 0.0022707  |   0.0 |  0.01
+Modify  | 5.0103     | 5.0103     | 5.0103     |   0.0 | 14.18
+Other   |            | 0.05914    |            |       |  0.17
+
+Nlocal:           8674 ave        8674 max        8674 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:          27366 ave       27366 max       27366 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    4.48585e+06 ave 4.48585e+06 max 4.48585e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 4485849
+Ave neighs/atom = 517.16036
+Ave special neighs/atom = 2.2573207
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:35

examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.6

@@ -0,0 +1,146 @@
+LAMMPS (8 Feb 2023)
+Processor partition = 6
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+variable ibead uloop 8 pad
+
+units           real
+neigh_modify    delay 2 every 1
+
+atom_style      full
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+
+pair_style      lj/charmm/coul/long 11 12
+pair_modify     mix arithmetic
+kspace_style    pppm 1e-4
+
+read_data system.data
+Reading data file ...
+  orthogonal box = (-23.109 -22.733 -23.141) to (22.853 22.912 22.8)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  8674 atoms
+  reading velocities ...
+  8674 velocities
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  18 = max dihedrals/atom
+  scanning impropers ...
+  1 = max impropers/atom
+  reading bonds ...
+  5869 bonds
+  reading angles ...
+  3264 angles
+  reading dihedrals ...
+  708 dihedrals
+  reading impropers ...
+  38 impropers
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     4 = max # of 1-2 neighbors
+     9 = max # of 1-3 neighbors
+    17 = max # of 1-4 neighbors
+    21 = max # of special neighbors
+  special bonds CPU = 0.004 seconds
+  read_data CPU = 0.139 seconds
+#read_restart    system_${ibead}.rest1
+special_bonds   charmm
+
+fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 300.0 nhc 4 sp 2.0
+
+thermo          10
+thermo_style    custom step temp pe etotal f_1[1] f_1[2] f_1[3]
+thermo_modify   colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial
+timestep        0.08
+
+# restart         100 system_${ibead}.rest1 system_${ibead}.rest2
+
+group prot id <= 256
+256 atoms in group prot
+# dump 1 prot dcd 100 prot_${ibead}.dcd
+
+run             200
+WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
+  G vector (1/distance) = 0.22071363
+  grid = 20 20 20
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.024910591
+  estimated relative force accuracy = 7.5017505e-05
+  using double precision KISS FFT
+  3d grid and FFT values/proc = 15625 8000
+Generated 231 of 231 mixed pair_coeff terms from arithmetic mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 2 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 14
+  ghost atom cutoff = 14
+  binsize = 7, bins = 7 7 7
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/charmm/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+WARNING: Inconsistent image flags (src/domain.cpp:815)
+Per MPI rank memory allocation (min/avg/max) = 84.59 | 84.59 | 84.59 Mbytes
+   Step          Temp          PotEng         TotEng        espring         T_ring         virial    
+         0   306.20099     -26166.171     -18250.089      0              0             -676.31071    
+        10   14.02002      -25861.333     -25498.879      45.268744      382.8946      -722.47561    
+        20   15.752886     -25289.441     -24882.188      135.42322      430.22014     -482.48877    
+        30   17.181691     -24659.071     -24214.881      316.76011      469.24159      115.80651    
+        40   11.76983      -24165.345     -23861.065      544.21259      321.44065      710.32531    
+        50   11.904289     -24034.29      -23726.534      812.12301      325.1128       1057.7309    
+        60   12.409559     -23964.986     -23644.167      1115.614       338.91201      1490.6948    
+        70   11.53241      -23718.204     -23420.061      1442.0767      314.95657      1654.3805    
+        80   12.377693     -23123.366     -22803.371      1794.1167      338.04173      2019.537     
+        90   11.21341      -22129.26      -21839.365      2172.5974      306.24451      2037.5349    
+       100   10.778526     -20922.126     -20643.474      2553.3173      294.36759      1922.6067    
+       110   10.656113     -19666.579     -19391.091      2944.1884      291.02442      1115.4533    
+       120   10.374573     -18508.305     -18240.096      3331.7564      283.3354       401.15223    
+       130   10.057534     -17613.953     -17353.939      3714.254       274.67688     -248.49945    
+       140   9.7972276     -16953.726     -16700.443      4076.4386      267.56777     -841.79062    
+       150   9.8266474     -16502.516     -16248.472      4422.7241      268.37124     -1155.8854    
+       160   9.9655308     -16127.142     -15869.507      4748.4514      272.16422     -1094.1994    
+       170   9.9292831     -15818.923     -15562.225      5045.9331      271.17428     -884.00102    
+       180   10.157102     -15473.205     -15210.618      5313.5511      277.39613     -553.25499    
+       190   10.068063     -15095.751     -14835.466      5545.0144      274.96443     -237.36247    
+       200   10.155151     -14754.017     -14491.48       5742.1288      277.34285     -332.89648    
+Loop time of 35.3338 on 1 procs for 200 steps with 8674 atoms
+
+Performance: 0.039 ns/day, 613.434 hours/ns, 5.660 timesteps/s, 49.098 katom-step/s
+97.5% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 27.875     | 27.875     | 27.875     |   0.0 | 78.89
+Bond    | 0.12707    | 0.12707    | 0.12707    |   0.0 |  0.36
+Kspace  | 2.4348     | 2.4348     | 2.4348     |   0.0 |  6.89
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.11906    | 0.11906    | 0.11906    |   0.0 |  0.34
+Output  | 0.0021503  | 0.0021503  | 0.0021503  |   0.0 |  0.01
+Modify  | 4.7164     | 4.7164     | 4.7164     |   0.0 | 13.35
+Other   |            | 0.05955    |            |       |  0.17
+
+Nlocal:           8674 ave        8674 max        8674 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:          27366 ave       27366 max       27366 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    4.48585e+06 ave 4.48585e+06 max 4.48585e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 4485849
+Ave neighs/atom = 517.16036
+Ave special neighs/atom = 2.2573207
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:35

examples/PACKAGES/pimd/prot-hairpin/log.25Feb23.scp.g++.8.7

@@ -0,0 +1,146 @@
+LAMMPS (8 Feb 2023)
+Processor partition = 7
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
+  using 1 OpenMP thread(s) per MPI task
+variable ibead uloop 8 pad
+
+units           real
+neigh_modify    delay 2 every 1
+
+atom_style      full
+bond_style      harmonic
+angle_style     charmm
+dihedral_style  charmm
+improper_style  harmonic
+
+pair_style      lj/charmm/coul/long 11 12
+pair_modify     mix arithmetic
+kspace_style    pppm 1e-4
+
+read_data system.data
+Reading data file ...
+  orthogonal box = (-23.109 -22.733 -23.141) to (22.853 22.912 22.8)
+  1 by 1 by 1 MPI processor grid
+  reading atoms ...
+  8674 atoms
+  reading velocities ...
+  8674 velocities
+  scanning bonds ...
+  4 = max bonds/atom
+  scanning angles ...
+  6 = max angles/atom
+  scanning dihedrals ...
+  18 = max dihedrals/atom
+  scanning impropers ...
+  1 = max impropers/atom
+  reading bonds ...
+  5869 bonds
+  reading angles ...
+  3264 angles
+  reading dihedrals ...
+  708 dihedrals
+  reading impropers ...
+  38 impropers
+Finding 1-2 1-3 1-4 neighbors ...
+  special bond factors lj:    0        0        0       
+  special bond factors coul:  0        0        0       
+     4 = max # of 1-2 neighbors
+     9 = max # of 1-3 neighbors
+    17 = max # of 1-4 neighbors
+    21 = max # of special neighbors
+  special bonds CPU = 0.004 seconds
+  read_data CPU = 0.138 seconds
+#read_restart    system_${ibead}.rest1
+special_bonds   charmm
+
+fix 1 all pimd/nvt method nmpimd fmass 1.0 temp 300.0 nhc 4 sp 2.0
+
+thermo          10
+thermo_style    custom step temp pe etotal f_1[1] f_1[2] f_1[3]
+thermo_modify   colname f_1[1] espring colname f_1[2] T_ring colname f_1[3] virial
+timestep        0.08
+
+# restart         100 system_${ibead}.rest1 system_${ibead}.rest2
+
+group prot id <= 256
+256 atoms in group prot
+# dump 1 prot dcd 100 prot_${ibead}.dcd
+
+run             200
+WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
+PPPM initialization ...
+  using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
+  G vector (1/distance) = 0.22071363
+  grid = 20 20 20
+  stencil order = 5
+  estimated absolute RMS force accuracy = 0.024910591
+  estimated relative force accuracy = 7.5017505e-05
+  using double precision KISS FFT
+  3d grid and FFT values/proc = 15625 8000
+Generated 231 of 231 mixed pair_coeff terms from arithmetic mixing rule
+Neighbor list info ...
+  update: every = 1 steps, delay = 2 steps, check = yes
+  max neighbors/atom: 2000, page size: 100000
+  master list distance cutoff = 14
+  ghost atom cutoff = 14
+  binsize = 7, bins = 7 7 7
+  1 neighbor lists, perpetual/occasional/extra = 1 0 0
+  (1) pair lj/charmm/coul/long, perpetual
+      attributes: half, newton on
+      pair build: half/bin/newton
+      stencil: half/bin/3d
+      bin: standard
+WARNING: Inconsistent image flags (src/domain.cpp:815)
+Per MPI rank memory allocation (min/avg/max) = 84.59 | 84.59 | 84.59 Mbytes
+   Step          Temp          PotEng         TotEng        espring         T_ring         virial    
+         0   306.20099     -26166.171     -18250.089      0              0             -676.31071    
+        10   11.858328     -24949.912     -24643.343      11.21746       379.42274     -589.42772    
+        20   13.313433     -22332.782     -21988.595      25.891404      425.98075     -189.42618    
+        30   14.492332     -18605.094     -18230.43       60.87232       463.70115      853.22726    
+        40   10.100576     -15158.156     -14897.03       103.87947      323.18115      1870.5664    
+        50   10.437976     -12976.762     -12706.913      161.50852      333.97672      2649.3283    
+        60   10.544993     -11868.561     -11595.946      225.58416      337.40089      3264.9267    
+        70   9.756396      -11851.23      -11599.002      303.66274      312.16868      3549.9084    
+        80   10.642372     -12316.225     -12041.092      392.92619      340.51663      3853.3301    
+        90   9.3834726     -12853.33      -12610.744      501.5373       300.2365       3943.7218    
+       100   8.9858656     -13254.517     -13022.21       619.67563      287.51455      3852.5038    
+       110   8.9674385     -13407.55      -13175.719      752.87088      286.92495      3047.0516    
+       120   8.7200626     -13430.184     -13204.748      897.34682      279.00983      2614.6547    
+       130   8.4404226     -13413.462     -13195.256      1051.1979      270.06239      2361.7563    
+       140   8.1867868     -13405.663     -13194.013      1215.2723      261.94697      2042.4666    
+       150   8.26024       -13427.11      -13213.561      1389.0864      264.29721      2179.5219    
+       160   8.2139102     -13403.956     -13191.605      1573.9454      262.81482      2489.6486    
+       170   8.2258918     -13367.291     -13154.631      1768.2198      263.19819      2793.6911    
+       180   8.4548603     -13245.62      -13027.04       1968.4468      270.52434      3070.2942    
+       190   8.4589955     -12920.954     -12702.268      2174.1321      270.65665      3360.4993    
+       200   8.537811      -12448.973     -12228.248      2382.746       273.17846      3370.2077    
+Loop time of 35.3334 on 1 procs for 200 steps with 8674 atoms
+
+Performance: 0.039 ns/day, 613.428 hours/ns, 5.660 timesteps/s, 49.098 katom-step/s
+99.1% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section |  min time  |  avg time  |  max time  |%varavg| %total
+---------------------------------------------------------------
+Pair    | 27.709     | 27.709     | 27.709     |   0.0 | 78.42
+Bond    | 0.13165    | 0.13165    | 0.13165    |   0.0 |  0.37
+Kspace  | 2.4416     | 2.4416     | 2.4416     |   0.0 |  6.91
+Neigh   | 0          | 0          | 0          |   0.0 |  0.00
+Comm    | 0.12826    | 0.12826    | 0.12826    |   0.0 |  0.36
+Output  | 0.002116   | 0.002116   | 0.002116   |   0.0 |  0.01
+Modify  | 4.863      | 4.863      | 4.863      |   0.0 | 13.76
+Other   |            | 0.05754    |            |       |  0.16
+
+Nlocal:           8674 ave        8674 max        8674 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost:          27366 ave       27366 max       27366 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs:    4.48585e+06 ave 4.48585e+06 max 4.48585e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 4485849
+Ave neighs/atom = 517.16036
+Ave special neighs/atom = 2.2573207
+Neighbor list builds = 0
+Dangerous builds = 0
+Total wall time: 0:00:35

lib/gpu/lal_device.cpp

@@ -389,6 +389,10 @@ int DeviceT::set_ocl_params(std::string s_config, const std::string &extra_args)
   #ifdef CL_VERSION_2_0
   _ocl_compile_string+="-cl-std=CL2.0 ";
   #endif
+  // workaround for double precision with Intel OpenCL
+  #ifdef _DOUBLE_DOUBLE
+  if (params[0] == "500") params[4] = "0";
+  #endif
   if (params[4] != "0") _ocl_compile_string+="-cl-fast-relaxed-math ";
   _ocl_compile_string+=std::string(OCL_INT_TYPE)+" "+
     std::string(OCL_PRECISION_COMPILE);

lib/gpu/lal_preprocessor.h

@@ -169,7 +169,7 @@
 #define ucl_abs fabs
 #define ucl_erfc erfc
 
-#if defined(FAST_MATH) && !defined(_DOUBLE_DOUBLE)
+#if defined(FAST_MATH) && (FAST_MATH > 0) && !defined(_DOUBLE_DOUBLE)
 
 #define ucl_exp native_exp
 #define ucl_pow pow

src/DPD-MESO/fix_mvv_dpd.cpp

@@ -22,11 +22,13 @@
 ------------------------------------------------------------------------- */
 
 #include "fix_mvv_dpd.h"
-#include <cstring>
+
 #include "atom.h"
+#include "error.h"
 #include "force.h"
 #include "update.h"
-#include "error.h"
+
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
@@ -65,6 +67,9 @@ void FixMvvDPD::init()
 
   dtv = update->dt;
   dtf = 0.5 * update->dt * force->ftm2v;
+
+  if (!force->pair_match("^edpd",0) && !force->pair_match("^dpd",0))
+    error->all(FLERR, "Must use a dpd or edpd pair style with fix mvv/edpd");
 }
 
 /* ----------------------------------------------------------------------

src/DPD-MESO/fix_mvv_edpd.cpp

@@ -31,11 +31,13 @@
 ------------------------------------------------------------------------- */
 
 #include "fix_mvv_edpd.h"
-#include <cstring>
+
 #include "atom.h"
+#include "error.h"
 #include "force.h"
 #include "update.h"
-#include "error.h"
+
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
@@ -71,6 +73,9 @@ void FixMvvEDPD::init()
 {
   dtv = update->dt;
   dtf = 0.5 * update->dt * force->ftm2v;
+
+  if (!force->pair_match("^edpd",0))
+    error->all(FLERR, "Must use pair style edpd with fix mvv/edpd");
 }
 
 /* ----------------------------------------------------------------------

src/DPD-MESO/fix_mvv_tdpd.cpp

@@ -27,11 +27,13 @@
 ------------------------------------------------------------------------- */
 
 #include "fix_mvv_tdpd.h"
-#include <cstring>
+
 #include "atom.h"
+#include "error.h"
 #include "force.h"
 #include "update.h"
-#include "error.h"
+
+#include <cstring>
 
 using namespace LAMMPS_NS;
 using namespace FixConst;
@@ -69,6 +71,8 @@ void FixMvvTDPD::init()
 {
   dtv = update->dt;
   dtf = 0.5 * update->dt * force->ftm2v;
+  if (!force->pair_match("^tdpd",0))
+    error->all(FLERR, "Must use pair style tdpd with fix mvv/tdpd");
 }
 
 /* ----------------------------------------------------------------------

src/EXTRA-FIX/fix_oneway.cpp

@@ -35,6 +35,7 @@ FixOneWay::FixOneWay(LAMMPS *lmp, int narg, char **arg) :
     Fix(lmp, narg, arg), region(nullptr), idregion(nullptr)
 {
   direction = NONE;
+  dynamic_group_allow = 1;
 
   if (narg < 6) error->all(FLERR, "Illegal fix oneway command");
 

src/ML-SNAP/pair_snap.cpp

@@ -796,6 +796,8 @@ double PairSNAP::memory_usage()
   return bytes;
 }
 
+/* ---------------------------------------------------------------------- */
+
 void *PairSNAP::extract(const char *str, int &dim)
 {
   dim = 2;

src/REPLICA/compute_pressure_alchemy.cpp

@@ -24,7 +24,7 @@ using namespace LAMMPS_NS;
 /* ---------------------------------------------------------------------- */
 
 ComputePressureAlchemy::ComputePressureAlchemy(LAMMPS *lmp, int narg, char **arg) :
-    Compute(lmp, narg, arg)
+    Compute(lmp, narg, arg), fix(nullptr)
 {
   if (narg != 4) error->all(FLERR, "Illegal compute pressure/alchemy command");
   if (igroup) error->all(FLERR, "Compute pressure/alchemy must use group all");

src/REPLICA/fix_alchemy.cpp

@@ -35,12 +35,12 @@ using namespace FixConst;
 
 FixAlchemy::FixAlchemy(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg), commbuf(nullptr)
 {
-  if (narg != 4) error->all(FLERR, "Incorrect number of arguments for fix alchemy");
+  if (narg != 4) error->universe_all(FLERR, "Incorrect number of arguments for fix alchemy");
-  if (universe->nworlds != 2) error->all(FLERR, "Must use exactly two partitions");
+  if (universe->nworlds != 2) error->universe_all(FLERR, "Must use exactly two partitions");
   if (utils::strmatch(arg[3], "^v_"))
     id_lambda = arg[3] + 2;
   else
-    error->all(FLERR, "Must use variable as lambda argument to fix alchemy");
+    error->universe_all(FLERR, "Must use variable as lambda argument to fix alchemy");
 
   lambda = epot[0] = epot[1] = epot[2] = 0.0;
   progress = 0;
@@ -53,8 +53,8 @@ FixAlchemy::FixAlchemy(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
   vector_flag = 1;
   size_vector = 3;
   extvector = 1;
-  ilevel_respa = 0;
   nmax = 6;
+  ivar = -1;
   sync_box = 0;
 
   // set up rank-to-rank communicator for inter-partition communication
@@ -73,7 +73,9 @@ FixAlchemy::FixAlchemy(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg),
   int allfail = 0;
   MPI_Allreduce(&fail, &allfail, 1, MPI_INT, MPI_MAX, universe->uworld);
   if (allfail)
-    error->all(FLERR, "Number of atoms and domain decomposition must match for both partitions");
+    error->universe_all(FLERR,
+                        "Number of atoms and domain decomposition must be the same "
+                        "on all partitions");
 
   id_pe = std::string(id) + "_pe";
   pe = modify->add_compute(id_pe + " all pe");
@@ -107,7 +109,51 @@ int FixAlchemy::setmask()
   return mask;
 }
 
-/* ---------------------------------------------------------------------- */
+/* ----------------------------------------------------------------------
+   check consistency of owned atom count and ordering
+   compare each pair of replica procs
+   checked before each exchange of atom coords or forces
+     to ensure the replicas have not become out of sync
+---------------------------------------------------------------------- */
+
+void FixAlchemy::check_consistency_atoms()
+{
+  // check that owned atom count is same for each pair of replica procs
+
+  const int nlocal = atom->nlocal;
+  int my_nlocal[2] = {0, 0};
+  int all_nlocal[2] = {0, 0};
+  my_nlocal[universe->iworld] = nlocal;
+  MPI_Allreduce(my_nlocal, all_nlocal, 2, MPI_INT, MPI_SUM, samerank);
+
+  int fail = (all_nlocal[0] == all_nlocal[1]) ? 0 : 1;
+  int allfail = 0;
+  MPI_Allreduce(&fail, &allfail, 1, MPI_INT, MPI_MAX, universe->uworld);
+  if (allfail) error->universe_all(FLERR, "Fix alchemy local atom count is inconsistent");
+
+  // check that owned atom ordering is same for each pair of replica procs
+  // re-use communication buffer for positions and forces
+
+  tagint *tagbuf = (tagint *) commbuf;
+  tagint *tag = atom->tag;
+  if (universe->iworld == 0) {
+    for (int i = 0; i < nlocal; ++i) tagbuf[i] = tag[i];
+  }
+  MPI_Bcast(tagbuf, nlocal, MPI_LMP_TAGINT, 0, samerank);
+
+  fail = allfail = 0;
+  if (universe->iworld > 0) {
+    for (int i = 0; i < nlocal; ++i)
+      if (tag[i] != tagbuf[i]) fail = 1;
+  }
+  MPI_Allreduce(&fail, &allfail, 1, MPI_INT, MPI_MAX, universe->uworld);
+  if (allfail) error->universe_all(FLERR, "Fix alchemy local atom ordering is inconsistent");
+}
+
+/* ----------------------------------------------------------------------
+   force simulation box size and shape to be identical for 2 replicas
+   invoked by post_integrate() after integration may have changed box
+---------------------------------------------------------------------- */
 
 static void synchronize_box(Domain *domain, MPI_Comm samerank)
 {
@@ -130,17 +176,19 @@ void FixAlchemy::init()
   memory->create(commbuf, sizeof(double) * nmax, "alchemy:nmax");
 
   if (modify->get_fix_by_style("^balance").size() > 0)
-    error->all(FLERR, "Fix alchemy is not compatible with load balancing");
+    error->universe_all(FLERR, "Fix alchemy is not compatible with load balancing");
 
   if (modify->get_fix_by_style("^alchemy").size() > 1)
-    error->all(FLERR, "There may only one fix alchemy at a time");
+    error->universe_all(FLERR, "There may only one fix alchemy at a time");
+
+  if (utils::strmatch(update->integrate_style, "^respa"))
+    error->universe_all(FLERR, "Must not use run style respa with fix alchemy");
 
   ivar = input->variable->find(id_lambda.c_str());
   if (ivar < 0)
-    error->universe_one(FLERR, fmt::format("Variable {} for fix alchemy does not exist", id_lambda));
+    error->universe_one(FLERR, fmt::format("Fix alchemy variable {} does not exist", id_lambda));
   if (!input->variable->equalstyle(ivar))
-    error->universe_one(FLERR,
+    error->universe_one(FLERR, fmt::format("Fix alchemy variable {} is invalid style", id_lambda));
-                        fmt::format("Variable {} for fix alchemy is invalid style", id_lambda));
   lambda = input->variable->compute_equal(ivar);
 
   // synchronize box dimensions, determine if resync during run will be needed.
@@ -156,33 +204,33 @@ void FixAlchemy::init()
 
 void FixAlchemy::setup(int vflag)
 {
-  if (utils::strmatch(update->integrate_style, "^respa")) {
-    auto respa = dynamic_cast<Respa *>(update->integrate);
-    respa->copy_flevel_f(ilevel_respa);
-    post_force_respa(vflag, ilevel_respa, 0);
-    respa->copy_f_flevel(ilevel_respa);
-  } else {
-    post_force(vflag);
-  }
-
   if (universe->me == 0) {
-    double delta = update->ntimestep - update->beginstep;
+    progress = 0;
-    if ((delta != 0.0) && (update->beginstep != update->endstep))
+    auto msg = fmt::format("Starting alchemical run\n");
-          delta /= update->endstep - update->beginstep;
-    progress = static_cast<int>(delta*100.0);
-    auto msg = fmt::format("Starting alchemical transformation at {:>3d}%\n", progress);
     if (universe->uscreen) fmt::print(universe->uscreen, msg);
     if (universe->ulogfile) fmt::print(universe->ulogfile, msg);
   }
+
+  // recheck domain decomposition, atom ordering, and synchronize positions
+
+  post_integrate();
+
+  // mix initial forces
+
+  post_force(vflag);
 }
 
 /* ---------------------------------------------------------------------- */
 
 void FixAlchemy::post_integrate()
 {
+  // check owned atom count and ordering between replicas
+
+  check_consistency_atoms();
+
   // synchronize atom positions
 
-  const int nall = atom->nlocal + atom->nghost;
+  const int nall = atom->nlocal;
   MPI_Bcast(&atom->x[0][0], 3 * nall, MPI_DOUBLE, 0, samerank);
 
   // synchronize box dimensions, if needed
@@ -194,15 +242,25 @@ void FixAlchemy::post_integrate()
 
 void FixAlchemy::post_force(int /*vflag*/)
 {
+  // grow commbuf if necessary
+
   if (3 * atom->nmax > nmax) {
     nmax = 3 * atom->nmax;
     memory->grow(commbuf, sizeof(double) * atom->nmax, "alchemy:commbuf");
   }
 
-  const int nall = 3 * atom->nlocal;
+  // check owned atom count and ordering between replicas
-  double *f = &atom->f[0][0];
+
+  check_consistency_atoms();
+
+  // evaluate lambda variable
+
   lambda = input->variable->compute_equal(ivar);
 
+  // sum forces multiplied by lambda across 2 replicas
+
+  const int nall = 3 * atom->nlocal;
+  double *f = &atom->f[0][0];
   for (int i = 0; i < nall; ++i) commbuf[i] = f[i] * lambda;
   MPI_Allreduce(commbuf, f, nall, MPI_DOUBLE, MPI_SUM, samerank);
 
@@ -222,7 +280,7 @@ void FixAlchemy::post_force(int /*vflag*/)
   MPI_Allreduce(commbuf, pressure, 6, MPI_DOUBLE, MPI_SUM, universe->uworld);
   press->addstep(update->ntimestep + 1);
 
-  // print progress info
+  // print progress info to universe screen/logfile
 
   if (universe->me == 0) {
     double delta = update->ntimestep - update->beginstep;
@@ -231,7 +289,7 @@ void FixAlchemy::post_force(int /*vflag*/)
     int status = static_cast<int>(delta * 100.0);
     if ((status / 10) > (progress / 10)) {
       progress = status;
-      auto msg = fmt::format("  Alchemical transformation progress: {:>3d}%\n", progress);
+      auto msg = fmt::format("  Alchemical run progress: {:>3d}%\n", progress);
       if (universe->uscreen) fmt::print(universe->uscreen, msg);
       if (universe->ulogfile) fmt::print(universe->ulogfile, msg);
     }

src/REPLICA/fix_alchemy.h

@@ -48,9 +48,10 @@ class FixAlchemy : public Fix {
   double pressure[6];    // joined pressure
   int progress;          // for progress indicator
   int sync_box;          // 1 of box dimensions need to be synchronized
-  int ilevel_respa;
   int nmax;
   int ivar;
+
+  void check_consistency_atoms();
 };
 }    // namespace LAMMPS_NS
 

src/REPLICA/fix_pimd_nvt.cpp

@@ -29,6 +29,7 @@
 #include "error.h"
 #include "force.h"
 #include "math_const.h"
+#include "math_special.h"
 #include "memory.h"
 #include "universe.h"
 #include "update.h"
@@ -40,6 +41,8 @@ using namespace LAMMPS_NS;
 using namespace FixConst;
 using namespace MathConst;
 
+using MathSpecial::powint;
+
 enum { PIMD, NMPIMD, CMD };
 
 /* ---------------------------------------------------------------------- */
@@ -69,6 +72,8 @@ FixPIMDNVT::FixPIMDNVT(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
   nhc_eta_dotdot = nullptr;
   nhc_eta_mass = nullptr;
 
+  spring_energy = t_sys = virial = 0.0;
+
   method = PIMD;
   fmass = 1.0;
   nhc_temp = 298.15;
@@ -234,7 +239,7 @@ void FixPIMDNVT::init()
   if (method == CMD || method == NMPIMD)
     nmpimd_init();
   else
-    for (int i = 1; i <= atom->ntypes; i++) mass[i] = atom->mass[i] / np * fmass;
+    for (int i = 1; i <= atom->ntypes; i++) mass[i] = atom->mass[i] * inverse_np * fmass;
 
   if (!nhc_ready) nhc_init();
 }
@@ -468,8 +473,8 @@ void FixPIMDNVT::nmpimd_init()
   // Set up eigenvectors for non-degenerated modes
 
   for (int i = 0; i < np; i++) {
-    M_x2xp[0][i] = 1.0 / np;
+    M_x2xp[0][i] = inverse_np;
-    if (np % 2 == 0) M_x2xp[np - 1][i] = 1.0 / np * pow(-1.0, i);
+    if (np % 2 == 0) M_x2xp[np - 1][i] = inverse_np * powint(-1.0, i);
   }
 
   // Set up eigenvectors for degenerated modes
@@ -880,8 +885,8 @@ int FixPIMDNVT::size_restart(int /*nlocal*/)
 
 double FixPIMDNVT::compute_vector(int n)
 {
-  if (n == 0) { return spring_energy; }
+  if (n == 0) return spring_energy;
-  if (n == 1) { return t_sys; }
+  if (n == 1) return t_sys;
-  if (n == 2) { return virial; }
+  if (n == 2) return virial;
   return 0.0;
 }

src/REPLICA/fix_pimd_nvt.h

@@ -52,6 +52,8 @@ class FixPIMDNVT : public Fix {
   int pack_forward_comm(int, int *, double *, int, int *) override;
   void unpack_forward_comm(int, int, double *) override;
 
+ protected:
+
   int method;
   int np;
   double inverse_np;

src/atom.cpp

@@ -1914,11 +1914,15 @@ void Atom::set_mass(const char *file, int line, const char *str, int type_offset
 
 void Atom::set_mass(const char *file, int line, int itype, double value)
 {
-  if (mass == nullptr) error->all(file,line, "Cannot set mass for atom style {}", atom_style);
+  if (mass == nullptr)
+    error->all(file,line, "Cannot set per-type mass for atom style {}", atom_style);
   if (itype < 1 || itype > ntypes)
     error->all(file,line,"Invalid type {} for atom mass {}", itype, value);
-  if (value <= 0.0) error->all(file,line,"Invalid atom mass value {}", value);
+  if (value <= 0.0) {
-
+    if (comm->me == 0)
+      error->warning(file,line,"Ignoring invalid mass value {} for atom type {}", value, itype);
+    return;
+  }
   mass[itype] = value;
   mass_setflag[itype] = 1;
 }

src/fix_efield.cpp

@@ -42,7 +42,7 @@ FixEfield::FixEfield(LAMMPS *lmp, int narg, char **arg) :
     Fix(lmp, narg, arg), xstr(nullptr), ystr(nullptr), zstr(nullptr), estr(nullptr),
     idregion(nullptr), region(nullptr), efield(nullptr)
 {
-  if (narg < 6) error->all(FLERR, "Illegal fix efield command");
+  if (narg < 6) utils::missing_cmd_args(FLERR, "fix efield", error);
 
   dynamic_group_allow = 1;
   vector_flag = 1;
@@ -85,20 +85,20 @@ FixEfield::FixEfield(LAMMPS *lmp, int narg, char **arg) :
   int iarg = 6;
   while (iarg < narg) {
     if (strcmp(arg[iarg], "region") == 0) {
-      if (iarg + 2 > narg) error->all(FLERR, "Illegal fix efield command");
+      if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix efield region", error);
       region = domain->get_region_by_id(arg[iarg + 1]);
       if (!region) error->all(FLERR, "Region {} for fix efield does not exist", arg[iarg + 1]);
       idregion = utils::strdup(arg[iarg + 1]);
       iarg += 2;
     } else if (strcmp(arg[iarg], "energy") == 0) {
-      if (iarg + 2 > narg) error->all(FLERR, "Illegal fix efield command");
+      if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "fix efield energy", error);
       if (utils::strmatch(arg[iarg + 1], "^v_")) {
         estr = utils::strdup(arg[iarg + 1] + 2);
       } else
-        error->all(FLERR, "Illegal fix efield command");
+        error->all(FLERR, "Illegal fix efield energy value argument");
       iarg += 2;
     } else
-      error->all(FLERR, "Illegal fix efield command");
+      error->all(FLERR, "Unknown fix efield keyword: {}", arg[iarg]);
   }
 
   force_flag = 0;
@@ -188,7 +188,7 @@ void FixEfield::init()
 
   if (idregion) {
     region = domain->get_region_by_id(idregion);
-    if (!region) error->all(FLERR, "Region {} for fix aveforce does not exist", idregion);
+    if (!region) error->all(FLERR, "Region {} for fix efield does not exist", idregion);
   }
 
   if (xstyle == ATOM || ystyle == ATOM || zstyle == ATOM)

src/fix_store_force.cpp

@@ -29,7 +29,7 @@ FixStoreForce::FixStoreForce(LAMMPS *lmp, int narg, char **arg) :
   Fix(lmp, narg, arg),
   foriginal(nullptr)
 {
-  if (narg < 3) error->all(FLERR,"Illegal fix store/coord command");
+  if (narg < 3) error->all(FLERR,"Illegal fix store/force command");
 
   peratom_flag = 1;
   size_peratom_cols = 3;

src/input.cpp

@@ -327,27 +327,28 @@ void Input::file(const char *filename)
   // call to file() will close filename and decrement nfile
 
   if (me == 0) {
-    if (nfile == maxfile)
+    if (nfile == maxfile) error->one(FLERR,"Too many nested levels of input scripts");
-      error->one(FLERR,"Too many nested levels of input scripts");
 
+    if (filename) {
       infile = fopen(filename,"r");
       if (infile == nullptr)
-      error->one(FLERR,"Cannot open input script {}: {}",
+        error->one(FLERR,"Cannot open input script {}: {}", filename, utils::getsyserror());
-                                   filename, utils::getsyserror());
-
       infiles[nfile++] = infile;
     }
+  }
 
   // process contents of file
 
   file();
 
   if (me == 0) {
+    if (filename) {
       fclose(infile);
       nfile--;
       infile = infiles[nfile-1];
     }
   }
+}
 
 /** Process a single command from a string in *single*
  *

src/library.cpp

@@ -532,8 +532,7 @@ void lammps_file(void *handle, const char *filename)
   BEGIN_CAPTURE
   {
     if (lmp->update->whichflag != 0)
-      lmp->error->all(FLERR,"Library error: issuing LAMMPS commands "
+      lmp->error->all(FLERR, "Library error: issuing LAMMPS commands during a run is not allowed");
-                      "during a run is not allowed.");
     else
       lmp->input->file(filename);
   }

src/read_data.cpp

@@ -336,8 +336,8 @@ void ReadData::command(int narg, char **arg)
     error->all(FLERR, "Cannot run 2d simulation with nonperiodic Z dimension");
   if ((domain->nonperiodic == 2) && utils::strmatch(force->kspace_style, "^msm"))
     error->all(FLERR,
-               "Reading a data file with shrinkwrap boundaries is "
+               "Reading a data file with shrinkwrap boundaries is not "
-               "not compatible with a MSM KSpace style");
+               "compatible with a MSM KSpace style");
   if (domain->box_exist && !addflag)
     error->all(FLERR, "Cannot use read_data without add keyword after simulation box is defined");
   if (!domain->box_exist && addflag)
@@ -617,8 +617,9 @@ void ReadData::command(int narg, char **arg)
         atomflag = 1;
         if (firstpass) {
           if (me == 0 && !style_match(style, atom->atom_style))
-            error->warning(FLERR,
+            error->warning(
-                           "Atom style in data file differs from currently defined atom style");
+                FLERR, "Atom style in data file {} differs from currently defined atom style {}",
+                style, atom->atom_style);
           atoms();
         } else
           skip_lines(natoms);
@@ -696,8 +697,9 @@ void ReadData::command(int narg, char **arg)
         if (force->pair == nullptr) error->all(FLERR, "Must define pair_style before Pair Coeffs");
         if (firstpass) {
           if (me == 0 && !style_match(style, force->pair_style))
-            error->warning(FLERR,
+            error->warning(
-                           "Pair style in data file differs from currently defined pair style");
+                FLERR, "Pair style {} in data file differs from currently defined pair style {}",
+                style, force->pair_style);
           paircoeffs();
         } else
           skip_lines(ntypes);
@@ -706,9 +708,9 @@ void ReadData::command(int narg, char **arg)
           error->all(FLERR, "Must define pair_style before PairIJ Coeffs");
         if (firstpass) {
           if (me == 0 && !style_match(style, force->pair_style))
-            error->warning(FLERR,
+            error->warning(
-                           "Pair style in data file differs "
+                FLERR, "Pair style {} in data file differs from currently defined pair style {}",
-                           "from currently defined pair style");
+                style, force->pair_style);
           pairIJcoeffs();
         } else
           skip_lines(ntypes * (ntypes + 1) / 2);
@@ -718,8 +720,9 @@ void ReadData::command(int narg, char **arg)
         if (force->bond == nullptr) error->all(FLERR, "Must define bond_style before Bond Coeffs");
         if (firstpass) {
           if (me == 0 && !style_match(style, force->bond_style))
-            error->warning(FLERR,
+            error->warning(
-                           "Bond style in data file differs from currently defined bond style");
+                FLERR, "Bond style {} in data file differs from currently defined bond style {}",
+                style, force->bond_style);
           bondcoeffs();
         } else
           skip_lines(nbondtypes);
@@ -730,8 +733,9 @@ void ReadData::command(int narg, char **arg)
           error->all(FLERR, "Must define angle_style before Angle Coeffs");
         if (firstpass) {
           if (me == 0 && !style_match(style, force->angle_style))
-            error->warning(FLERR,
+            error->warning(
-                           "Angle style in data file differs from currently defined angle style");
+                FLERR, "Angle style {} in data file differs from currently defined angle style {}",
+                style, force->angle_style);
           anglecoeffs(0);
         } else
           skip_lines(nangletypes);
@@ -742,9 +746,10 @@ void ReadData::command(int narg, char **arg)
           error->all(FLERR, "Must define dihedral_style before Dihedral Coeffs");
         if (firstpass) {
           if (me == 0 && !style_match(style, force->dihedral_style))
-            error->warning(FLERR,
+            error->warning(
-                           "Dihedral style in data file differs "
+                FLERR,
-                           "from currently defined dihedral style");
+                "Dihedral style {} in data file differs from currently defined dihedral style {}",
+                style, force->dihedral_style);
           dihedralcoeffs(0);
         } else
           skip_lines(ndihedraltypes);
@@ -755,9 +760,10 @@ void ReadData::command(int narg, char **arg)
           error->all(FLERR, "Must define improper_style before Improper Coeffs");
         if (firstpass) {
           if (me == 0 && !style_match(style, force->improper_style))
-            error->warning(FLERR,
+            error->warning(
-                           "Improper style in data file differs "
+                FLERR,
-                           "from currently defined improper style");
+                "Improper style {} in data file differs from currently defined improper style {}",
+                style, force->improper_style);
           impropercoeffs(0);
         } else
           skip_lines(nimpropertypes);
@@ -1985,7 +1991,8 @@ void ReadData::paircoeffs()
     next = strchr(buf, '\n');
     *next = '\0';
     parse_coeffs(buf, nullptr, 1, 2, toffset, tlabelflag, lmap->lmap2lmap.atom);
-    if (ncoeffarg == 0) error->all(FLERR, "Unexpected empty line in PairCoeffs section");
+    if (ncoeffarg == 0)
+      error->all(FLERR, "Unexpected empty line in PairCoeffs section. Expected {} lines.", ntypes);
     force->pair->coeff(ncoeffarg, coeffarg);
     buf = next + 1;
   }
@@ -2016,7 +2023,11 @@ void ReadData::pairIJcoeffs()
       next = strchr(buf, '\n');
       *next = '\0';
       parse_coeffs(buf, nullptr, 0, 2, toffset, tlabelflag, lmap->lmap2lmap.atom);
-      if (ncoeffarg == 0) error->all(FLERR, "Unexpected empty line in PairCoeffs section");
+      if (ncoeffarg == 0)
+        error->all(FLERR,
+                   "Unexpected empty line in PairIJCoeffs section. "
+                   "Expected {} lines.",
+                   (ntypes - 1) * ntypes);
       force->pair->coeff(ncoeffarg, coeffarg);
       buf = next + 1;
     }
@@ -2045,7 +2056,9 @@ void ReadData::bondcoeffs()
     next = strchr(buf, '\n');
     *next = '\0';
     parse_coeffs(buf, nullptr, 0, 1, boffset, blabelflag, lmap->lmap2lmap.bond);
-    if (ncoeffarg == 0) error->all(FLERR, "Unexpected empty line in BondCoeffs section");
+    if (ncoeffarg == 0)
+      error->all(FLERR, "Unexpected empty line in BondCoeffs section. Expected {} lines.",
+                 nbondtypes);
     force->bond->coeff(ncoeffarg, coeffarg);
     buf = next + 1;
   }

tools/msi2lmp/README

@@ -76,10 +76,14 @@ This program uses the .car and .mdf files from MSI/Biosyms's INSIGHT
     The program is started by supplying information at the command prompt
     according to the usage described below.  
 
-    USAGE: msi2lmp.exe <ROOTNAME> {-print #} {-class #} {-frc FRC_FILE}
+    USAGE: msi2lmp.exe [-help] <ROOTNAME> [-print #] [-class #] [-frc FRC_FILE]
-                {-ignore} {-nocenter} {-shift # # #}
+                [-ignore] [-nocenter] [-shift # # #]
 
    -- msi2lmp.exe is the name of the executable
+
+   -- -help (or -h)
+        Print detailed this help message and exit.
+
    -- <ROOTNAME> is the base name of the .car and .mdf files
 
    -- -print (or -p)
@@ -148,6 +152,15 @@ msi2lmp has the following known limitations:
 
 CHANGELOG
 
+10 Mar 2023 Axel Kohlmeyer <akohlmey@gmail.com>
+
+Substitute UTF-8 characters in .frc files with known ASCII equivalents
+and add help message output
+
+05 Nov 2018 Axel Kohlmeyer <akohlmey@gmail.com>
+
+Teach msi2lmp to not generate dihedrals with identical 1-4 atoms
+
 06 Oct 2016 Axel Kohlmeyer <akohlmey@gmail.com>
 
 Improved whitespace handling in parsing topology and force field
@@ -239,5 +252,5 @@ for number_of_dihedrals, etc. could be unpredictable in these systems.
 
 -----------------------------
 
- msi2lmp v3.9.8 6/10/2016
+ msi2lmp v3.9.10 3/10/2023
 

tools/msi2lmp/src/SearchAndFill.c

@@ -48,6 +48,7 @@ const char *SearchAndCheck(const char *keyword)
       fprintf(stderr," Exiting....\n");
       exit(1);
     }
+    if (has_utf8(line)) utf8_subst(line);
     if (line[0] == '@') {
       if (string_match(strtok(line+1," '\t\n\r\f("),keyword)) {
         got_it = 1;
@@ -82,6 +83,7 @@ void SearchAndFill(struct FrcFieldItem *item)
       fprintf(stderr," Exiting....\n");
       exit(1);
     }
+    if (has_utf8(line)) utf8_subst(line);
     if (line[0] == '#') {
       if (string_match(strtok(line," '\t\r\n("),item->keyword)) got_it = 1;
     }
@@ -116,13 +118,16 @@ void SearchAndFill(struct FrcFieldItem *item)
   ctr = 0;
   while ( strncmp(line,"!---", 4) != 0 ) {
     fgets(line, MAX_LINE_LENGTH, FrcF);
+    if (has_utf8(line)) utf8_subst(line);
   }
 
   /* Get first line of data that isn't commented out */
 
   fgets(line, MAX_LINE_LENGTH, FrcF);
+  if (has_utf8(line)) utf8_subst(line);
   while (strncmp(line,"!",1) == 0) {
     fgets( line, MAX_LINE_LENGTH, FrcF);
+    if (has_utf8(line)) utf8_subst(line);
   }
 
   /* Read data into structure */
@@ -225,11 +230,13 @@ void SearchAndFill(struct FrcFieldItem *item)
       ctr++;
     }
     fgets( line, MAX_LINE_LENGTH, FrcF);
+    if (has_utf8(line)) utf8_subst(line);
+
     /*if blank line encountered, get next */
-    while((blank_line(line)) ||
+    while((blank_line(line)) || (strncmp(line,"!",1) == 0)) {
-          (strncmp(line,"!",1) == 0)) {
       status = fgets( line, MAX_LINE_LENGTH, FrcF);
       if (status == NULL) break;
+      if (has_utf8(line)) utf8_subst(line);
     }
   }
   item->entries = ctr;

tools/msi2lmp/src/msi2lmp.c

@@ -2,6 +2,9 @@
 *
 *  msi2lmp.exe
 *
+*   v3.9.10 AK - Substitute UTF-8 characters in .frc files with known ASCII equivalents
+*              - add help message output
+*
 *   v3.9.9 AK - Teach msi2lmp to not generate dihedrals with identical 1-4 atoms
 *
 *   v3.9.8 AK - Improved whitespace handling in parsing topology and force
@@ -156,6 +159,59 @@
 #include <ctype.h>
 #endif
 
+const char helpmesg[] =
+  "  USAGE: msi2lmp [-help] ROOTNAME [-print #] [-class #] [-frc FRC_FILE] [-ignore] [-nocenter] [-oldstyle]\n"
+  "\n"
+  "  -- msi2lmp is the name of the executable\n"
+  "\n"
+  "  -- -help or -h triggers printing this message and exits\n"
+  "\n"
+  "  -- ROOTNAME is the base name of the .car and .mdf files\n"
+  "  -- all opther flags are optional and can be abbreviated (e.g. -p instead of -print)\n"
+  "\n"
+  "  -- -print\n"
+  "        # is the print level:  0  - silent except for errors\n"
+  "                               1  - minimal (default)\n"
+  "                               2  - more verbose\n"
+  "                               3  - even more verbose\n"
+  "  -- -class\n"
+  "        # is the class of forcefield to use (I  or 1 = Class I e.g., CVFF, clayff)\n"
+  "                                            (II or 2 = Class II e.g., CFFx, COMPASS)\n"
+  "                                            (O  or 0 = OPLS-AA)\n"
+  "     default is -class I\n"
+  "\n"
+  "  -- -ignore   - tells msi2lmp to ignore warnings and errors and keep going\n"
+  "\n"
+  "  -- -nocenter - tells msi2lmp to not center the box around the (geometrical)\n"
+  "                 center of the atoms, but around the origin\n"
+  "\n"
+  "  -- -oldstyle - tells msi2lmp to write out a data file without style hints\n"
+  "                 (to be compatible with older LAMMPS versions)\n"
+  "\n"
+  "  -- -shift    - tells msi2lmp to shift the entire system (box and coordinates)\n"
+  "                 by a vector (default: 0.0 0.0 0.0)\n"
+  "\n"
+  "  -- -frc      - specifies name of the forcefield file (e.g., cff91)\n"
+  "\n"
+  "     If the name includes a hard wired directory (i.e., if the name\n"
+  "     starts with . or /), then the name is used alone. Otherwise,\n"
+  "     the program looks for the forcefield file in $MSI2LMP_LIBRARY.\n"
+  "     If $MSI2LMP_LIBRARY is not set, then the current directory is\n"
+  "     used.\n"
+  "\n"
+  "     If the file name does not include a dot after the first\n"
+  "     character, then .frc is appended to the name.\n"
+  "\n"
+  "     For example,  -frc cvff (assumes cvff.frc is in $MSI2LMP_LIBRARY or .)\n"
+  "\n"
+  "                   -frc cff/cff91 (assumes cff91.frc is in $MSI2LMP_LIBRARY/cff or ./cff)\n"
+  "\n"
+  "                   -frc /usr/local/forcefields/cff95 (absolute location)\n"
+  "\n"
+  "     By default, the program uses $MSI2LMP_LIBRARY/cvff.frc\n"
+  "\n"
+  "  -- output is written to a file called ROOTNAME.data\n";
+
 /* global variables */
 
 char  *rootname;
@@ -239,9 +295,14 @@ int main (int argc, char *argv[])
   frc_dir_name = getenv("MSI2LMP_LIBRARY");
 
   if (argc < 2) {
-    printf("usage: %s <rootname> [-class <I|1|II|2>] [-frc <path to frc file>] [-print #] [-ignore] [-nocenter] [-oldstyle]\n",argv[0]);
+    printf("usage: %s [-help|-h] <rootname> [-class <I|1|II|2|O|0>] [-frc <path to frc file>] [-print #] [-ignore] [-nocenter] [-oldstyle]\n",argv[0]);
     return 1;
-  } else { /* rootname was supplied as first argument, copy to rootname */
+  } else {
+    if ((strcmp(argv[1],"-help") == 0) || (strcmp(argv[1],"-h") == 0)) {
+      puts(helpmesg);
+      return 1;
+    }
+    /* rootname was supplied as first argument, copy to rootname */
     int len = strlen(argv[1]) + 1;
     rootname = (char *)malloc(len);
     strcpy(rootname,argv[1]);
@@ -249,6 +310,10 @@ int main (int argc, char *argv[])
 
   n = 2;
   while (n < argc) {
+    if ((strcmp(argv[n],"-help") == 0) || (strcmp(argv[1],"-h") == 0)) {
+      puts(helpmesg);
+      return 1;
+    }
     if (strncmp(argv[n],"-c",2) == 0) {
       n++;
       if (check_arg(argv,"-class",n,argc))
@@ -444,3 +509,101 @@ int main (int argc, char *argv[])
     printf("\nNormal program termination\n");
   return 0;
 }
+
+/* detect if a line has UTF-8 characters */
+
+int has_utf8(const char *line)
+{
+  const unsigned char *c = (const unsigned char *)line;
+
+  while (*c != '\0') {
+    if (*c & 0x80U) return 1;
+    ++c;
+  }
+  return 0;
+}
+
+/* replace UTF-8 characters with ASCII counterparts where known and possible */
+
+void utf8_subst(char *line)
+{
+  unsigned char *buf, *in, *out;
+  int i, len;
+
+  in = (unsigned char *)line;
+  len = strlen(line);
+  buf = (unsigned char *)malloc(len+1);
+  out = buf;
+
+  for (i = 0; i < len; ++i) {
+
+    /* UTF-8 2-byte character */
+    if ((in[i] & 0xe0U) == 0xc0U) {
+      if ((i + 1) < len) {
+        /* NON-BREAKING SPACE (U+00A0) */
+        if ((in[i] == 0xc2U) && (in[i + 1] == 0xa0U)) *out++ = ' ', ++i;
+        /* MODIFIER LETTER PLUS SIGN (U+02D6) */
+        if ((in[i] == 0xcbU) && (in[i + 1] == 0x96U)) *out++ = '+', ++i;
+        /* MODIFIER LETTER MINUS SIGN (U+02D7) */
+        if ((in[i] == 0xcbU) && (in[i + 1] == 0x97U)) *out++ = '-', ++i;
+      }
+      /* UTF-8 3-byte character */
+    } else if ((in[i] & 0xf0U) == 0xe0U) {
+      if ((i + 2) < len) {
+        /* EN QUAD (U+2000) */
+        if ((in[i] == 0xe2U) && (in[i + 1] == 0x80U) && (in[i + 2] == 0x80U)) *out++ = ' ', i += 2;
+        /* EM QUAD (U+2001) */
+        if ((in[i] == 0xe2U) && (in[i + 1] == 0x80U) && (in[i + 2] == 0x81U)) *out++ = ' ', i += 2;
+        /* EN SPACE (U+2002) */
+        if ((in[i] == 0xe2U) && (in[i + 1] == 0x80U) && (in[i + 2] == 0x82U)) *out++ = ' ', i += 2;
+        /* EM SPACE (U+2003) */
+        if ((in[i] == 0xe2U) && (in[i + 1] == 0x80U) && (in[i + 2] == 0x83U)) *out++ = ' ', i += 2;
+        /* THREE-PER-EM SPACE (U+2004) */
+        if ((in[i] == 0xe2U) && (in[i + 1] == 0x80U) && (in[i + 2] == 0x84U)) *out++ = ' ', i += 2;
+        /* FOUR-PER-EM SPACE (U+2005) */
+        if ((in[i] == 0xe2U) && (in[i + 1] == 0x80U) && (in[i + 2] == 0x85U)) *out++ = ' ', i += 2;
+        /* SIX-PER-EM SPACE (U+2006) */
+        if ((in[i] == 0xe2U) && (in[i + 1] == 0x80U) && (in[i + 2] == 0x86U)) *out++ = ' ', i += 2;
+        /* FIGURE SPACE (U+2007) */
+        if ((in[i] == 0xe2U) && (in[i + 1] == 0x80U) && (in[i + 2] == 0x87U)) *out++ = ' ', i += 2;
+        /* PUNCTUATION SPACE (U+2008) */
+        if ((in[i] == 0xe2U) && (in[i + 1] == 0x80U) && (in[i + 2] == 0x88U)) *out++ = ' ', i += 2;
+        /* THIN SPACE (U+2009) */
+        if ((in[i] == 0xe2U) && (in[i + 1] == 0x80U) && (in[i + 2] == 0x89U)) *out++ = ' ', i += 2;
+        /* HAIR SPACE (U+200A) */
+        if ((in[i] == 0xe2U) && (in[i + 1] == 0x80U) && (in[i + 2] == 0x8aU)) *out++ = ' ', i += 2;
+        /* ZERO WIDTH SPACE (U+200B) */
+        if ((in[i] == 0xe2U) && (in[i + 1] == 0x80U) && (in[i + 2] == 0x8bU)) *out++ = ' ', i += 2;
+        /* LEFT SINGLE QUOTATION MARK (U+2018) */
+        if ((in[i] == 0xe2U) && (in[i + 1] == 0x80U) && (in[i + 2] == 0x98U)) *out++ = '\'', i += 2;
+        /* RIGHT SINGLE QUOTATION MARK (U+2019) */
+        if ((in[i] == 0xe2U) && (in[i + 1] == 0x80U) && (in[i + 2] == 0x99U)) *out++ = '\'', i += 2;
+        /* LEFT DOUBLE QUOTATION MARK (U+201C) */
+        if ((in[i] == 0xe2U) && (in[i + 1] == 0x80U) && (in[i + 2] == 0x9cU)) *out++ = '"', i += 2;
+        /* RIGHT DOUBLE QUOTATION MARK (U+201D) */
+        if ((in[i] == 0xe2U) && (in[i + 1] == 0x80U) && (in[i + 2] == 0x9dU)) *out++ = '"', i += 2;
+        /* NARROW NO-BREAK SPACE (U+202F) */
+        if ((in[i] == 0xe2U) && (in[i + 1] == 0x80U) && (in[i + 2] == 0xafU)) *out++ = ' ', i += 2;
+        /* WORD JOINER (U+2060) */
+        if ((in[i] == 0xe2U) && (in[i + 1] == 0x81U) && (in[i + 2] == 0xa0U)) *out++ = ' ', i += 2;
+        /* INVISIBLE SEPARATOR (U+2063) */
+        if ((in[i] == 0xe2U) && (in[i + 1] == 0x81U) && (in[i + 2] == 0xa3U)) *out++ = ' ', i += 2;
+        /* INVISIBLE PLUS (U+2064) */
+        if ((in[i] == 0xe2U) && (in[i + 1] == 0x81U) && (in[i + 2] == 0xa4U)) *out++ = '+', i += 2;
+        /* MINUS SIGN (U+2212) */
+        if ((in[i] == 0xe2U) && (in[i + 1] == 0x88U) && (in[i + 2] == 0x92U)) *out++ = '-', i += 2;
+        /* ZERO WIDTH NO-BREAK SPACE (U+FEFF) */
+        if ((in[i] == 0xefU) && (in[i + 1] == 0xbbU) && (in[i + 2] == 0xbfU)) *out++ = ' ', i += 2;
+      }
+      /* UTF-8 4-byte character */
+    } else if ((in[i] & 0xf8U) == 0xf0U) {
+      if ((i + 3) < len) { ; }
+    } else {
+      *out++ = in[i];
+    }
+  }
+
+  *out = '\0';
+  strncpy(line, (char *)buf, len);
+  free(buf);
+}

tools/msi2lmp/src/msi2lmp.h

@@ -36,7 +36,7 @@
 
 #include <stdio.h>              /* IWYU pragma: export */
 
-#define MSI2LMP_VERSION "v3.9.9 / 05 Nov 2018"
+#define MSI2LMP_VERSION "v3.9.10 / 10 Mar 2023"
 
 #define PI_180  0.01745329251994329576
 
@@ -226,3 +226,6 @@ extern void lamda2x(double *lamda, double *x, double *h, double *boxlo);
 extern void x2lamda(double *x, double *lamda, double *h_inv, double *boxlo);
 
 extern void condexit(int);
+
+extern int has_utf8(const char *line);
+extern void utf8_subst(char *line);