Merge branch 'develop' into collected-small-fixes

doc/src/Commands_fix.rst

@@ -171,6 +171,7 @@ OPT.
    * :doc:`pafi <fix_pafi>`
    * :doc:`pair <fix_pair>`
    * :doc:`phonon <fix_phonon>`
+   * :doc:`pimd/langevin <fix_pimd>`
    * :doc:`pimd/nvt <fix_pimd>`
    * :doc:`planeforce <fix_planeforce>`
    * :doc:`plumed <fix_plumed>`

doc/src/compute_stress_mop.rst

@@ -18,7 +18,7 @@ Syntax
 * style = *stress/mop* or *stress/mop/profile*
 * dir = *x* or *y* or *z* is the direction normal to the plane
 * args = argument specific to the compute style
-* keywords = *kin* or *conf* or *total* (one of more can be specified)
+* keywords = *kin* or *conf* or *total* or *pair* or *bond* or *angle* (one or more can be specified)
 
 .. parsed-literal::
 
@@ -45,85 +45,107 @@ Examples
 Description
 """""""""""
 
-Compute *stress/mop* and compute *stress/mop/profile* define computations that
+Compute *stress/mop* and compute *stress/mop/profile* define
-calculate components of the local stress tensor using the method of
+computations that calculate components of the local stress tensor using
-planes :ref:`(Todd) <mop-todd>`.  Specifically in compute *stress/mop* calculates 3
+the method of planes :ref:`(Todd) <mop-todd>`.  Specifically in compute
-components are computed in directions *dir*,\ *x*\ ; *dir*,\ *y*\ ; and
+*stress/mop* calculates 3 components are computed in directions *dir*,\
-*dir*,\ *z*\ ; where *dir* is the direction normal to the plane, while
+*x*\ ; *dir*,\ *y*\ ; and *dir*,\ *z*\ ; where *dir* is the direction
-in compute *stress/mop/profile* the profile of the stress is computed.
+normal to the plane, while in compute *stress/mop/profile* the profile
+of the stress is computed.
 
 Contrary to methods based on histograms of atomic stress (i.e., using
-:doc:`compute stress/atom <compute_stress_atom>`), the method of planes is
+:doc:`compute stress/atom <compute_stress_atom>`), the method of planes
-compatible with mechanical balance in heterogeneous systems and at
+is compatible with mechanical balance in heterogeneous systems and at
 interfaces :ref:`(Todd) <mop-todd>`.
 
 The stress tensor is the sum of a kinetic term and a configurational
 term, which are given respectively by Eq. (21) and Eq. (16) in
-:ref:`(Todd) <mop-todd>`. For the kinetic part, the algorithm considers that
+:ref:`(Todd) <mop-todd>`. For the kinetic part, the algorithm considers
-atoms have crossed the plane if their positions at times :math:`t-\Delta t`
+that atoms have crossed the plane if their positions at times
-and :math:`t` are one on either side of the plane, and uses the velocity at
+:math:`t-\Delta t` and :math:`t` are one on either side of the plane,
-time :math:`t-\Delta t/2` given by the velocity Verlet algorithm.
+and uses the velocity at time :math:`t-\Delta t/2` given by the velocity
+Verlet algorithm.
 
-Between one and three keywords can be used to indicate which
+.. versionadded:: TBD
-contributions to the stress must be computed: kinetic stress (kin),
-configurational stress (conf), and/or total stress (total).
 
-NOTE 1: The configurational stress is computed considering all pairs of atoms where at least one atom belongs to group group-ID.
+   contributions from bond and angle potentials
+
+Between one and six keywords can be used to indicate which contributions
+to the stress must be computed: total stress (total), kinetic stress
+(kin), configurational stress (conf), stress due to bond stretching
+(bond), stress due to angle bending (angle) and/or due to pairwise
+non-bonded interactions (pair).  The angle keyword is currently
+available only for the *stress/mop* command and **not** the
+*stress/mop/profile* command.
+
+NOTE 1: The configurational stress is computed considering all pairs of
+atoms where at least one atom belongs to group group-ID.
 
 NOTE 2: The local stress does not include any Lennard-Jones tail
-corrections to the stress added by the :doc:`pair_modify tail yes <pair_modify>`
+corrections to the stress added by the :doc:`pair_modify tail yes
-command, since those are contributions to the global system pressure.
+<pair_modify>` command, since those are contributions to the global
+system pressure.
 
-NOTE 3: The local stress profile generated by compute *stress/mop/profile*
+NOTE 3: The local stress profile generated by compute
-is similar to that obtained by compute
+*stress/mop/profile* is similar to that obtained by compute
-:doc:`stress/cartesian <compute_stress_profile>`.
+:doc:`stress/cartesian <compute_stress_profile>`.  A key difference is
-A key difference is that compute *stress/mop/profile* considers particles
+that compute *stress/mop/profile* considers particles crossing a set of
-crossing a set of planes, while compute *stress/cartesian* computes averages
+planes, while compute *stress/cartesian* computes averages for a set of
-for a set of small volumes.  More information
+small volumes.  More information on the similarities and differences can
-on the similarities and differences can be found in
+be found in :ref:`(Ikeshoji)<Ikeshoji2>`.
-:ref:`(Ikeshoji)<Ikeshoji2>`.
 
 Output info
 """""""""""
 
-Compute *stress/mop* calculates a global vector (indices starting at 1), with 3
+Compute *stress/mop* calculates a global vector (indices starting at 1),
-values for each declared keyword (in the order the keywords have been
+with 3 values for each declared keyword (in the order the keywords have
-declared). For each keyword, the stress tensor components are ordered as
+been declared). For each keyword, the stress tensor components are
-follows: stress_dir,x, stress_dir,y, and stress_dir,z.
+ordered as follows: stress_dir,x, stress_dir,y, and stress_dir,z.
 
-Compute *stress/mop/profile* instead calculates a global array, with 1 column
+Compute *stress/mop/profile* instead calculates a global array, with 1
-giving the position of the planes where the stress tensor was computed,
+column giving the position of the planes where the stress tensor was
-and with 3 columns of values for each declared keyword (in the order the
+computed, and with 3 columns of values for each declared keyword (in the
-keywords have been declared). For each keyword, the profiles of stress
+order the keywords have been declared). For each keyword, the profiles
-tensor components are ordered as follows: stress_dir,x; stress_dir,y;
+of stress tensor components are ordered as follows: stress_dir,x;
-and stress_dir,z.
+stress_dir,y; and stress_dir,z.
 
 The values are in pressure :doc:`units <units>`.
 
-The values produced by this compute can be accessed by various :doc:`output commands <Howto_output>`.
+The values produced by this compute can be accessed by various
-For instance, the results can be written to a file using the
+:doc:`output commands <Howto_output>`.  For instance, the results can be
-:doc:`fix ave/time <fix_ave_time>` command. Please see the example
+written to a file using the :doc:`fix ave/time <fix_ave_time>`
-in the examples/PACKAGES/mop folder.
+command. Please see the example in the examples/PACKAGES/mop folder.
 
 Restrictions
 """"""""""""
 
-These styles are part of the EXTRA-COMPUTE package. They are only enabled if
+These styles are part of the EXTRA-COMPUTE package. They are only
-LAMMPS is built with that package. See the :doc:`Build package <Build_package>`
+enabled if LAMMPS is built with that package. See the :doc:`Build
-doc page on for more info.
+package <Build_package>` doc page on for more info.
 
 The method is only implemented for 3d orthogonal simulation boxes whose
 size does not change in time, and axis-aligned planes.
 
 The method only works with two-body pair interactions, because it
-requires the class method pair->single() to be implemented. In
+requires the class method ``Pair::single()`` to be implemented, which is
-particular, it does not work with more than two-body pair interactions,
+not possible for manybody potentials.  In particular, compute
-intra-molecular interactions, and long range (kspace) interactions.
+*stress/mop/profile* does not work with more than two-body pair
+interactions, long range (kspace) interactions and
+angle/dihedral/improper intramolecular interactions. Similarly, compute
+*stress/mop* does not work with more than two-body pair interactions,
+long range (kspace) interactions and dihedral/improper intramolecular
+interactions but works with all bond interactions with the class method
+single() implemented and all angle interactions with the class method
+born_matrix() implemented.
 
 Related commands
 """"""""""""""""
 
-:doc:`compute stress/atom <compute_stress_atom>`, :doc:`compute pressure <compute_pressure>`, :doc:`compute stress/cartesian <compute_stress_profile>`, :doc:`compute stress/cylinder <compute_stress_profile>`, :doc:`compute stress/spherical <compute_stress_profile>`
+:doc:`compute stress/atom <compute_stress_atom>`,
+:doc:`compute pressure <compute_pressure>`,
+:doc:`compute stress/cartesian <compute_stress_profile>`,
+:doc:`compute stress/cylinder <compute_stress_profile>`,
+:doc:`compute stress/spherical <compute_stress_profile>`
 
 Default
 """""""

doc/src/fix.rst

@@ -323,7 +323,8 @@ accelerated styles exist.
 * :doc:`pafi <fix_pafi>` - constrained force averages on hyper-planes to compute free energies (PAFI)
 * :doc:`pair <fix_pair>` - access per-atom info from pair styles
 * :doc:`phonon <fix_phonon>` - calculate dynamical matrix from MD simulations
-* :doc:`pimd/nvt <fix_pimd>` - Feynman path integral molecular dynamics with Nose-Hoover thermostat
+* :doc:`pimd/langevin <fix_pimd>` - Feynman path-integral molecular dynamics with stochastic thermostat
+* :doc:`pimd/nvt <fix_pimd>` - Feynman path-integral molecular dynamics with Nose-Hoover thermostat
 * :doc:`planeforce <fix_planeforce>` - constrain atoms to move in a plane
 * :doc:`plumed <fix_plumed>` - wrapper on PLUMED free energy library
 * :doc:`poems <fix_poems>` - constrain clusters of atoms to move as coupled rigid bodies

doc/src/fix_pimd.rst

@@ -1,5 +1,9 @@
+.. index:: fix pimd/langevin
 .. index:: fix pimd/nvt
 
+fix pimd/langevin command
+=========================
+
 fix pimd/nvt command
 ====================
 
@@ -8,72 +12,107 @@ Syntax
 
 .. parsed-literal::
 
-   fix ID group-ID pimd/nvt keyword value ...
+   fix ID group-ID style keyword value ...
 
 * ID, group-ID are documented in :doc:`fix <fix>` command
-* pimd/nvt = style name of this fix command
+* style = *pimd/langevin* or *pimd/nvt* = style name of this fix command
 * zero or more keyword/value pairs may be appended
-* keyword = *method* or *fmass* or *sp* or *temp* or *nhc*
+* keywords for style *pimd/nvt*
 
   .. parsed-literal::
-
+       *keywords* = *method* or *fmass* or *sp* or *temp* or *nhc*
        *method* value = *pimd* or *nmpimd* or *cmd*
        *fmass* value = scaling factor on mass
        *sp* value = scaling factor on Planck constant
-       *temp* value = temperature (temperarate units)
+       *temp* value = temperature (temperature units)
        *nhc* value = Nc = number of chains in Nose-Hoover thermostat
 
+* keywords for style *pimd/langevin*
+
+  .. parsed-literal::
+       *keywords* = *method* or *integrator* or *ensemble* or *fmmode* or *fmass* or *scale* or *temp* or *thermostat* or *tau* or *iso* or *aniso* or *barostat* or *taup* or *fixcom* or *lj*
+       *method* value = *nmpimd*
+       *integrator* value = *obabo* or *baoab*
+       *fmmode* value = *physical* or *normal*
+       *fmass* value = scaling factor on mass
+       *temp* value = temperature (temperature unit)
+          temperature = target temperature of the thermostat
+       *thermostat* values = style seed
+          style value = *PILE_L*
+          seed = random number generator seed
+       *tau* value = thermostat damping parameter (time unit)
+       *scale* value = scaling factor of the damping times of non-centroid modes of PILE_L thermostat
+       *iso* or *aniso* values = pressure (pressure unit)
+         pressure = scalar external pressure of the barostat
+       *barostat* value = *BZP* or *MTTK*
+       *taup* value = barostat damping parameter (time unit)
+       *fixcom* value = *yes* or *no*
+       *lj* values = epsilon sigma mass planck mvv2e
+          epsilon = energy scale for reduced units (energy units)
+          sigma = length scale for reduced units (length units)
+          mass = mass scale for reduced units (mass units)
+          planck = Planck's constant for other unit style
+          mvv2e = mass * velocity^2 to energy conversion factor for other unit style
+
 Examples
 """"""""
 
 .. code-block:: LAMMPS
 
    fix 1 all pimd/nvt method nmpimd fmass 1.0 sp 2.0 temp 300.0 nhc 4
+   fix 1 all pimd/langevin ensemble npt integrator obabo temp 113.15 thermostat PILE_L 1234 tau 1.0 iso 1.0 barostat BZP taup 1.0
 
 Description
 """""""""""
 
 .. versionchanged:: 28Mar2023
 
-Fix pimd was renamed to fix pimd/nvt.
+Fix pimd was renamed to fix *pimd/nvt* and fix *pimd/langevin* was added.
 
-This command performs quantum molecular dynamics simulations based on
+These fix commands perform quantum molecular dynamics simulations based
-the Feynman path integral to include effects of tunneling and
+on the Feynman path-integral to include effects of tunneling and
 zero-point motion.  In this formalism, the isomorphism of a quantum
 partition function for the original system to a classical partition
 function for a ring-polymer system is exploited, to efficiently sample
 configurations from the canonical ensemble :ref:`(Feynman) <Feynman>`.
+
 The classical partition function and its components are given
 by the following equations:
 
 .. math::
 
    Z = & \int d{\bf q} d{\bf p} \cdot \textrm{exp} [ -\beta H_{eff} ] \\
-   H_{eff} = & \bigg(\sum_{i=1}^P \frac{p_i^2}{2m_i}\bigg) + V_{eff} \\
+   H_{eff} = & \bigg(\sum_{i=1}^P \frac{p_i^2}{2M_i}\bigg) + V_{eff} \\
    V_{eff} = & \sum_{i=1}^P \bigg[ \frac{mP}{2\beta^2 \hbar^2} (q_i - q_{i+1})^2 + \frac{1}{P} V(q_i)\bigg]
 
+:math:`M_i` is the fictitious mass of the :math:`i`-th mode, and m is the actual mass of the atoms.
+
 The interested user is referred to any of the numerous references on
-this methodology, but briefly, each quantum particle in a path
+this methodology, but briefly, each quantum particle in a path integral
-integral simulation is represented by a ring-polymer of P quasi-beads,
+simulation is represented by a ring-polymer of P quasi-beads, labeled
-labeled from 1 to P.  During the simulation, each quasi-bead interacts
+from 1 to P.  During the simulation, each quasi-bead interacts with
-with beads on the other ring-polymers with the same imaginary time
+beads on the other ring-polymers with the same imaginary time index (the
-index (the second term in the effective potential above).  The
+second term in the effective potential above).  The quasi-beads also
-quasi-beads also interact with the two neighboring quasi-beads through
+interact with the two neighboring quasi-beads through the spring
-the spring potential in imaginary-time space (first term in effective
+potential in imaginary-time space (first term in effective potential).
-potential).  To sample the canonical ensemble, a Nose-Hoover massive
+To sample the canonical ensemble, any thermostat can be applied.
-chain thermostat is applied :ref:`(Tuckerman) <pimd-Tuckerman>`.  With the
+
-massive chain algorithm, a chain of NH thermostats is coupled to each
+Fix *pimd/nvt* applies a Nose-Hoover massive chain thermostat
-degree of freedom for each quasi-bead.  The keyword *temp* sets the
+:ref:`(Tuckerman) <pimd-Tuckerman>`.  With the massive chain
-target temperature for the system and the keyword *nhc* sets the
+algorithm, a chain of NH thermostats is coupled to each degree of
-number *Nc* of thermostats in each chain.  For example, for a
+freedom for each quasi-bead.  The keyword *temp* sets the target
-simulation of N particles with P beads in each ring-polymer, the total
+temperature for the system and the keyword *nhc* sets the number *Nc* of
-number of NH thermostats would be 3 x N x P x Nc.
+thermostats in each chain.  For example, for a simulation of N particles
+with P beads in each ring-polymer, the total number of NH thermostats
+would be 3 x N x P x Nc.
+
+Fix *pimd/langevin* implements a Langevin thermostat in the normal mode
+representation, and also provides a barostat to sample the NPH/NPT ensembles.
 
 .. note::
 
-   Fix pimd/nvt implements a complete velocity-verlet integrator
+   Both these *fix* styles implement a complete velocity-verlet integrator
-   combined with NH massive chain thermostat, so no other time
+   combined with a thermostat, so no other time integration fix should be used.
-   integration fix should be used.
 
 The *method* keyword determines what style of PIMD is performed.  A
 value of *pimd* is standard PIMD.  A value of *nmpimd* is for
@@ -81,7 +120,7 @@ normal-mode PIMD.  A value of *cmd* is for centroid molecular dynamics
 (CMD).  The difference between the styles is as follows.
 
    In standard PIMD, the value used for a bead's fictitious mass is
-   arbitrary.  A common choice is to use Mi = m/P, which results in the
+   arbitrary.  A common choice is to use :math:`M_i = m/P`, which results in the
    mass of the entire ring-polymer being equal to the real quantum
    particle.  But it can be difficult to efficiently integrate the
    equations of motion for the stiff harmonic interactions in the ring
@@ -97,6 +136,10 @@ normal-mode PIMD.  A value of *cmd* is for centroid molecular dynamics
    overall translation of the ring-polymer and is assigned the mass of
    the real particle.
 
+.. note::
+   Fix pimd/langevin only supports *method* value *nmpimd*. This should be enough
+   for most PIMD applications for quantum thermodynamics purpose.
+
    Motion of the centroid can be effectively uncoupled from the other
    normal modes by scaling the fictitious masses to achieve a partial
    adiabatic separation.  This is called a Centroid Molecular Dynamics
@@ -108,17 +151,86 @@ normal-mode PIMD.  A value of *cmd* is for centroid molecular dynamics
    only the k > 0 modes are thermostatted, not the centroid degrees of
    freedom.
 
+The keyword *integrator* specifies the Trotter splitting method used by *fix pimd/langevin*.
+See :ref:`(Liu) <Liu>` for a discussion on the OBABO and BAOAB splitting schemes. Typically
+either of the two should work fine.
+
 The keyword *fmass* sets a further scaling factor for the fictitious
 masses of beads, which can be used for the Partial Adiabatic CMD
 :ref:`(Hone) <Hone>`, or to be set as P, which results in the fictitious
 masses to be equal to the real particle masses.
 
+The keyword *fmmode* of *fix pimd/langevin* determines the mode of fictitious
+mass preconditioning. There are two options: *physical* and *normal*. If *fmmode* is
+*physical*, then the physical mass of the particles are used (and then multiplied by
+*fmass*). If *fmmode* is *normal*, then the physical mass is first multiplied by the
+eigenvalue of each normal mode, and then multiplied by *fmass*. More precisely, the
+fictitious mass of *fix pimd/langevin* is determined by two factors: *fmmode* and *fmass*.
+If *fmmode* is *physical*, then the fictitious mass is
+
+.. math::
+
+   M_i = \mathrm{fmass} \times m
+
+If *fmmode* is *normal*, then the fictitious mass is
+
+.. math::
+
+   M_i = \mathrm{fmass} \times \lambda_i \times m
+
+where :math:`\lambda_i` is the eigenvalue of the :math:`i`-th normal mode.
+
+.. note::
+
+   Fictitious mass is only used in the momentum of the equation of motion
+   (:math:`\mathbf{p}_i=M_i\mathbf{v}_i`), and not used in the spring elastic energy
+   (:math:`\sum_{i=1}^P \frac{1}{2}m\omega_P^2(q_i - q_{i+1})^2`, :math:`m` is always the
+   actual mass of the particles).
+
 The keyword *sp* is a scaling factor on Planck's constant, which can
 be useful for debugging or other purposes.  The default value of 1.0
 is appropriate for most situations.
 
+The keyword *ensemble* for fix style *pimd/langevin* determines which ensemble is it
+going to sample. The value can be *nve* (microcanonical), *nvt* (canonical), *nph* (isoenthalpic),
+and *npt* (isothermal-isobaric).
+
+The keyword *temp* specifies temperature parameter for fix styles *pimd/nvt* and *pimd/langevin*. It should read
+a positive floating-point number.
+
+.. note::
+
+   For pimd simulations, a temperature values should be specified even for nve ensemble. Temperature will make a difference
+   for nve pimd, since the spring elastic frequency between the beads will be affected by the temperature.
+
+The keyword *thermostat* reads *style* and *seed* of thermostat for fix style *pimd/langevin*. *style* can only
+be *PILE_L* (path integral Langevin equation local thermostat, as described in :ref:`Ceriotti <Ceriotti2>`), and *seed* should a positive integer number, which serves as the seed of the pseudo random number generator.
+
+.. note::
+   The fix style *pimd/langevin* uses the stochastic PILE_L thermostat to control temperature. This thermostat works on the normal modes
+   of the ring polymer. The *tau* parameter controls the centroid mode, and the *scale* parameter controls the non-centroid modes.
+
+The keyword *tau* specifies the thermostat damping time parameter for fix style *pimd/langevin*. It is in time unit. It only works on the centroid mode.
+
+The keyword *scale* specifies a scaling parameter for the damping times of the non-centroid modes for fix style *pimd/langevin*. The default
+damping time of the non-centroid mode :math:`i` is :math:`\frac{P}{\beta\hbar}\sqrt{\lambda_i\times\mathrm{fmass}}` (*fmmode* is *physical*) or  :math:`\frac{P}{\beta\hbar}\sqrt{\mathrm{fmass}}` (*fmmode* is *normal*). The damping times of all non-centroid modes are the default values divided by *scale*.
+
+The barostat parameters for fix style *pimd/langevin* with *npt* or *nph* ensemble is specified using one of *iso* and *aniso*
+keywords. A *pressure* value should be given with pressure unit. The keyword *iso* means couple all 3 diagonal components together when pressure is computed (hydrostatic pressure), and dilate/contract the dimensions together. The keyword *aniso* means x, y, and z dimensions are controlled independently using the Pxx, Pyy, and Pzz components of the stress tensor as the driving forces, and the specified scalar external pressure.
+
+The keyword *barostat* reads *style* of barostat for fix style *pimd/langevin*. *style* can
+be *BZP* (Bussi-Zykova-Parrinello, as described in :ref:`Bussi <Bussi>`) or *MTTK* (Martyna-Tuckerman-Tobias-Klein, as described in :ref:`Martyna1 <Martyna3>` and :ref:`Martyna2 <Martyna4>`).
+
+The keyword *taup* specifies the barostat damping time parameter for fix style *pimd/langevin*. It is in time unit.
+
+The keyword *fixcom* specifies whether the center-of-mass of the extended ring-polymer system is fixed during the pimd simulation.
+Once *fixcom* is set to be *yes*, the center-of-mass velocity will be distracted from the centroid-mode velocities in each step.
+
+The keyword *lj* should be used if :doc:`lj units <units>` is used for *fix pimd/langevin*. Typically one may want to use
+reduced units to run the simulation, and then convert the results into some physical units (for example, :doc:`metal units <units>`). In this case, the 5 quantities in the physical mass units are needed: epsilon (energy scale), sigma (length scale), mass, Planck's constant, mvv2e (mass * velocity^2 to energy conversion factor). Planck's constant and mvv2e can be found in src/update.cpp. If there is no need to convert reduced units to physical units, set all these five value to 1.
+
 The PIMD algorithm in LAMMPS is implemented as a hyper-parallel scheme
-as described in :ref:`(Calhoun) <Calhoun>`.  In LAMMPS this is done by using
+as described in :ref:`Calhoun <Calhoun>`.  In LAMMPS this is done by using
 :doc:`multi-replica feature <Howto_replica>` in LAMMPS, where each
 quasi-particle system is stored and simulated on a separate partition
 of processors.  The following diagram illustrates this approach.  The
@@ -152,22 +264,49 @@ related tasks for each of the partitions, e.g.
 .. code-block:: LAMMPS
 
    dump dcd all dcd 10 system_${ibead}.dcd
+   dump 1 all custom 100 ${ibead}.xyz id type x y z vx vy vz ix iy iz fx fy fz
    restart 1000 system_${ibead}.restart1 system_${ibead}.restart2
    read_restart system_${ibead}.restart2
 
+.. note::
+   Fix *pimd/langevin* dumps the Cartesian coordinates, but dumps the velocities and
+   forces in the normal mode representation. If the Cartesian velocities and forces are
+   needed, it is easy to perform the transformation when doing post-processing.
+
+   It is recommended to dump the image flags (*ix iy iz*) for fix *pimd/langevin*. It
+   will be useful if you want to calculate some estimators during post-processing.
+
+Major differences of *fix pimd/nvt* and *fix pimd/langevin* are:
+
+   #. *Fix pimd/nvt* includes Cartesian pimd, normal mode pimd, and centroid md. *Fix pimd/langevin* only intends to support normal mode pimd, as it is commonly enough for thermodynamic sampling.
+   #. *Fix pimd/nvt* uses Nose-Hoover chain thermostat. *Fix pimd/langevin* uses Langevin thermostat.
+   #. *Fix pimd/langevin* provides barostat, so the npt ensemble can be sampled. *Fix pimd/nvt* only support nvt ensemble.
+   #. *Fix pimd/langevin* provides several quantum estimators in output.
+   #. *Fix pimd/langevin* allows multiple processes for each bead. For *fix pimd/nvt*, there is a large chance that multi-process tasks for each bead may fail.
+   #. The dump of *fix pimd/nvt* are all Cartesian. *Fix pimd/langevin* dumps normal-mode velocities and forces, and Cartesian coordinates.
+
+Initially, the inter-replica communication and normal mode transformation parts of *fix pimd/langevin* are written based on
+those of *fix pimd/nvt*, but are significantly revised.
+
 Restart, fix_modify, output, run start/stop, minimize info
 """""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
-Fix pimd/nvt writes the state of the Nose/Hoover thermostat over all
+Fix *pimd/nvt* writes the state of the Nose/Hoover thermostat over all
 quasi-beads to :doc:`binary restart files <restart>`.  See the
 :doc:`read_restart <read_restart>` command for info on how to re-specify
 a fix in an input script that reads a restart file, so that the
 operation of the fix continues in an uninterrupted fashion.
 
+Fix *pimd/langevin* writes the state of the barostat overall beads to
+:doc:`binary restart files <restart>`. Since it uses a stochastic thermostat,
+the state of the thermostat is not written. However, the state of the system
+can be restored by reading the restart file, except that it will re-initialize
+the random number generator.
+
 None of the :doc:`fix_modify <fix_modify>` options
 are relevant to fix pimd/nvt.
 
-Fix pimd/nvt computes a global 3-vector, which can be accessed by
+Fix *pimd/nvt* computes a global 3-vector, which can be accessed by
 various :doc:`output commands <Howto_output>`.  The three quantities in
 the global vector are:
 
@@ -176,21 +315,80 @@ the global vector are:
    #. the current value of the scalar virial estimator for the kinetic
       energy of the quantum system :ref:`(Herman) <Herman>`.
 
-The vector values calculated by fix pimd/nvt are "extensive", except for the
+The vector values calculated by fix *pimd/nvt* are "extensive", except for the
 temperature, which is "intensive".
 
-No parameter of fix pimd/nvt can be used with the *start/stop* keywords
+Fix *pimd/langevin* computes a global vector of quantities, which
-of the :doc:`run <run>` command.  Fix pimd/nvt is not invoked during
+can be accessed by various :doc:`output commands <Howto_output>`. Note that
+it outputs multiple log files, and different log files contain information
+about different beads or modes (see detailed explanations below). If *ensemble*
+is *nve* or *nvt*, the vector has 10 values:
+
+   #. kinetic energy of the normal mode
+   #. spring elastic energy of the normal mode
+   #. potential energy of the bead
+   #. total energy of all beads (conserved if *ensemble* is *nve*)
+   #. primitive kinetic energy estimator
+   #. virial energy estimator
+   #. centroid-virial energy estimator
+   #. primitive pressure estimator
+   #. thermodynamic pressure estimator
+   #. centroid-virial pressure estimator
+
+The first 3 are different for different log files, and the others are the same for different log files.
+
+If *ensemble* is *nph* or *npt*, the vector stores internal variables of the barostat. If *iso* is used,
+the vector has 15 values:
+
+   #. kinetic energy of the normal mode
+   #. spring elastic energy of the normal mode
+   #. potential energy of the bead
+   #. total energy of all beads (conserved if *ensemble* is *nve*)
+   #. primitive kinetic energy estimator
+   #. virial energy estimator
+   #. centroid-virial energy estimator
+   #. primitive pressure estimator
+   #. thermodynamic pressure estimator
+   #. centroid-virial pressure estimator
+   #. barostat velocity
+   #. barostat kinetic energy
+   #. barostat potential energy
+   #. barostat cell Jacobian
+   #. enthalpy of the extended system (sum of 4, 12, 13, and 14; conserved if *ensemble* is *nph*)
+
+If *aniso* or *x* or *y* or *z* is used for the barostat, the vector has 17 values:
+
+   #. kinetic energy of the normal mode
+   #. spring elastic energy of the normal mode
+   #. potential energy of the bead
+   #. total energy of all beads (conserved if *ensemble* is *nve*)
+   #. primitive kinetic energy estimator
+   #. virial energy estimator
+   #. centroid-virial energy estimator
+   #. primitive pressure estimator
+   #. thermodynamic pressure estimator
+   #. centroid-virial pressure estimator
+   #. x component of barostat velocity
+   #. y component of barostat velocity
+   #. z component of barostat velocity
+   #. barostat kinetic energy
+   #. barostat potential energy
+   #. barostat cell Jacobian
+   #. enthalpy of the extended system (sum of 4, 14, 15, and 16; conserved if *ensemble* is *nph*)
+
+No parameter of fix *pimd/nvt* or *pimd/langevin* can be used with the *start/stop* keywords
+of the :doc:`run <run>` command.  Fix *pimd/nvt* or *pimd/langevin* is not invoked during
 :doc:`energy minimization <minimize>`.
 
 Restrictions
 """"""""""""
 
-This fix is part of the REPLICA package.  It is only enabled if LAMMPS
+These fixes are part of the REPLICA package.  They are only enabled if
-was built with that package.  See the :doc:`Build package
+LAMMPS was built with that package.  See the :doc:`Build package
 <Build_package>` page for more info.
 
-Fix pimd/nvt cannot be used with :doc:`lj units <units>`.
+Fix *pimd/nvt* cannot be used with :doc:`lj units <units>`.
+Fix *pimd/langevin* can be used with :doc:`lj units <units>`. See the above part for how to use it.
 
 A PIMD simulation can be initialized with a single data file read via
 the :doc:`read_data <read_data>` command.  However, this means all
@@ -207,7 +405,7 @@ variable, e.g.
 Default
 """""""
 
-The keyword defaults for fix pimd/nvt are method = pimd, fmass = 1.0, sp
+The keyword defaults for fix *pimd/nvt* are method = pimd, fmass = 1.0, sp
 = 1.0, temp = 300.0, and nhc = 2.
 
 ----------
@@ -243,3 +441,22 @@ Path Integrals, McGraw-Hill, New York (1965).
 
 **(Herman)** M. F. Herman, E. J. Bruskin, B. J. Berne, J Chem Phys, 76, 5150 (1982).
 
+.. _Bussi:
+
+**(Bussi)** G. Bussi, T. Zykova-Timan, M. Parrinello, J Chem Phys, 130, 074101 (2009).
+
+.. _Ceriotti3:
+
+**(Ceriotti)** M. Ceriotti, M. Parrinello, T. Markland, D. Manolopoulos, J. Chem. Phys. 133, 124104 (2010).
+
+.. _Martyna3:
+
+**(Martyna1)** G. Martyna, D. Tobias, M. Klein, J. Chem. Phys. 101, 4177 (1994).
+
+.. _Martyna4:
+
+**(Martyna2)** G. Martyna, A. Hughes, M. Tuckerman, J. Chem. Phys. 110, 3275 (1999).
+
+.. _Liujian:
+
+**(Liu)** J. Liu, D. Li, X. Liu, J. Chem. Phys. 145, 024103 (2016).

doc/utils/sphinx-config/false_positives.txt

@@ -1621,6 +1621,7 @@ Izumi
 Izvekov
 izz
 Izz
+Jacobian
 Jacobsen
 Jadhao
 Jadhav
@@ -2027,6 +2028,7 @@ Marchetti
 Marchi
 Mariella
 Marinica
+Markland
 Marrink
 Marroquin
 Marsaglia
@@ -3595,6 +3597,7 @@ THz
 Tigran
 Tij
 Tildesley
+Timan
 timeI
 timespan
 timestamp
@@ -4091,4 +4094,5 @@ zu
 zx
 zy
 Zybin
+Zykova
 zz

examples/PACKAGES/pimd/lj/data.metalnpt01

@@ -0,0 +1,422 @@
+LAMMPS data file via write_data, version 8 Feb 2023, timestep = 100000
+
+200 atoms
+1 atom types
+
+-11.876696863105703 11.876696863105703 xlo xhi
+-11.876696863105703 11.876696863105703 ylo yhi
+-11.876696863105703 11.876696863105703 zlo zhi
+
+Masses
+
+1 39.948
+
+Pair Coeffs # lj/cut
+
+1 0.00965188 3.4
+
+Atoms # atomic
+
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examples/PACKAGES/pimd/lj/data.metalnpt02

@@ -0,0 +1,422 @@
+LAMMPS data file via write_data, version 8 Feb 2023, timestep = 100000
+
+200 atoms
+1 atom types
+
+-11.876696863105703 11.876696863105703 xlo xhi
+-11.876696863105703 11.876696863105703 ylo yhi
+-11.876696863105703 11.876696863105703 zlo zhi
+
+Masses
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+1 39.948
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+Pair Coeffs # lj/cut
+
+1 0.00965188 3.4
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+Atoms # atomic
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examples/PACKAGES/pimd/lj/data.metalnpt03

@@ -0,0 +1,422 @@
+LAMMPS data file via write_data, version 8 Feb 2023, timestep = 100000
+
+200 atoms
+1 atom types
+
+-11.876696863105703 11.876696863105703 xlo xhi
+-11.876696863105703 11.876696863105703 ylo yhi
+-11.876696863105703 11.876696863105703 zlo zhi
+
+Masses
+
+1 39.948
+
+Pair Coeffs # lj/cut
+
+1 0.00965188 3.4
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+Atoms # atomic
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examples/PACKAGES/pimd/lj/data.metalnpt04

@@ -0,0 +1,422 @@
+LAMMPS data file via write_data, version 8 Feb 2023, timestep = 100000
+
+200 atoms
+1 atom types
+
+-11.876696863105703 11.876696863105703 xlo xhi
+-11.876696863105703 11.876696863105703 ylo yhi
+-11.876696863105703 11.876696863105703 zlo zhi
+
+Masses
+
+1 39.948
+
+Pair Coeffs # lj/cut
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+1 0.00965188 3.4
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+Atoms # atomic
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+171 -1.3488599922862394 -0.40015537573335275 5.541824987776105
+94 2.7016234671889183 -4.500360725821148 -0.3771036206116729
+41 0.040051409073174504 1.3144504850460685 -2.628956804481983
+141 0.8101589418958534 -0.40901282998394567 2.3777914588666906
+159 -2.168905163137191 -3.9077440516609387 3.1238186982134213

examples/PACKAGES/pimd/lj/in.lmp

@@ -0,0 +1,28 @@
+variable ibead uloop 99 pad
+
+units metal
+atom_style atomic
+atom_modify map yes
+boundary p p p
+pair_style lj/cut 9.5251
+read_data data.metalnpt${ibead}
+
+pair_coeff    * * 0.00965188 3.4
+pair_modify shift yes
+
+mass 1 39.948
+
+timestep 0.001
+
+velocity all create 0.0 ${ibead}
+
+fix 1 all pimd/langevin ensemble npt integrator obabo thermostat PILE_L 1234 tau 1.0 temp 113.15 iso 1.0 barostat BZP taup 1.0 fixcom no
+
+thermo_style custom step temp f_1[*] vol press
+thermo 100
+thermo_modify norm no format line "%d %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f"
+
+dump dcd all custom 100 ${ibead}.xyz id type xu yu zu vx vy vz ix iy iz fx fy fz
+dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f"
+
+run 1000

examples/PACKAGES/pimd/lj/run.sh

@@ -0,0 +1 @@
+mpirun -np 4 $LMP -in in.lmp -p 4x1 -log log -screen screen

examples/PACKAGES/pimd/lj_reduced_units/data.lj01

@@ -0,0 +1,219 @@
+LAMMPS data file via write_data, version 8 Feb 2023, timestep = 2000
+
+200 atoms
+1 atom types
+
+-3.4945130603740377 3.4945130603740377 xlo xhi
+-3.4945130603740377 3.4945130603740377 ylo yhi
+-3.4945130603740377 3.4945130603740377 zlo zhi
+
+Masses
+
+1 1
+
+Pair Coeffs # lj/cut
+
+1 1 1
+
+Atoms # atomic
+
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+169 1 2.1185477137097575 2.27540363851787 2.3296903855745934 0 0 0

examples/PACKAGES/pimd/lj_reduced_units/data.lj02

@@ -0,0 +1,219 @@
+LAMMPS data file via write_data, version 8 Feb 2023, timestep = 8000
+
+200 atoms
+1 atom types
+
+-3.4945130603740377 3.4945130603740377 xlo xhi
+-3.4945130603740377 3.4945130603740377 ylo yhi
+-3.4945130603740377 3.4945130603740377 zlo zhi
+
+Masses
+
+1 1
+
+Pair Coeffs # lj/cut
+
+1 1 1
+
+Atoms # atomic
+
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examples/PACKAGES/pimd/lj_reduced_units/in.lmp

@@ -0,0 +1,26 @@
+variable ibead uloop 32 pad
+
+units lj
+atom_style atomic
+atom_modify map yes
+boundary p p p
+pair_style lj/cut 2.8015
+read_data data.lj${ibead}
+
+pair_coeff    * * 1.0 1.0
+pair_modify shift yes
+
+mass 1 1.0
+
+timestep 0.00044905847
+
+fix 1 all pimd/langevin ensemble nvt integrator obabo temp 1.00888 lj 0.00965188 3.4 39.948 4.135667403e-3 1.03646168908e-4 thermostat PILE_L ${ibead}
+
+thermo_style custom step temp f_1[*] vol press
+thermo 100
+thermo_modify norm no format line "%d %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f %.16f"
+
+dump dcd all custom 1 ${ibead}.xyz id type x y z vx vy vz ix iy iz fx fy fz
+dump_modify dcd sort id format line "%d %d %.16f %.16f %.16f %.16f %.16f %.16f %d %d %d %.16f %.16f %.16f"
+
+run 1000

examples/PACKAGES/pimd/lj_reduced_units/run.sh

@@ -0,0 +1 @@
+mpirun -np 2 $LMP -in in.lmp -p 2x1 -log log -screen screen

src/.gitignore

@@ -1549,6 +1549,10 @@
 /fix_langevin_drude.h
 /fix_mol_swap.cpp
 /fix_mol_swap.h
+/fix_pimd.cpp
+/fix_pimd.h
+/fix_pimd_langevin.cpp
+/fix_pimd_langevin.h
 /fix_alchemy.cpp
 /fix_alchemy.h
 /fix_pimd_nvt.cpp

src/EXTRA-COMPUTE/compute_stress_mop.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -14,15 +13,21 @@
 
 /*------------------------------------------------------------------------
   Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon)
+  Support for bonds and angles added by : Evangelos Voyiatzis (NovaMechanics)
   --------------------------------------------------------------------------*/
 
 #include "compute_stress_mop.h"
 
+#include "angle.h"
 #include "atom.h"
+#include "atom_vec.h"
+#include "bond.h"
+#include "comm.h"
 #include "domain.h"
 #include "error.h"
 #include "force.h"
 #include "memory.h"
+#include "molecule.h"
 #include "neigh_list.h"
 #include "neighbor.h"
 #include "pair.h"
@@ -33,40 +38,52 @@
 
 using namespace LAMMPS_NS;
 
-enum{X,Y,Z};
+enum { X, Y, Z };
-enum{TOTAL,CONF,KIN};
+enum { TOTAL, CONF, KIN, PAIR, BOND, ANGLE };
-
-#define BIG 1000000000
 
+// clang-format off
 /* ---------------------------------------------------------------------- */
 
 ComputeStressMop::ComputeStressMop(LAMMPS *lmp, int narg, char **arg) :
   Compute(lmp, narg, arg)
 {
-  if (narg < 6) error->all(FLERR,"Illegal compute stress/mop command");
+  if (narg < 6) utils::missing_cmd_args(FLERR, "compute stress/mop", error);
 
-  MPI_Comm_rank(world,&me);
+  bondflag = 0;
+  angleflag = 0;
 
   // set compute mode and direction of plane(s) for pressure calculation
 
-  if (strcmp(arg[3],"x")==0) {
+  if (strcmp(arg[3],"x") == 0) {
     dir = X;
-  } else if (strcmp(arg[3],"y")==0) {
+  } else if (strcmp(arg[3],"y") == 0) {
     dir = Y;
-  } else if (strcmp(arg[3],"z")==0) {
+  } else if (strcmp(arg[3],"z") == 0) {
     dir = Z;
   } else error->all(FLERR,"Illegal compute stress/mop command");
 
   // Position of the plane
 
-  if (strcmp(arg[4],"lower")==0) {
+  if (strcmp(arg[4],"lower") == 0) {
     pos = domain->boxlo[dir];
-  } else if (strcmp(arg[4],"upper")==0) {
+  } else if (strcmp(arg[4],"upper") == 0) {
     pos = domain->boxhi[dir];
-  } else if (strcmp(arg[4],"center")==0) {
+  } else if (strcmp(arg[4],"center") == 0) {
     pos = 0.5*(domain->boxlo[dir]+domain->boxhi[dir]);
   } else pos = utils::numeric(FLERR,arg[4],false,lmp);
 
+  // plane inside the box
+  if ((pos > domain->boxhi[dir]) || (pos < domain->boxlo[dir])) {
+    error->warning(FLERR, "The specified initial plane lies outside of the simulation box");
+    double dx[3] = {0.0, 0.0, 0.0};
+    dx[dir] = pos - 0.5*(domain->boxhi[dir] + domain->boxlo[dir]);
+    domain->minimum_image(dx[0], dx[1], dx[2]);
+    pos = 0.5*(domain->boxhi[dir] + domain->boxlo[dir]) + dx[dir];
+
+    if ((pos > domain->boxhi[dir]) || (pos < domain->boxlo[dir]))
+      error->all(FLERR, "Plane for compute stress/mop is out of bounds");
+  }
+
   if (pos < (domain->boxlo[dir]+domain->prd_half[dir])) {
     pos1 = pos + domain->prd[dir];
   } else {
@@ -96,34 +113,53 @@ ComputeStressMop::ComputeStressMop(LAMMPS *lmp, int narg, char **arg) :
         which[nvalues] = TOTAL;
         nvalues++;
       }
+    } else if (strcmp(arg[iarg],"pair") == 0) {
+      for (i=0; i<3; i++) {
+        which[nvalues] = PAIR;
+        nvalues++;
+      }
+    } else if (strcmp(arg[iarg],"bond") == 0) {
+      for (i=0; i<3; i++) {
+        which[nvalues] = BOND;
+        nvalues++;
+      }
+    } else if (strcmp(arg[iarg],"angle") == 0) {
+      for (i=0; i<3; i++) {
+        which[nvalues] = ANGLE;
+        nvalues++;
+      }
     } else error->all(FLERR, "Illegal compute stress/mop command"); //break;
 
     iarg++;
   }
 
-  // Error check
+  // Error checks
   // 3D only
 
-  if (domain->dimension < 3)
+  if (domain->dimension != 3)
-    error->all(FLERR, "Compute stress/mop incompatible with simulation dimension");
+    error->all(FLERR, "Compute stress/mop requires a 3d system");
 
   // orthogonal simulation box
   if (domain->triclinic != 0)
-    error->all(FLERR, "Compute stress/mop incompatible with triclinic simulation box");
+    error->all(FLERR, "Compute stress/mop is incompatible with triclinic simulation box");
-  // plane inside the box
-  if (pos >domain->boxhi[dir] || pos <domain->boxlo[dir])
-    error->all(FLERR, "Plane for compute stress/mop is out of bounds");
-
 
   // Initialize some variables
 
   values_local = values_global = vector = nullptr;
+  bond_local = nullptr;
+  bond_global = nullptr;
+  angle_local = nullptr;
+  angle_global = nullptr;
 
   // this fix produces a global vector
 
   memory->create(vector,nvalues,"stress/mop:vector");
-  memory->create(values_local,nvalues,"stress/mop/spatial:values_local");
+  memory->create(values_local,nvalues,"stress/mop:values_local");
-  memory->create(values_global,nvalues,"stress/mop/spatial:values_global");
+  memory->create(values_global,nvalues,"stress/mop:values_global");
+  memory->create(bond_local,nvalues,"stress/mop:bond_local");
+  memory->create(bond_global,nvalues,"stress/mop:bond_global");
+  memory->create(angle_local,nvalues,"stress/mop:angle_local");
+  memory->create(angle_global,nvalues,"stress/mop:angle_global");
   size_vector = nvalues;
 
   vector_flag = 1;
@@ -135,11 +171,14 @@ ComputeStressMop::ComputeStressMop(LAMMPS *lmp, int narg, char **arg) :
 
 ComputeStressMop::~ComputeStressMop()
 {
-
+  delete[] which;
-  delete [] which;
 
   memory->destroy(values_local);
   memory->destroy(values_global);
+  memory->destroy(bond_local);
+  memory->destroy(bond_global);
+  memory->destroy(angle_local);
+  memory->destroy(angle_global);
   memory->destroy(vector);
 }
 
@@ -169,31 +208,39 @@ void ComputeStressMop::init()
 
   // Compute stress/mop requires fixed simulation box
   if (domain->box_change_size || domain->box_change_shape || domain->deform_flag)
-    error->all(FLERR, "Compute stress/mop requires a fixed simulation box");
+    error->all(FLERR, "Compute stress/mop requires a fixed size simulation box");
 
   // This compute requires a pair style with pair_single method implemented
 
-  if (force->pair == nullptr)
+  if (!force->pair)
     error->all(FLERR,"No pair style is defined for compute stress/mop");
   if (force->pair->single_enable == 0)
     error->all(FLERR,"Pair style does not support compute stress/mop");
 
-  // Warnings
+  // Errors
 
-  if (me==0) {
+  if (comm->me == 0) {
 
-    //Compute stress/mop only accounts for pair interactions.
+    // issue an error for unimplemented intramolecular potentials or Kspace.
-    // issue a warning if any intramolecular potential or Kspace is defined.
 
-    if (force->bond!=nullptr)
+    if (force->bond) bondflag = 1;
-      error->warning(FLERR,"compute stress/mop does not account for bond potentials");
+    if (force->angle) {
-    if (force->angle!=nullptr)
+      if (force->angle->born_matrix_enable == 0) {
-      error->warning(FLERR,"compute stress/mop does not account for angle potentials");
+        if ((strcmp(force->angle_style, "zero") != 0) && (strcmp(force->angle_style, "none") != 0))
-    if (force->dihedral!=nullptr)
+          error->all(FLERR,"compute stress/mop does not account for angle potentials");
-      error->warning(FLERR,"compute stress/mop does not account for dihedral potentials");
+      } else {
-    if (force->improper!=nullptr)
+         angleflag = 1;
-      error->warning(FLERR,"compute stress/mop does not account for improper potentials");
+      }
-    if (force->kspace!=nullptr)
+    }
+    if (force->dihedral) {
+      if ((strcmp(force->dihedral_style, "zero") != 0) && (strcmp(force->dihedral_style, "none") != 0))
+        error->all(FLERR,"compute stress/mop does not account for dihedral potentials");
+    }
+    if (force->improper) {
+      if ((strcmp(force->improper_style, "zero") != 0) && (strcmp(force->improper_style, "none") != 0))
+        error->all(FLERR,"compute stress/mop does not account for improper potentials");
+    }
+    if (force->kspace)
       error->warning(FLERR,"compute stress/mop does not account for kspace contributions");
   }
 
@@ -221,14 +268,31 @@ void ComputeStressMop::compute_vector()
   compute_pairs();
 
   // sum pressure contributions over all procs
-  MPI_Allreduce(values_local,values_global,nvalues,
+  MPI_Allreduce(values_local,values_global,nvalues,MPI_DOUBLE,MPI_SUM,world);
-                MPI_DOUBLE,MPI_SUM,world);
 
-  int m;
+  if (bondflag) {
-  for (m=0; m<nvalues; m++) {
+    //Compute bond contribution on separate procs
-    vector[m] = values_global[m];
+    compute_bonds();
+  } else {
+    for (int i=0; i<nvalues; i++) bond_local[i] = 0.0;
   }
 
+  // sum bond contribution over all procs
+  MPI_Allreduce(bond_local,bond_global,nvalues,MPI_DOUBLE,MPI_SUM,world);
+
+  if (angleflag) {
+    //Compute angle contribution on separate procs
+    compute_angles();
+  } else {
+    for (int i=0; i<nvalues; i++) angle_local[i] = 0.0;
+  }
+
+  // sum angle contribution over all procs
+  MPI_Allreduce(angle_local,angle_global,nvalues,MPI_DOUBLE,MPI_SUM,world);
+
+  for (int m=0; m<nvalues; m++) {
+    vector[m] = values_global[m] + bond_global[m] + angle_global[m];
+  }
 }
 
 
@@ -280,8 +344,8 @@ void ComputeStressMop::compute_pairs()
   double xj[3];
 
   m = 0;
-  while (m<nvalues) {
+  while (m < nvalues) {
-    if (which[m] == CONF || which[m] == TOTAL) {
+    if ((which[m] == CONF) || (which[m] == TOTAL) || (which[m] == PAIR)) {
 
       //Compute configurational contribution to pressure
       for (ii = 0; ii < inum; ii++) {
@@ -316,47 +380,34 @@ void ComputeStressMop::compute_pairs()
           if (newton_pair || j < nlocal) {
 
             //check if ij pair is across plane, add contribution to pressure
-            if (((xi[dir]>pos) && (xj[dir]<pos)) || ((xi[dir]>pos1) && (xj[dir]<pos1))) {
+            if (((xi[dir] > pos) && (xj[dir] < pos)) || ((xi[dir] > pos1) && (xj[dir] < pos1))) {
-
               pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
-
               values_local[m] += fpair*(xi[0]-xj[0])/area*nktv2p;
               values_local[m+1] += fpair*(xi[1]-xj[1])/area*nktv2p;
               values_local[m+2] += fpair*(xi[2]-xj[2])/area*nktv2p;
-            }
+            } else if (((xi[dir] < pos) && (xj[dir] > pos)) || ((xi[dir] < pos1) && (xj[dir] > pos1))) {
-            else if (((xi[dir]<pos) && (xj[dir]>pos)) || ((xi[dir]<pos1) && (xj[dir]>pos1))) {
-
               pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
-
               values_local[m] -= fpair*(xi[0]-xj[0])/area*nktv2p;
               values_local[m+1] -= fpair*(xi[1]-xj[1])/area*nktv2p;
               values_local[m+2] -= fpair*(xi[2]-xj[2])/area*nktv2p;
             }
-
           } else {
-
+            if (((xi[dir] > pos) && (xj[dir] < pos)) || ((xi[dir] > pos1) && (xj[dir] < pos1))) {
-            if (((xi[dir]>pos) && (xj[dir]<pos)) || ((xi[dir]>pos1) && (xj[dir]<pos1))) {
-
               pair->single(i,j,itype,jtype,rsq,factor_coul,factor_lj,fpair);
-
               values_local[m] += fpair*(xi[0]-xj[0])/area*nktv2p;
               values_local[m+1] += fpair*(xi[1]-xj[1])/area*nktv2p;
               values_local[m+2] += fpair*(xi[2]-xj[2])/area*nktv2p;
             }
-
           }
-
         }
-
       }
-
     }
 
 
     // Compute kinetic contribution to pressure
     // counts local particles transfers across the plane
 
-    if (which[m] == KIN || which[m] == TOTAL) {
+    if ((which[m] == KIN) || (which[m] == TOTAL)) {
       double sgn;
 
       for (int i = 0; i < nlocal; i++) {
@@ -383,13 +434,13 @@ void ComputeStressMop::compute_pairs()
 
           //coordinates at t-dt (based on Velocity-Verlet alg.)
           if (rmass) {
-            xj[0] = xi[0]-vi[0]*dt+fi[0]/2/rmass[i]*dt*dt*ftm2v;
+            xj[0] = xi[0]-vi[0]*dt+fi[0]/2.0/rmass[i]*dt*dt*ftm2v;
-            xj[1] = xi[1]-vi[1]*dt+fi[1]/2/rmass[i]*dt*dt*ftm2v;
+            xj[1] = xi[1]-vi[1]*dt+fi[1]/2.0/rmass[i]*dt*dt*ftm2v;
-            xj[2] = xi[2]-vi[2]*dt+fi[2]/2/rmass[i]*dt*dt*ftm2v;
+            xj[2] = xi[2]-vi[2]*dt+fi[2]/2.0/rmass[i]*dt*dt*ftm2v;
           } else {
-            xj[0] = xi[0]-vi[0]*dt+fi[0]/2/mass[itype]*dt*dt*ftm2v;
+            xj[0] = xi[0]-vi[0]*dt+fi[0]/2.0/mass[itype]*dt*dt*ftm2v;
-            xj[1] = xi[1]-vi[1]*dt+fi[1]/2/mass[itype]*dt*dt*ftm2v;
+            xj[1] = xi[1]-vi[1]*dt+fi[1]/2.0/mass[itype]*dt*dt*ftm2v;
-            xj[2] = xi[2]-vi[2]*dt+fi[2]/2/mass[itype]*dt*dt*ftm2v;
+            xj[2] = xi[2]-vi[2]*dt+fi[2]/2.0/mass[itype]*dt*dt*ftm2v;
           }
 
           // because LAMMPS does not put atoms back in the box
@@ -399,21 +450,21 @@ void ComputeStressMop::compute_pairs()
           double pos_temp = pos+copysign(1.0,domain->prd_half[dir]-pos)*domain->prd[dir];
           if (fabs(xi[dir]-pos)<fabs(xi[dir]-pos_temp)) pos_temp = pos;
 
-          if (((xi[dir]-pos_temp)*(xj[dir]-pos_temp)<0)) {
+          if (((xi[dir]-pos_temp)*(xj[dir]-pos_temp)) < 0) {
 
-            //sgn = copysign(1.0,vi[dir]-vcm[dir]);
+            // sgn = copysign(1.0,vi[dir]-vcm[dir]);
             sgn = copysign(1.0,vi[dir]);
 
-            //approximate crossing velocity by v(t-dt/2) (based on Velocity-Verlet alg.)
+            // approximate crossing velocity by v(t-dt/2) (based on Velocity-Verlet alg.)
             double vcross[3];
             if (rmass) {
-              vcross[0] = vi[0]-fi[0]/rmass[i]/2*ftm2v*dt;
+              vcross[0] = vi[0]-fi[0]/rmass[i]/2.0*ftm2v*dt;
-              vcross[1] = vi[1]-fi[1]/rmass[i]/2*ftm2v*dt;
+              vcross[1] = vi[1]-fi[1]/rmass[i]/2.0*ftm2v*dt;
-              vcross[2] = vi[2]-fi[2]/rmass[i]/2*ftm2v*dt;
+              vcross[2] = vi[2]-fi[2]/rmass[i]/2.0*ftm2v*dt;
             } else {
-              vcross[0] = vi[0]-fi[0]/mass[itype]/2*ftm2v*dt;
+              vcross[0] = vi[0]-fi[0]/mass[itype]/2.0*ftm2v*dt;
-              vcross[1] = vi[1]-fi[1]/mass[itype]/2*ftm2v*dt;
+              vcross[1] = vi[1]-fi[1]/mass[itype]/2.0*ftm2v*dt;
-              vcross[2] = vi[2]-fi[2]/mass[itype]/2*ftm2v*dt;
+              vcross[2] = vi[2]-fi[2]/mass[itype]/2.0*ftm2v*dt;
             }
 
             values_local[m] += mass[itype]*vcross[0]*sgn/dt/area*nktv2p/ftm2v;
@@ -423,7 +474,288 @@ void ComputeStressMop::compute_pairs()
         }
       }
     }
-    m+=3;
+    m += 3;
   }
 }
 
+/*------------------------------------------------------------------------
+ *   compute bond contribution to pressure of local proc
+ *-------------------------------------------------------------------------*/
+
+void ComputeStressMop::compute_bonds()
+{
+  int i, nb, atom1, atom2, imol, iatom, btype;
+  tagint tagprev;
+  double rsq, fpair;
+
+  double **x = atom->x;
+  tagint *tag = atom->tag;
+  int *num_bond = atom->num_bond;
+  tagint **bond_atom = atom->bond_atom;
+  int **bond_type = atom->bond_type;
+  int *mask = atom->mask;
+
+  int *molindex = atom->molindex;
+  int *molatom = atom->molatom;
+  Molecule **onemols = atom->avec->onemols;
+
+  int nlocal = atom->nlocal;
+  int newton_bond = force->newton_bond;
+  int molecular = atom->molecular;
+
+  Bond *bond = force->bond;
+
+  double dx[3] = {0.0, 0.0, 0.0};
+  double x_bond_1[3] = {0.0, 0.0, 0.0};
+  double x_bond_2[3] = {0.0, 0.0, 0.0};
+  double local_contribution[3] = {0.0, 0.0, 0.0};
+
+  // initialization
+  for (int i = 0; i < nvalues; i++) bond_local[i] = 0.0;
+
+  // loop over all bonded atoms in the current proc
+  for (atom1 = 0; atom1 < nlocal; atom1++) {
+    if (!(mask[atom1] & groupbit)) continue;
+
+    if (molecular == 1)
+      nb = num_bond[atom1];
+    else {
+      if (molindex[atom1] < 0) continue;
+      imol = molindex[atom1];
+      iatom = molatom[atom1];
+      nb = onemols[imol]->num_bond[iatom];
+    }
+
+    for (i = 0; i < nb; i++) {
+      if (molecular == 1) {
+        btype = bond_type[atom1][i];
+        atom2 = atom->map(bond_atom[atom1][i]);
+      } else {
+        tagprev = tag[atom1] - iatom - 1;
+        btype = onemols[imol]->bond_type[iatom][i];
+        atom2 = atom->map(onemols[imol]->bond_atom[iatom][i] + tagprev);
+      }
+
+      if (atom2 < 0 || !(mask[atom2] & groupbit)) continue;
+      if (newton_bond == 0 && tag[atom1] > tag[atom2]) continue;
+      if (btype <= 0) continue;
+
+      // minimum image of atom1 with respect to the plane of interest
+      dx[0] = x[atom1][0];
+      dx[1] = x[atom1][1];
+      dx[2] = x[atom1][2];
+      dx[dir] -= pos;
+      domain->minimum_image(dx[0], dx[1], dx[2]);
+      x_bond_1[0] = dx[0];
+      x_bond_1[1] = dx[1];
+      x_bond_1[2] = dx[2];
+      x_bond_1[dir] += pos;
+
+      // minimum image of atom2 with respect to atom1
+      dx[0] = x[atom2][0] - x_bond_1[0];
+      dx[1] = x[atom2][1] - x_bond_1[1];
+      dx[2] = x[atom2][2] - x_bond_1[2];
+      domain->minimum_image(dx[0], dx[1], dx[2]);
+      x_bond_2[0] = x_bond_1[0] + dx[0];
+      x_bond_2[1] = x_bond_1[1] + dx[1];
+      x_bond_2[2] = x_bond_1[2] + dx[2];
+
+      // check if the bond vector crosses the plane of interest
+      double tau = (x_bond_1[dir] - pos) / (x_bond_1[dir] - x_bond_2[dir]);
+      if ((tau <= 1) && (tau >= 0)) {
+        dx[0] = x_bond_1[0] - x_bond_2[0];
+        dx[1] = x_bond_1[1] - x_bond_2[1];
+        dx[2] = x_bond_1[2] - x_bond_2[2];
+        rsq = dx[0] * dx[0] + dx[1] * dx[1] + dx[2] * dx[2];
+        bond->single(btype, rsq, atom1, atom2, fpair);
+
+        double sgn = copysign(1.0, x_bond_1[dir] - pos);
+        local_contribution[0] += sgn*fpair*dx[0]/area*nktv2p;
+        local_contribution[1] += sgn*fpair*dx[1]/area*nktv2p;
+        local_contribution[2] += sgn*fpair*dx[2]/area*nktv2p;
+      }
+    }
+  }
+
+  // loop over the keywords and if necessary add the bond contribution
+  int m = 0;
+  while (m<nvalues) {
+    if (which[m] == CONF || which[m] == TOTAL || which[m] == BOND) {
+      bond_local[m] = local_contribution[0];
+      bond_local[m+1] = local_contribution[1];
+      bond_local[m+2] = local_contribution[2];
+    }
+    m += 3;
+  }
+}
+
+/*------------------------------------------------------------------------
+  compute angle contribution to pressure of local proc
+  -------------------------------------------------------------------------*/
+
+void ComputeStressMop::compute_angles()
+{
+  int na, atom1, atom2, atom3, imol, iatom, atype;
+  tagint tagprev;
+  double r1, r2, cos_theta;
+
+  double **x = atom->x;
+  tagint *tag = atom->tag;
+  int *num_angle = atom->num_angle;
+  tagint **angle_atom1 = atom->angle_atom1;
+  tagint **angle_atom2 = atom->angle_atom2;
+  tagint **angle_atom3 = atom->angle_atom3;
+  int **angle_type = atom->angle_type;
+  int *mask = atom->mask;
+
+  int *molindex = atom->molindex;
+  int *molatom = atom->molatom;
+  Molecule **onemols = atom->avec->onemols;
+
+  int nlocal = atom->nlocal;
+  int molecular = atom->molecular;
+
+  // loop over all atoms and their angles
+
+  Angle *angle = force->angle;
+
+  double duang, du2ang;
+  double dx[3] = {0.0, 0.0, 0.0};
+  double dx_left[3] = {0.0, 0.0, 0.0};
+  double dx_right[3] = {0.0, 0.0, 0.0};
+  double x_angle_left[3] = {0.0, 0.0, 0.0};
+  double x_angle_middle[3] = {0.0, 0.0, 0.0};
+  double x_angle_right[3] = {0.0, 0.0, 0.0};
+  double dcos_theta[3] = {0.0, 0.0, 0.0};
+  double local_contribution[3] = {0.0, 0.0, 0.0};
+
+  // initialization
+  for (int i = 0; i < nvalues; i++) angle_local[i] = 0.0;
+
+  for (atom2 = 0; atom2 < nlocal; atom2++) {
+    if (!(mask[atom2] & groupbit)) continue;
+
+    if (molecular == 1)
+      na = num_angle[atom2];
+    else {
+      if (molindex[atom2] < 0) continue;
+      imol = molindex[atom2];
+      iatom = molatom[atom2];
+      na = onemols[imol]->num_angle[iatom];
+    }
+
+    for (int i = 0; i < na; i++) {
+      if (molecular == 1) {
+        if (tag[atom2] != angle_atom2[atom2][i]) continue;
+        atype = angle_type[atom2][i];
+        atom1 = atom->map(angle_atom1[atom2][i]);
+        atom3 = atom->map(angle_atom3[atom2][i]);
+      } else {
+        if (tag[atom2] != onemols[imol]->angle_atom2[atom2][i]) continue;
+        atype = onemols[imol]->angle_type[atom2][i];
+        tagprev = tag[atom2] - iatom - 1;
+        atom1 = atom->map(onemols[imol]->angle_atom1[atom2][i] + tagprev);
+        atom3 = atom->map(onemols[imol]->angle_atom3[atom2][i] + tagprev);
+      }
+
+      if (atom1 < 0 || !(mask[atom1] & groupbit)) continue;
+      if (atom3 < 0 || !(mask[atom3] & groupbit)) continue;
+      if (atype <= 0) continue;
+
+      // minimum image of atom1 with respect to the plane of interest
+      dx[0] = x[atom1][0];
+      dx[1] = x[atom1][1];
+      dx[2] = x[atom1][2];
+      dx[dir] -= pos;
+      domain->minimum_image(dx[0], dx[1], dx[2]);
+      x_angle_left[0] = dx[0];
+      x_angle_left[1] = dx[1];
+      x_angle_left[2] = dx[2];
+      x_angle_left[dir] += pos;
+      // minimum image of atom2 with respect to atom1
+      dx_left[0] = x[atom2][0] - x_angle_left[0];
+      dx_left[1] = x[atom2][1] - x_angle_left[1];
+      dx_left[2] = x[atom2][2] - x_angle_left[2];
+      domain->minimum_image(dx_left[0], dx_left[1], dx_left[2]);
+      x_angle_middle[0] = x_angle_left[0] + dx_left[0];
+      x_angle_middle[1] = x_angle_left[1] + dx_left[1];
+      x_angle_middle[2] = x_angle_left[2] + dx_left[2];
+
+      // minimum image of atom3 with respect to atom2
+      dx_right[0] = x[atom3][0] - x_angle_middle[0];
+      dx_right[1] = x[atom3][1] - x_angle_middle[1];
+      dx_right[2] = x[atom3][2] - x_angle_middle[2];
+      domain->minimum_image(dx_right[0], dx_right[1], dx_right[2]);
+      x_angle_right[0] = x_angle_middle[0] + dx_right[0];
+      x_angle_right[1] = x_angle_middle[1] + dx_right[1];
+      x_angle_right[2] = x_angle_middle[2] + dx_right[2];
+
+      // check if any bond vector crosses the plane of interest
+      double tau_right = (x_angle_right[dir] - pos) / (x_angle_right[dir] - x_angle_middle[dir]);
+      double tau_left = (x_angle_middle[dir] - pos) / (x_angle_middle[dir] - x_angle_left[dir]);
+      bool right_cross = ((tau_right >=0) && (tau_right  <= 1));
+      bool left_cross = ((tau_left >=0) && (tau_left <= 1));
+
+      // no bonds crossing the plane
+      if (!right_cross && !left_cross) continue;
+
+      // compute the cos(theta) of the angle
+      r1 = sqrt(dx_left[0]*dx_left[0] + dx_left[1]*dx_left[1] + dx_left[2]*dx_left[2]);
+      r2 = sqrt(dx_right[0]*dx_right[0] + dx_right[1]*dx_right[1] + dx_right[2]*dx_right[2]);
+      cos_theta = -(dx_right[0]*dx_left[0] + dx_right[1]*dx_left[1] + dx_right[2]*dx_left[2])/(r1*r2);
+
+      if (cos_theta >  1.0) cos_theta = 1.0;
+      if (cos_theta < -1.0) cos_theta = -1.0;
+
+      // The method returns derivative with regards to cos(theta)
+      angle->born_matrix(atype, atom1, atom2, atom3, duang, du2ang);
+      // only right bond crossing the plane
+      if (right_cross && !left_cross)
+      {
+        double sgn = copysign(1.0, x_angle_right[dir] - pos);
+        dcos_theta[0] = sgn*(dx_right[0]*cos_theta/r2 + dx_left[0]/r1)/r2;
+        dcos_theta[1] = sgn*(dx_right[1]*cos_theta/r2 + dx_left[1]/r1)/r2;
+        dcos_theta[2] = sgn*(dx_right[2]*cos_theta/r2 + dx_left[2]/r1)/r2;
+      }
+
+      // only left bond crossing the plane
+      if (!right_cross && left_cross)
+      {
+        double sgn = copysign(1.0, x_angle_left[dir] - pos);
+        dcos_theta[0] = -sgn*(dx_left[0]*cos_theta/r1 + dx_right[0]/r2)/r1;
+        dcos_theta[1] = -sgn*(dx_left[1]*cos_theta/r1 + dx_right[1]/r2)/r1;
+        dcos_theta[2] = -sgn*(dx_left[2]*cos_theta/r1 + dx_right[2]/r2)/r1;
+      }
+
+      // both bonds crossing the plane
+      if (right_cross && left_cross)
+      {
+        // due to right bond
+        double sgn = copysign(1.0, x_angle_middle[dir] - pos);
+        dcos_theta[0] = -sgn*(dx_right[0]*cos_theta/r2 + dx_left[0]/r1)/r2;
+        dcos_theta[1] = -sgn*(dx_right[1]*cos_theta/r2 + dx_left[1]/r1)/r2;
+        dcos_theta[2] = -sgn*(dx_right[2]*cos_theta/r2 + dx_left[2]/r1)/r2;
+
+        // due to left bond
+        dcos_theta[0] += sgn*(dx_left[0]*cos_theta/r1 + dx_right[0]/r2)/r1;
+        dcos_theta[1] += sgn*(dx_left[1]*cos_theta/r1 + dx_right[1]/r2)/r1;
+        dcos_theta[2] += sgn*(dx_left[2]*cos_theta/r1 + dx_right[2]/r2)/r1;
+      }
+
+      // final contribution of the given angle term
+      local_contribution[0] += duang*dcos_theta[0]/area*nktv2p;
+      local_contribution[1] += duang*dcos_theta[1]/area*nktv2p;
+      local_contribution[2] += duang*dcos_theta[2]/area*nktv2p;
+    }
+  }
+  // loop over the keywords and if necessary add the angle contribution
+  int m = 0;
+  while (m < nvalues) {
+    if (which[m] == CONF || which[m] == TOTAL || which[m] == ANGLE) {
+      angle_local[m] = local_contribution[0];
+      angle_local[m+1] = local_contribution[1];
+      angle_local[m+2] = local_contribution[2];
+    }
+    m += 3;
+  }
+}

src/EXTRA-COMPUTE/compute_stress_mop.h

@@ -38,11 +38,17 @@ class ComputeStressMop : public Compute {
 
  private:
   void compute_pairs();
+  void compute_bonds();
+  void compute_angles();
 
-  int me, nvalues, dir;
+  int nvalues, dir;
   int *which;
 
+  int bondflag, angleflag;
+
   double *values_local, *values_global;
+  double *bond_local, *bond_global;
+  double *angle_local, *angle_global;
   double pos, pos1, dt, nktv2p, ftm2v;
   double area;
   class NeighList *list;

src/EXTRA-COMPUTE/compute_stress_mop_profile.cpp

@@ -1,4 +1,3 @@
-// clang-format off
 /* ----------------------------------------------------------------------
    LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
    https://www.lammps.org/, Sandia National Laboratories
@@ -14,47 +13,51 @@
 
 /*------------------------------------------------------------------------
   Contributing Authors : Romain Vermorel (LFCR), Laurent Joly (ULyon)
+  Support for bonds added by : Evangelos Voyiatzis (NovaMechanics)
   --------------------------------------------------------------------------*/
 
 #include "compute_stress_mop_profile.h"
 
 #include "atom.h"
-#include "update.h"
+#include "atom_vec.h"
+#include "bond.h"
+#include "comm.h"
 #include "domain.h"
-#include "neighbor.h"
-#include "force.h"
-#include "pair.h"
-#include "neigh_list.h"
 #include "error.h"
+#include "force.h"
 #include "memory.h"
+#include "molecule.h"
+#include "neigh_list.h"
+#include "neighbor.h"
+#include "pair.h"
+#include "update.h"
 
 #include <cmath>
 #include <cstring>
 
 using namespace LAMMPS_NS;
 
-enum{X,Y,Z};
+enum { X, Y, Z };
-enum{LOWER,CENTER,UPPER,COORD};
+enum { LOWER, CENTER, UPPER, COORD };
-enum{TOTAL,CONF,KIN};
+enum { TOTAL, CONF, KIN, PAIR, BOND };
-
-#define BIG 1000000000
 
+// clang-format off
 /* ---------------------------------------------------------------------- */
 
 ComputeStressMopProfile::ComputeStressMopProfile(LAMMPS *lmp, int narg, char **arg) :
   Compute(lmp, narg, arg)
 {
-  if (narg < 7) error->all(FLERR,"Illegal compute stress/mop/profile command");
+  if (narg < 7) utils::missing_cmd_args(FLERR, "compute stress/mop/profile", error);
 
-  MPI_Comm_rank(world,&me);
+  bondflag = 0;
 
   // set compute mode and direction of plane(s) for pressure calculation
 
-  if (strcmp(arg[3],"x")==0) {
+  if (strcmp(arg[3],"x") == 0) {
     dir = X;
-  } else if (strcmp(arg[3],"y")==0) {
+  } else if (strcmp(arg[3],"y") == 0) {
     dir = Y;
-  } else if (strcmp(arg[3],"z")==0) {
+  } else if (strcmp(arg[3],"z") == 0) {
     dir = Z;
   } else error->all(FLERR,"Illegal compute stress/mop/profile command");
 
@@ -64,8 +67,7 @@ ComputeStressMopProfile::ComputeStressMopProfile(LAMMPS *lmp, int narg, char **a
   else if (strcmp(arg[4],"center") == 0) originflag = CENTER;
   else if (strcmp(arg[4],"upper") == 0) originflag = UPPER;
   else originflag = COORD;
-  if (originflag == COORD)
+  if (originflag == COORD) origin = utils::numeric(FLERR,arg[4],false,lmp);
-    origin = utils::numeric(FLERR,arg[4],false,lmp);
   delta = utils::numeric(FLERR,arg[5],false,lmp);
   invdelta = 1.0/delta;
 
@@ -92,6 +94,16 @@ ComputeStressMopProfile::ComputeStressMopProfile(LAMMPS *lmp, int narg, char **a
         which[nvalues] = TOTAL;
         nvalues++;
       }
+    } else if (strcmp(arg[iarg],"pair") == 0) {
+      for (i=0; i<3; i++) {
+        which[nvalues] = PAIR;
+        nvalues++;
+      }
+    } else if (strcmp(arg[iarg],"bond") == 0) {
+      for (i=0; i<3; i++) {
+        which[nvalues] = BOND;
+        nvalues++;
+      }
     } else error->all(FLERR, "Illegal compute stress/mop/profile command"); //break;
 
     iarg++;
@@ -114,6 +126,9 @@ ComputeStressMopProfile::ComputeStressMopProfile(LAMMPS *lmp, int narg, char **a
   nbins = 0;
   coord = coordp = nullptr;
   values_local = values_global = array = nullptr;
+  bond_local = nullptr;
+  bond_global = nullptr;
+  local_contribution = nullptr;
 
   // bin setup
 
@@ -133,13 +148,15 @@ ComputeStressMopProfile::ComputeStressMopProfile(LAMMPS *lmp, int narg, char **a
 
 ComputeStressMopProfile::~ComputeStressMopProfile()
 {
-
+  delete[] which;
-  delete [] which;
 
   memory->destroy(coord);
   memory->destroy(coordp);
   memory->destroy(values_local);
   memory->destroy(values_global);
+  memory->destroy(bond_local);
+  memory->destroy(bond_global);
+  memory->destroy(local_contribution);
   memory->destroy(array);
 }
 
@@ -147,7 +164,6 @@ ComputeStressMopProfile::~ComputeStressMopProfile()
 
 void ComputeStressMopProfile::init()
 {
-
   // conversion constants
 
   nktv2p = force->nktv2p;
@@ -173,27 +189,30 @@ void ComputeStressMopProfile::init()
 
   //This compute requires a pair style with pair_single method implemented
 
-  if (force->pair == nullptr)
+  if (!force->pair)
     error->all(FLERR,"No pair style is defined for compute stress/mop/profile");
   if (force->pair->single_enable == 0)
     error->all(FLERR,"Pair style does not support compute stress/mop/profile");
 
-  // Warnings
+  // Errors
 
-  if (me==0) {
+  if (comm->me == 0) {
 
     //Compute stress/mop/profile only accounts for pair interactions.
-    // issue a warning if any intramolecular potential or Kspace is defined.
+    // issue an error if any intramolecular potential or Kspace is defined.
 
-    if (force->bond!=nullptr)
+    if (force->bond) bondflag = 1;
-      error->warning(FLERR,"compute stress/mop/profile does not account for bond potentials");
+
-    if (force->angle!=nullptr)
+    if (force->angle)
-      error->warning(FLERR,"compute stress/mop/profile does not account for angle potentials");
+      if ((strcmp(force->angle_style, "zero") != 0) && (strcmp(force->angle_style, "none") != 0))
-    if (force->dihedral!=nullptr)
+        error->all(FLERR,"compute stress/mop/profile does not account for angle potentials");
-      error->warning(FLERR,"compute stress/mop/profile does not account for dihedral potentials");
+    if (force->dihedral)
-    if (force->improper!=nullptr)
+      if ((strcmp(force->dihedral_style, "zero") != 0) && (strcmp(force->dihedral_style, "none") != 0))
-      error->warning(FLERR,"compute stress/mop/profile does not account for improper potentials");
+        error->all(FLERR,"compute stress/mop/profile does not account for dihedral potentials");
-    if (force->kspace!=nullptr)
+    if (force->improper)
+      if ((strcmp(force->improper_style, "zero") != 0) && (strcmp(force->improper_style, "none") != 0))
+        error->all(FLERR,"compute stress/mop/profile does not account for improper potentials");
+    if (force->kspace)
       error->warning(FLERR,"compute stress/mop/profile does not account for kspace contributions");
   }
 
@@ -222,17 +241,29 @@ void ComputeStressMopProfile::compute_array()
   compute_pairs();
 
   // sum pressure contributions over all procs
-  MPI_Allreduce(&values_local[0][0],&values_global[0][0],nbins*nvalues,
+  MPI_Allreduce(&values_local[0][0],&values_global[0][0],nbins*nvalues,MPI_DOUBLE,MPI_SUM,world);
-                MPI_DOUBLE,MPI_SUM,world);
 
-  int ibin,m,mo;
+  if (bondflag) {
-  for (ibin=0; ibin<nbins; ibin++) {
+    //Compute bond contribution on separate procs
+    compute_bonds();
+  } else {
+    for (int m = 0; m < nbins; m++) {
+      for (int i = 0; i < nvalues; i++) {
+        bond_local[m][i] = 0.0;
+      }
+    }
+  }
+
+  // sum bond contribution over all procs
+  MPI_Allreduce(&bond_local[0][0],&bond_global[0][0],nbins*nvalues,MPI_DOUBLE,MPI_SUM,world);
+
+  for (int ibin=0; ibin<nbins; ibin++) {
     array[ibin][0] = coord[ibin][0];
-    mo=1;
 
-    m = 0;
+    int mo = 1;
-    while (m<nvalues) {
+    int m = 0;
-      array[ibin][m+mo] = values_global[ibin][m];
+    while (m < nvalues) {
+      array[ibin][m+mo] = values_global[ibin][m] + bond_global[ibin][m];
       m++;
     }
   }
@@ -289,8 +320,8 @@ void ComputeStressMopProfile::compute_pairs()
   double xj[3];
 
   m = 0;
-  while (m<nvalues) {
+  while (m < nvalues) {
-    if (which[m] == CONF || which[m] == TOTAL) {
+    if ((which[m] == CONF) || (which[m] == TOTAL) || (which[m] == PAIR)) {
 
       // Compute configurational contribution to pressure
 
@@ -377,7 +408,7 @@ void ComputeStressMopProfile::compute_pairs()
     // compute kinetic contribution to pressure
     // counts local particles transfers across the plane
 
-    if (which[m] == KIN || which[m] == TOTAL) {
+    if ((which[m] == KIN) || (which[m] == TOTAL)) {
 
       double sgn;
 
@@ -415,7 +446,7 @@ void ComputeStressMopProfile::compute_pairs()
             xj[2] = xi[2]-vi[2]*dt+fi[2]/2/mass[itype]*dt*dt*ftm2v;
           }
 
-          for (ibin=0;ibin<nbins;ibin++) {
+          for (ibin = 0; ibin < nbins; ibin++) {
             pos = coord[ibin][0];
             pos1 = coordp[ibin][0];
 
@@ -452,6 +483,129 @@ void ComputeStressMopProfile::compute_pairs()
   }
 }
 
+/*------------------------------------------------------------------------
+  compute bond contribution to pressure of local proc
+  -------------------------------------------------------------------------*/
+
+void ComputeStressMopProfile::compute_bonds()
+{
+  int i, nb, atom1, atom2, imol, iatom, btype;
+  tagint tagprev;
+  double rsq, fpair;
+
+  double **x = atom->x;
+  tagint *tag = atom->tag;
+  int *num_bond = atom->num_bond;
+  tagint **bond_atom = atom->bond_atom;
+  int **bond_type = atom->bond_type;
+  int *mask = atom->mask;
+
+  int *molindex = atom->molindex;
+  int *molatom = atom->molatom;
+  Molecule **onemols = atom->avec->onemols;
+
+  int nlocal = atom->nlocal;
+  int newton_bond = force->newton_bond;
+  int molecular = atom->molecular;
+
+  Bond *bond = force->bond;
+
+  double dx[3] = {0.0, 0.0, 0.0};
+  double x_bond_1[3] = {0.0, 0.0, 0.0};
+  double x_bond_2[3] = {0.0, 0.0, 0.0};
+
+  // initialization
+  for (int m = 0; m < nbins; m++) {
+    for (int i = 0; i < nvalues; i++) {
+      bond_local[m][i] = 0.0;
+    }
+    local_contribution[m][0] = 0.0;
+    local_contribution[m][1] = 0.0;
+    local_contribution[m][2] = 0.0;
+  }
+
+  // loop over all bonded atoms in the current proc
+  for (atom1 = 0; atom1 < nlocal; atom1++) {
+    if (!(mask[atom1] & groupbit)) continue;
+
+    if (molecular == 1)
+      nb = num_bond[atom1];
+    else {
+      if (molindex[atom1] < 0) continue;
+      imol = molindex[atom1];
+      iatom = molatom[atom1];
+      nb = onemols[imol]->num_bond[iatom];
+    }
+
+    for (i = 0; i < nb; i++) {
+      if (molecular == 1) {
+        btype = bond_type[atom1][i];
+        atom2 = atom->map(bond_atom[atom1][i]);
+      } else {
+        tagprev = tag[atom1] - iatom - 1;
+        btype = onemols[imol]->bond_type[iatom][i];
+        atom2 = atom->map(onemols[imol]->bond_atom[iatom][i] + tagprev);
+      }
+
+      if (atom2 < 0 || !(mask[atom2] & groupbit)) continue;
+      if (newton_bond == 0 && tag[atom1] > tag[atom2]) continue;
+      if (btype <= 0) continue;
+
+      for (int ibin = 0; ibin<nbins; ibin++) {
+        double pos = coord[ibin][0];
+
+        // minimum image of atom1 with respect to the plane of interest
+        dx[0] = x[atom1][0];
+        dx[1] = x[atom1][1];
+        dx[2] = x[atom1][2];
+        dx[dir] -= pos;
+        domain->minimum_image(dx[0], dx[1], dx[2]);
+        x_bond_1[0] = dx[0];
+        x_bond_1[1] = dx[1];
+        x_bond_1[2] = dx[2];
+        x_bond_1[dir] += pos;
+
+        // minimum image of atom2 with respect to atom1
+        dx[0] = x[atom2][0] - x_bond_1[0];
+        dx[1] = x[atom2][1] - x_bond_1[1];
+        dx[2] = x[atom2][2] - x_bond_1[2];
+        domain->minimum_image(dx[0], dx[1], dx[2]);
+        x_bond_2[0] = x_bond_1[0] + dx[0];
+        x_bond_2[1] = x_bond_1[1] + dx[1];
+        x_bond_2[2] = x_bond_1[2] + dx[2];
+
+        // check if the bond vector crosses the plane of interest
+        double tau = (x_bond_1[dir] - pos) / (x_bond_1[dir] - x_bond_2[dir]);
+        if ((tau <= 1) && (tau >= 0)) {
+          dx[0] = x_bond_1[0] - x_bond_2[0];
+          dx[1] = x_bond_1[1] - x_bond_2[1];
+          dx[2] = x_bond_1[2] - x_bond_2[2];
+          rsq = dx[0] * dx[0] + dx[1] * dx[1] + dx[2] * dx[2];
+          bond->single(btype, rsq, atom1, atom2, fpair);
+
+          double sgn = copysign(1.0, x_bond_1[dir] - pos);
+          local_contribution[ibin][0] += sgn*fpair*dx[0]/area*nktv2p;
+          local_contribution[ibin][1] += sgn*fpair*dx[1]/area*nktv2p;
+          local_contribution[ibin][2] += sgn*fpair*dx[2]/area*nktv2p;
+        }
+      }
+    }
+  }
+
+  // loop over the keywords and if necessary add the bond contribution
+  int m = 0;
+  while (m < nvalues) {
+    if ((which[m] == CONF) || (which[m] == TOTAL) || (which[m] == BOND)) {
+      for (int ibin = 0; ibin < nbins; ibin++) {
+        bond_local[ibin][m] = local_contribution[ibin][0];
+        bond_local[ibin][m+1] = local_contribution[ibin][1];
+        bond_local[ibin][m+2] = local_contribution[ibin][2];
+      }
+    }
+    m += 3;
+  }
+}
+
 /* ----------------------------------------------------------------------
    setup 1d bins and their extent and coordinates
    called at init()
@@ -492,6 +646,9 @@ void ComputeStressMopProfile::setup_bins()
   memory->create(coordp,nbins,1,"stress/mop/profile:coordp");
   memory->create(values_local,nbins,nvalues,"stress/mop/profile:values_local");
   memory->create(values_global,nbins,nvalues,"stress/mop/profile:values_global");
+  memory->create(bond_local,nbins,nvalues,"stress/mop/profile:bond_local");
+  memory->create(bond_global,nbins,nvalues,"stress/mop/profile:bond_global");
+  memory->create(local_contribution,nbins,3,"stress/mop/profile:local_contribution");
 
   // set bin coordinates
   for (i = 0; i < nbins; i++) {

src/EXTRA-COMPUTE/compute_stress_mop_profile.h

@@ -38,16 +38,21 @@ class ComputeStressMopProfile : public Compute {
 
  private:
   void compute_pairs();
+  void compute_bonds();
   void setup_bins();
 
-  int me, nvalues, dir;
+  int nvalues, dir;
   int *which;
 
+  int bondflag;
+
   int originflag;
   double origin, delta, offset, invdelta;
   int nbins;
   double **coord, **coordp;
   double **values_local, **values_global;
+  double **bond_local, **bond_global;
+  double **local_contribution;
 
   double dt, nktv2p, ftm2v;
   double area;

src/REPLICA/fix_pimd_langevin.h

@@ -0,0 +1,186 @@
+/* -*- c++ -*- ----------------------------------------------------------
+   LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
+   https://www.lammps.org/, Sandia National Laboratories
+   LAMMPS development team: developers@lammps.org
+
+   Copyright (2003) Sandia Corporation.  Under the terms of Contract
+   DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
+   certain rights in this software.  This software is distributed under
+   the GNU General Public License.
+
+   See the README file in the top-level LAMMPS directory.
+------------------------------------------------------------------------- */
+
+#ifdef FIX_CLASS
+// clang-format off
+FixStyle(pimd/langevin,FixPIMDLangevin);
+// clang-format on
+#else
+
+#ifndef FIX_PIMD_LANGEVIN_H
+#define FIX_PIMD_LANGEVIN_H
+
+#include "fix.h"
+
+namespace LAMMPS_NS {
+
+class FixPIMDLangevin : public Fix {
+ public:
+  FixPIMDLangevin(class LAMMPS *, int, char **);
+  ~FixPIMDLangevin() override;
+
+  int setmask() override;
+
+  void init() override;
+  void setup(int) override;
+  void post_force(int) override;
+  void initial_integrate(int) override;
+  void final_integrate() override;
+  void end_of_step() override;
+
+  double compute_vector(int) override;
+
+ protected:
+  /* System setting variables */
+  int method;                              // PIMD or NMPIMD or CMD
+  int fmmode;                              // physical or normal
+  int np;                                  // number of beads
+  double inverse_np;                       // 1.0/np
+  double temp;                             // temperature
+  double hbar;                             // Planck's constant
+  double lj_epsilon, lj_sigma, lj_mass;    // LJ unit energy, length, and mass scales
+  double other_planck;
+  double other_mvv2e;
+  double kt;              // k_B * temp
+  double beta, beta_np;    // beta = 1./kBT beta_np = 1./kBT/np
+  int thermostat;          // NHC or PILE_L
+  int barostat;            // BZP
+  int integrator;          // obabo or baoab
+  int ensemble;            // nve or nvt or nph or npt
+  int mapflag;             // should be 1 if number of beads > 1
+  int removecomflag;
+  double masstotal;
+
+  double fixedpoint[3];    // location of dilation fixed-point
+  /* ring-polymer model */
+
+  double omega_np, fbond, spring_energy, sp;
+
+  /* fictitious mass */
+
+  double fmass, *mass;
+
+  /* inter-partition communication */
+
+  MPI_Comm rootworld;
+  int me, nprocs, ireplica, nreplica, nprocs_universe;
+  int ntotal, maxlocal;
+
+  int cmode;
+  int sizeplan;
+  int *plansend, *planrecv;
+
+  tagint *tagsend, *tagrecv;
+  double **bufsend, **bufrecv, **bufbeads;
+  double **bufsorted, **bufsortedall;
+  double **outsorted, **buftransall;
+
+  tagint *tagsendall, *tagrecvall;
+  double **bufsendall, **bufrecvall;
+
+  int *counts, *displacements;
+
+  void comm_init();
+  void inter_replica_comm(double **ptr);
+
+  /* normal-mode operations */
+
+  double *lam, **M_x2xp, **M_xp2x, **M_f2fp, **M_fp2f;
+  int *modeindex;
+
+  void reallocate();
+  void nmpimd_init();
+  void nmpimd_transform(double **, double **, double *);
+
+  /* Langevin integration */
+
+  double dtv, dtf, dtv2, dtv3;
+  double gamma, c1, c2, tau;
+  double *tau_k, *c1_k, *c2_k;
+  double pilescale;
+  double Lan_temp;
+  double r1, r2, r3;
+  double _omega_np, *_omega_k, *Lan_s, *Lan_c;    // sin(omega_k*dt*0.5), cos(omega_k*dt*0.5)
+
+  class RanMars *random;
+
+  int tstat_flag;    // tstat_flat = 1 if thermostat if used
+  void langevin_init();
+  void b_step();    // integrate for dt/2 according to B part (v <- v + f * dt/2)
+  void a_step();    // integrate for dt/2 according to A part (non-centroid mode, harmonic force between replicas)
+  void qc_step();    // integrate for dt/2 for the centroid mode (x <- x + v * dt/2)
+  void o_step();     // integrate for dt according to O part (O-U process, for thermostating)
+
+  /* Bussi-Zykova-Parrinello barostat */
+
+  double f_omega, mtk_term1;
+  int pstat_flag;    // pstat_flag = 1 if barostat is used
+  int pstyle;        // pstyle = ISO or ANISO (will support TRICLINIC in the future)
+  double W, tau_p, Pext, p_hydro, totenthalpy, Vcoeff;
+  int pdim;
+  int p_flag[6];
+  double p_target[6];
+  double vw[6];               // barostat velocity
+  double ke_tensor[6];        // kinetic energy tensor
+  double c_vir_tensor[6];     // centroid-virial tensor
+  double stress_tensor[6];    // path integral centroid-virial stress tensor
+
+  void baro_init();
+  void press_v_step();
+  void press_o_step();
+
+  /* centroid-virial estimator computation */
+  double vol0 = 0.0;
+  double volume;
+  double **xc, *xcall;
+  int maxxc;
+  int maxunwrap;
+  double **x_unwrap;
+  void reallocate_x_unwrap();
+  void reallocate_xc();
+  void collect_xc();
+  void remove_com_motion();
+  double xf, vir, vir_, xcf, centroid_vir;
+  double t_prim, t_vir, t_cv, p_prim, p_vir, p_cv, p_md;
+
+  /* Computes */
+  double kine, pote, tote, totke;
+  double ke_bead, se_bead, pe_bead, pot_energy_partition;
+  double total_spring_energy;
+  char *id_pe;
+  char *id_press;
+  class Compute *c_pe;
+  class Compute *c_press;
+
+  void compute_totke();            // 1: kinetic energy
+  void compute_spring_energy();    // 2: spring elastic energy
+  void compute_pote();             // 3: potential energy
+  void compute_tote();             // 4: total energy: 1+2+3 for all the beads
+  void compute_stress_tensor();
+  void compute_t_prim();
+  void compute_t_vir();
+  void compute_t_cv();
+  void compute_p_prim();
+  void compute_p_cv();    // centroid-virial pressure estimator
+  void compute_vir();
+  void compute_cvir();
+  void compute_totenthalpy();
+
+  void write_restart(FILE *fp) override;
+  int size_restart_global();
+  int pack_restart_data(double *list);
+  void restart(char *buf) override;
+};
+}    // namespace LAMMPS_NS
+#endif
+#endif

src/REPLICA/fix_pimd_nvt.cpp

@@ -219,7 +219,7 @@ void FixPIMDNVT::init()
   const double Boltzmann = force->boltz;
   const double Plank = force->hplanck;
 
-  double hbar = Plank / (2.0 * MY_PI);
+  double hbar = Plank / (2.0 * MY_PI) * sp;
   double beta = 1.0 / (Boltzmann * nhc_temp);
   double _fbond = 1.0 * np / (beta * beta * hbar * hbar);
 

src/domain.cpp

@@ -1432,6 +1432,29 @@ void Domain::remap_near(double *xnew, double *xold)
   if (triclinic) lamda2x(coordnew,xnew);
 }
 
+/* ----------------------------------------------------------------------
+   remap the point to specific image flags
+   x overwritten with result, reset image flag
+   for triclinic, use h[] to add in tilt factors in other dims as needed
+------------------------------------------------------------------------- */
+
+void Domain::unmap_inv(double *x, imageint image)
+{
+  int xbox = (image & IMGMASK) - IMGMAX;
+  int ybox = (image >> IMGBITS & IMGMASK) - IMGMAX;
+  int zbox = (image >> IMG2BITS) - IMGMAX;
+
+  if (triclinic == 0) {
+    x[0] -= xbox*xprd;
+    x[1] -= ybox*yprd;
+    x[2] -= zbox*zprd;
+  } else {
+    x[0] -= h[0]*xbox + h[5]*ybox + h[4]*zbox;
+    x[1] -= h[1]*ybox + h[3]*zbox;
+    x[2] -= h[2]*zbox;
+  }
+}
+
 /* ----------------------------------------------------------------------
    unmap the point via image flags
    x overwritten with result, don't reset image flag

src/domain.h

@@ -125,6 +125,7 @@ class Domain : protected Pointers {
   void remap(double *, imageint &);
   void remap(double *);
   void remap_near(double *, double *);
+  void unmap_inv(double *x, imageint);
   void unmap(double *, imageint);
   void unmap(const double *, imageint, double *);
   void image_flip(int, int, int);

unittest/commands/test_compute_global.cpp

@@ -169,7 +169,7 @@ TEST_F(ComputeGlobalTest, Geometry)
         command("compute mom1 all momentum");
         command("compute mom2 allwater momentum");
         command("compute mop1 all stress/mop x 0.0 total");
-        command("compute mop2 all stress/mop/profile z lower 0.5 kin conf");
+        command("compute mop2 all stress/mop/profile z lower 0.5 kin pair");
         thermo_style += " c_mu1 c_mu2 c_mop1[*] c_mop2[1][1]";
     }
 
@@ -225,9 +225,9 @@ TEST_F(ComputeGlobalTest, Geometry)
         EXPECT_DOUBLE_EQ(mom2[0], -0.022332069630161717);
         EXPECT_DOUBLE_EQ(mom2[1], -0.056896553865696115);
         EXPECT_DOUBLE_EQ(mom2[2], 0.069179891052881484);
-        EXPECT_DOUBLE_EQ(mop1[0], 3522311.3572200728);
+        EXPECT_DOUBLE_EQ(mop1[0], 3536584.0880458541);
-        EXPECT_DOUBLE_EQ(mop1[1], 2871104.9055934539);
+        EXPECT_DOUBLE_EQ(mop1[1], 2887485.033995091);
-        EXPECT_DOUBLE_EQ(mop1[2], -4136077.5224247416);
+        EXPECT_DOUBLE_EQ(mop1[2], -4154145.8952306858);
         EXPECT_DOUBLE_EQ(mop2[0][0], -8.0869239999999998);
         EXPECT_DOUBLE_EQ(mop2[0][1], 0.0);
         EXPECT_DOUBLE_EQ(mop2[0][2], 0.0);