doc pages and sync qm vs qmmm fixes
This commit is contained in:
Steve Plimpton
@ -13,7 +13,7 @@ Syntax
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* mdi/qm = style name of this fix command
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* zero or more keyword/value pairs may be appended
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* keyword = *virial* or *add* or *every* or *connect* or *elements*
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* keyword = *virial* or *add* or *every* or *connect* or *elements* or *mc*
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.. parsed-literal::
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@ -29,7 +29,9 @@ Syntax
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yes = perform a one-time connection to the MDI engine code
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no = do not perform the connection operation
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*elements* args = N_1 N_2 ... N_ntypes
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N_1,N_2,...N_ntypes = atomic number for each of ntypes LAMMPS atom types
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N_1,N_2,...N_ntypes = chemical symbol for each of ntypes LAMMPS atom types
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*mc* args = mcfixID
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mcfixID = ID of a Monte Carlo fix designed to work with this fix
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Examples
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""""""""
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@ -38,7 +40,7 @@ Examples
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fix 1 all mdi/qm
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fix 1 all mdi/qm virial yes
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fix 1 all mdi/qm add no every 100 elements 13 29
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fix 1 all mdi/qm add no every 100 elements C C H O
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Description
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"""""""""""
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@ -57,12 +59,25 @@ The server code must support use of the `MDI Library
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<https://molssi-mdi.github.io/MDI_Library/html/index.html>`_ as
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explained below.
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Typically, to use this fix, the input script should not define any
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other classical force field components, e.g. a pair style, bond style,
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etc.
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These are example use cases for this fix, discussed further below:
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* perform an ab initio MD (AIMD) simulation with quantum forces
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* perform an energy minimization with quantum forces
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* perform a nudged elastic band (NEB) calculation with quantum forces
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* perform a QM calculation for a series of independent systems which LAMMPS reads or generates
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* perform a QM calculation for a series of independent systems which LAMMPS reads or generates once
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* run a classical MD simulation and calculate QM energy/forces once every N steps on the current configuration
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More generally any command which calulates per-atom forces can instead
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use quantum forces be defining this fix. Examples are the Monte Carlo
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commands :doc:`fix gcmc <fix_gcmc>` and :doc:`fix atom/swap
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<fix_atom_swap>`, as well as the :doc:`compute born <compute_born>`
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command. The only requirement is that internally the commmand invokes
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the post_force() method of fixes such as this one, which will trigger
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the quantum calculation.
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The code coupling performed by this command is done via the `MDI
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Library <https://molssi-mdi.github.io/MDI_Library/html/index.html>`_.
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@ -80,19 +95,23 @@ to launch two codes so that they communicate via the MDI library using
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either MPI or sockets. Any QM code that supports MDI could be used in
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place of LAMMPS acting as a QM surrogate. See the :doc:`Howto mdi
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<Howto_mdi>` page for a current list (March 2022) of such QM codes.
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The examples/QUANTUM directory has examples for coupling LAMMPS to 3
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QM codes either via this fix or the :doc:`fix mdi/qmmm <fix_mdi_qmmm>`
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command.
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Note that an engine code can support MDI in either or both of two
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modes. It can be used as a stand-alone code, launched at the same
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time as LAMMPS. Or it can be used as a plugin library, which LAMMPS
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loads. See the :doc:`mdi plugin <mdi>` command for how to trigger
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LAMMPS to load a plugin library. The examples/mdi/README file
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explains how to launch the two codes in either mode.
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LAMMPS to load a plugin library. The examples/mdi/README file and
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examples/QUANTUM/QM-code/README files explain how to launch the two
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codes in either mode.
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----------
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The *virial* keyword setting of yes or no determines whether
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LAMMPS will request the QM code to also compute and return
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a 6-element symmetric virial tensor for the system.
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The *virial* keyword setting of yes or no determines whether LAMMPS
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will request the QM code to also compute and return a symmetric virial
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tensor for the system.
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The *add* keyword setting of *yes* or *no* determines whether the
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energy and forces and virial returned by the QM code will be added to
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@ -109,25 +128,27 @@ commands. See details below.
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The *every* keyword determines how often the QM code will be invoked
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during a dynamics run with the current LAMMPS simulation box and
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configuration of atoms. The QM code will be called once every
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*Nevery* timesteps.
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*Nevery* timesteps. By default *Nevery* = 1.
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The *connect* keyword determines whether this fix performs a one-time
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connection to the QM code. The default is *yes*. The only time a
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*no* is needed is if this command is used multiple times in an input
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script. E.g. if it used inside a loop which also uses the :doc:`clear
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<clear>` command to destroy the system (including any defined fixes).
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See the examples/mdi/in.series.driver script as an example of this,
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where LAMMPS is using the QM code to compute energy and forces for a
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series of system configurations. In this use case *connect no*
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is used along with the :doc:`mdi connect and exit <mdi>` command
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to one-time initiate/terminate the connection outside the loop.
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script and the MDI coupling is between two stand-alone codes (not
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plugin mode). E.g. if it used inside a loop which also uses the
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:doc:`clear <clear>` command to destroy the system (including this
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fix). See the examples/mdi/in.series.driver script as an example of
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this, where LAMMPS is using the QM code to compute energy and forces
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for a series of system configurations. In this use case *connect no*
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is used along with the :doc:`mdi connect and exit <mdi>` command to
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one-time initiate/terminate the connection outside the loop.
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The *elements* keyword allows specification of what element each
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LAMMPS atom type corresponds to. This is specified by the atomic
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number of the element, e.g. 13 for Al. An atomic number must be
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specified for each of the ntypes LAMMPS atom types. Ntypes is
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typically specified via the create_box command or in the data file
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read by the read_data command.
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LAMMPS atom type corresponds to. This is specified by the chemical
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symbol of the element, e.g. C or Al or Si. A symbol must be specified
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for each of the ntypes LAMMPS atom types. Multiple LAMMPS types can
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represent the same element. Ntypes is typically specified via the
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:doc:`create_box <create_box>` command or in the data file read by the
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:doc:`read_data <read_data>` command.
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If this keyword is specified, then this fix will send the MDI
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">ELEMENTS" command to the engine, to ensure the two codes are
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@ -136,6 +157,14 @@ not specified, then this fix will send the MDI >TYPES command to the
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engine. This is fine if both the LAMMPS driver and the MDI engine are
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initialized so that the atom type values are consistent in both codes.
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The *mc* keyword enables this fix to be used with a Monte Carlo (MC)
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fix to calculate before/after quantum energies as part of the MC
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accept/reject criterion. The :doc:`fix gcmc <fix_gcmc>` and :doc:`fix
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atom/swap <fix_atom_swap>` commands can be used in this manner.
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Specify the ID of the MC fix following the *mc* keyword. This allows
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the two fixes to coordinate when MC events are being calculated versus
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MD timesteps between the MC events.
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----------
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The following 3 example use cases are illustrated in the examples/mdi
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@ -265,7 +294,8 @@ unit conversions between LAMMPS and MDI units. The other code will
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also perform similar unit conversions into its preferred units.
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LAMMPS can also be used as an MDI driver in other unit choices it
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supports, e.g. *lj*, but then no unit conversion is performed.
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supports, e.g. *lj*, but then no unit conversion to MDI units is
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performed.
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Related commands
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""""""""""""""""
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@ -1,6 +1,6 @@
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.. index:: fix mdi/qm
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.. index:: fix mdi/qmmm
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fix mdi/qm command
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fix mdi/qmmm command
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======================
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Syntax
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@ -11,7 +11,7 @@ Syntax
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fix ID group-ID mdi/qmmm mode keyword value(s) keyword value(s) ...
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* ID, group-ID are documented in :doc:`fix <fix>` command
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* mdi/qm = style name of this fix command
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* mdi/qmmm = style name of this fix command
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* mode = *direct* or *potential*
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* zero or more keyword/value pairs may be appended
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* keyword = *virial* or *add* or *every* or *connect* or *elements*
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@ -25,7 +25,7 @@ Syntax
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yes = perform a one-time connection to the MDI engine code
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no = do not perform the connection operation
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*elements* args = N_1 N_2 ... N_ntypes
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N_1,N_2,...N_ntypes = atomic number for each of ntypes LAMMPS atom types
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N_1,N_2,...N_ntypes = chemical symbol for each of ntypes LAMMPS atom types
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Examples
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""""""""
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@ -40,14 +40,29 @@ Description
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"""""""""""
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This command enables LAMMPS to act as a client with another server
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code to perform a couple QMMM (quantum-mechanics molecular-mechanics)
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simulation. LAMMPS will perform classical MD (molecular-mechnanics)
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for the (typically larger) MM portion of the system. A quantum
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mechanics code will calculate quantum effects for the QM portion of
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the system. The QM server code must support use of the `MDI Library
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code to perform a coupled QMMM (quantum-mechanics/molecular-mechanics)
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simulation. LAMMPS will perform classical MD (molecular-mechnanics
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or MM) for the (typically larger) MM portion of the system. A quantum
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mechanics code will calculate quantum energy and forces for the QM
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portion of the system. The two codes work together to calculate the
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energy and forces due to the cross interactions between QM and MM
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atoms. The QM server code must support use of the `MDI Library
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<https://molssi-mdi.github.io/MDI_Library/html/index.html>`_ as
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explained below.
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The partitioning of the system between QM and MM atoms is determined
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by the specified group. Atoms in that group are QM atoms; the remaining
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atoms are MM atoms. The input script should
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need to remove bonds/etc between QM atoms
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currently no bonds between QM/MM atoms are allowed
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need to be able to compute Coulomb only portion of the force
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field in a pair style, use hybrid
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must be a charged system
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explain the 2 algs: DIRECT and POTENTIAL
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The code coupling performed by this command is done via the `MDI
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Library <https://molssi-mdi.github.io/MDI_Library/html/index.html>`_.
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LAMMPS runs as an MDI driver (client), and sends MDI commands to an
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@ -56,11 +71,6 @@ support for MDI. See the :doc:`Howto mdi <Howto_mdi>` page for more
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information about how LAMMPS can operate as either an MDI driver or
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engine.
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Q: provide an example where LAMMPS is also the QM code ?
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similar to fix mdi/qm ?
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The examples/mdi directory contains input scripts using this fix in
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the various use cases discussed below. In each case, two instances of
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LAMMPS are used, once as an MDI driver, once as an MDI engine
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@ -79,6 +89,8 @@ explains how to launch the two codes in either mode.
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----------
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----------
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The *virial* keyword setting of yes or no determines whether
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LAMMPS will request the QM code to also compute and return
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a 6-element symmetric virial tensor for the system.
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@ -87,19 +99,20 @@ The *connect* keyword determines whether this fix performs a one-time
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connection to the QM code. The default is *yes*. The only time a
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*no* is needed is if this command is used multiple times in an input
|
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script. E.g. if it used inside a loop which also uses the :doc:`clear
|
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<clear>` command to destroy the system (including any defined fixes).
|
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See the examples/mdi/in.series.driver script as an example of this,
|
||||
where LAMMPS is using the QM code to compute energy and forces for a
|
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series of system configurations. In this use case *connect no*
|
||||
is used along with the :doc:`mdi connect and exit <mdi>` command
|
||||
to one-time initiate/terminate the connection outside the loop.
|
||||
<clear>` command to destroy the system (including this fix). As
|
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example would be a script which loop over a series of independent QMMM
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simulations, e.g. each with their own data file. In this use case
|
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*connect no* could be used along with the :doc:`mdi connect and exit
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<mdi>` command to one-time initiate/terminate the connection outside
|
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the loop.
|
||||
|
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The *elements* keyword allows specification of what element each
|
||||
LAMMPS atom type corresponds to. This is specified by the atomic
|
||||
number of the element, e.g. 13 for Al. An atomic number must be
|
||||
specified for each of the ntypes LAMMPS atom types. Ntypes is
|
||||
typically specified via the create_box command or in the data file
|
||||
read by the read_data command.
|
||||
LAMMPS atom type corresponds to. This is specified by the chemical
|
||||
symbol of the element, e.g. C or Al or Si. A symbol must be specified
|
||||
for each of the ntypes LAMMPS atom types. Multiple LAMMPS types can
|
||||
represent the same element. Ntypes is typically specified via the
|
||||
:doc:`create_box <create_box>` command or in the data file read by the
|
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:doc:`read_data <read_data>` command.
|
||||
|
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If this keyword is specified, then this fix will send the MDI
|
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">ELEMENTS" command to the engine, to insure the two codes are
|
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@ -236,9 +249,6 @@ used to specify *real* or *metal* units. This will ensure the correct
|
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unit conversions between LAMMPS and MDI units. The other code will
|
||||
also perform similar unit conversions into its preferred units.
|
||||
|
||||
LAMMPS can also be used as an MDI driver in other unit choices it
|
||||
supports, e.g. *lj*, but then no unit conversion is performed.
|
||||
|
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Related commands
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""""""""""""""""
|
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|
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@ -56,4 +56,4 @@ thermo_style custom step cpu temp ke evdwl ecoul epair emol elong &
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f_2 pe etotal press
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thermo 1
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run 2
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run 10
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@ -60,4 +60,4 @@ variable p equal extract_setting(world_size)
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mdi plugin nwchem_mdi mdi "-role ENGINE -name NWChem -method LINK" &
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extra "template.water.nw water.nw log.water.pwdft.qmmm.plugin.$p" &
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command "run 1"
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command "run 10"
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File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@ -94,7 +94,7 @@ fix_modify 2 energy yes
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thermo_style custom step cpu temp ke evdwl ecoul epair emol elong f_2 pe etotal press
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thermo 1
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run 2
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run 10
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Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update: every = 1 steps, delay = 0 steps, check = yes
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@ -115,24 +115,32 @@ Neighbor list info ...
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 7.445 | 7.445 | 7.445 Mbytes
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Step CPU Temp KinEng E_vdwl E_coul E_pair E_mol E_long f_2 PotEng TotEng Press
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0 0 0 0 0.95937448 -170.68735 -169.72797 3.3962859 0 -10627.878 -10794.209 -10794.209 -374.81058
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1 1.3827511 1.1713705 0.017458165 0.95934217 -170.68987 -169.73053 3.3804649 0 -10627.878 -10794.229 -10794.211 -376.91596
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2 4.3658207 4.6633575 0.069502914 0.95924532 -170.70698 -169.74773 3.3333254 0 -10627.871 -10794.286 -10794.216 -383.31463
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Loop time of 4.36586 on 1 procs for 2 steps with 6 atoms
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0 0 0 0 0.95937448 -170.68735 -169.72798 3.3962859 0 -10627.878 -10794.209 -10794.209 -374.81058
|
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1 1.3998539 1.1713705 0.017458165 0.95934217 -170.68987 -169.73053 3.3804649 0 -10627.878 -10794.229 -10794.211 -376.91596
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2 4.2727994 4.6633575 0.069502914 0.95924532 -170.70698 -169.74773 3.3333254 0 -10627.871 -10794.286 -10794.216 -383.31463
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3 8.6537003 10.410148 0.15515337 0.95908482 -170.73725 -169.77816 3.2558316 0 -10627.857 -10794.38 -10794.224 -393.99
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4 14.050859 18.303344 0.27279397 0.95886179 -170.78053 -169.82167 3.1495694 0 -10627.837 -10794.509 -10794.236 -408.93357
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5 19.424842 28.194049 0.42020553 0.9585778 -170.83354 -169.87496 3.016716 0 -10627.813 -10794.671 -10794.251 -428.10518
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6 25.315002 39.895741 0.59460812 0.95823491 -170.90236 -169.94412 2.8599973 0 -10627.779 -10794.864 -10794.269 -451.5421
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7 31.945826 53.187854 0.79271445 0.95783553 -170.98485 -170.02702 2.6826348 0 -10627.739 -10795.083 -10794.29 -479.20295
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8 38.843432 67.819953 1.010792 0.95738252 -171.0742 -170.11682 2.4882829 0 -10627.697 -10795.325 -10794.314 -510.99723
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9 46.718156 83.516497 1.2447341 0.95687915 -171.17882 -170.22194 2.2809581 0 -10627.645 -10795.586 -10794.342 -546.9588
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10 54.366233 99.982124 1.4901386 0.95632904 -171.28928 -170.33295 2.0649603 0 -10627.594 -10795.862 -10794.372 -586.9531
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Loop time of 54.3663 on 1 procs for 10 steps with 6 atoms
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Performance: 0.004 ns/day, 6063.691 hours/ns, 0.458 timesteps/s, 2.749 atom-step/s
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Performance: 0.002 ns/day, 15101.736 hours/ns, 0.184 timesteps/s, 1.104 atom-step/s
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100.0% CPU use with 1 MPI tasks x no OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
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Pair | 7.572e-06 | 7.572e-06 | 7.572e-06 | 0.0 | 0.00
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||||
Bond | 5.119e-06 | 5.119e-06 | 5.119e-06 | 0.0 | 0.00
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Pair | 3.4059e-05 | 3.4059e-05 | 3.4059e-05 | 0.0 | 0.00
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||||
Bond | 1.1659e-05 | 1.1659e-05 | 1.1659e-05 | 0.0 | 0.00
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 2.881e-06 | 2.881e-06 | 2.881e-06 | 0.0 | 0.00
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||||
Output | 5.439e-05 | 5.439e-05 | 5.439e-05 | 0.0 | 0.00
|
||||
Modify | 4.3658 | 4.3658 | 4.3658 | 0.0 |100.00
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Other | | 6.093e-06 | | | 0.00
|
||||
Comm | 1.0583e-05 | 1.0583e-05 | 1.0583e-05 | 0.0 | 0.00
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||||
Output | 0.00016554 | 0.00016554 | 0.00016554 | 0.0 | 0.00
|
||||
Modify | 54.366 | 54.366 | 54.366 | 0.0 |100.00
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||||
Other | | 1.567e-05 | | | 0.00
|
||||
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||||
Nlocal: 6 ave 6 max 6 min
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||||
Histogram: 1 0 0 0 0 0 0 0 0 0
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||||
@ -146,4 +154,4 @@ Ave neighs/atom = 2
|
||||
Ave special neighs/atom = 1
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:11
|
||||
Total wall time: 0:01:59
|
||||
|
||||
@ -96,8 +96,8 @@ thermo 1
|
||||
|
||||
variable p equal extract_setting(world_size)
|
||||
|
||||
mdi plugin nwchem_mdi mdi "-role ENGINE -name NWChem -method LINK" extra "template.water.nw water.dimer.nw log.water.pwdft.qmmm.plugin.$p" command "run 1"
|
||||
run 1
|
||||
mdi plugin nwchem_mdi mdi "-role ENGINE -name NWChem -method LINK" extra "template.water.nw water.nw log.water.pwdft.qmmm.plugin.$p" command "run 10"
|
||||
run 10
|
||||
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
@ -118,23 +118,32 @@ Neighbor list info ...
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 7.453 | 7.453 | 7.453 Mbytes
|
||||
Step CPU Temp KinEng E_vdwl E_coul E_pair E_mol E_long f_2 PotEng TotEng Press
|
||||
0 0 0 0 0.95937448 -170.68735 -169.72797 3.3962859 0 -10627.878 -10794.209 -10794.209 -374.81058
|
||||
1 1.2206038 1.1713705 0.017458165 0.95934217 -170.68987 -169.73053 3.3804649 0 -10627.878 -10794.229 -10794.211 -376.91596
|
||||
Loop time of 1.22062 on 2 procs for 1 steps with 6 atoms
|
||||
0 0 0 0 0.95937448 -170.68735 -169.72798 3.3962859 0 -10627.878 -10794.209 -10794.209 -374.81058
|
||||
1 1.2511997 1.1713705 0.017458165 0.95934217 -170.68987 -169.73053 3.3804649 0 -10627.878 -10794.229 -10794.211 -376.91596
|
||||
2 3.8385452 4.6633575 0.069502914 0.95924532 -170.70698 -169.74773 3.3333254 0 -10627.871 -10794.286 -10794.216 -383.31463
|
||||
3 7.7938711 10.410148 0.15515337 0.95908482 -170.73725 -169.77816 3.2558316 0 -10627.857 -10794.38 -10794.224 -393.99
|
||||
4 12.421381 18.303344 0.27279396 0.95886179 -170.78051 -169.82164 3.1495694 0 -10627.837 -10794.509 -10794.236 -408.93334
|
||||
5 17.269932 28.194049 0.42020553 0.9585778 -170.83354 -169.87496 3.016716 0 -10627.813 -10794.671 -10794.251 -428.10518
|
||||
6 22.792492 39.895742 0.59460814 0.95823491 -170.90235 -169.94412 2.8599973 0 -10627.779 -10794.864 -10794.269 -451.54206
|
||||
7 28.768848 53.187856 0.79271447 0.95783553 -170.98485 -170.02701 2.6826348 0 -10627.739 -10795.083 -10794.29 -479.20292
|
||||
8 34.74838 67.819955 1.010792 0.95738253 -171.07427 -170.11688 2.4882829 0 -10627.697 -10795.325 -10794.314 -510.99784
|
||||
9 41.409904 83.516502 1.2447341 0.95687915 -171.17899 -170.22211 2.2809581 0 -10627.645 -10795.586 -10794.342 -546.96024
|
||||
10 48.305399 99.982132 1.4901387 0.95632904 -171.28935 -170.33302 2.0649603 0 -10627.594 -10795.862 -10794.372 -586.95371
|
||||
Loop time of 48.3054 on 2 procs for 10 steps with 6 atoms
|
||||
|
||||
Performance: 0.007 ns/day, 3390.614 hours/ns, 0.819 timesteps/s, 4.916 atom-step/s
|
||||
88.7% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
Performance: 0.002 ns/day, 13418.171 hours/ns, 0.207 timesteps/s, 1.242 atom-step/s
|
||||
93.0% CPU use with 2 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 4.563e-06 | 4.9165e-06 | 5.27e-06 | 0.0 | 0.00
|
||||
Bond | 1.201e-06 | 2.0745e-06 | 2.948e-06 | 0.0 | 0.00
|
||||
Pair | 4.6638e-05 | 4.8108e-05 | 4.9577e-05 | 0.0 | 0.00
|
||||
Bond | 1.5399e-05 | 2.157e-05 | 2.7741e-05 | 0.0 | 0.00
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 7.511e-06 | 8.0675e-06 | 8.624e-06 | 0.0 | 0.00
|
||||
Output | 1.7987e-05 | 1.9748e-05 | 2.151e-05 | 0.0 | 0.00
|
||||
Modify | 1.2206 | 1.2206 | 1.2206 | 0.0 |100.00
|
||||
Other | | 7.148e-06 | | | 0.00
|
||||
Comm | 7.9132e-05 | 8.3424e-05 | 8.7716e-05 | 0.0 | 0.00
|
||||
Output | 0.0001854 | 0.00020373 | 0.00022205 | 0.0 | 0.00
|
||||
Modify | 48.305 | 48.305 | 48.305 | 0.0 |100.00
|
||||
Other | | 4.187e-05 | | | 0.00
|
||||
|
||||
Nlocal: 3 ave 4 max 2 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
@ -148,4 +157,4 @@ Ave neighs/atom = 2
|
||||
Ave special neighs/atom = 1
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:00
|
||||
Total wall time: 0:01:45
|
||||
|
||||
@ -58,9 +58,9 @@ FixMDIQM::FixMDIQM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
|
||||
addflag = 1;
|
||||
every = 1;
|
||||
connectflag = 1;
|
||||
elements = nullptr;
|
||||
mcflag = 0;
|
||||
id_mcfix = nullptr;
|
||||
elements = nullptr;
|
||||
|
||||
int iarg = 3;
|
||||
while (iarg < narg) {
|
||||
@ -96,12 +96,6 @@ FixMDIQM::FixMDIQM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
|
||||
else
|
||||
error->all(FLERR, "Illegal fix mdi/qm command");
|
||||
iarg += 2;
|
||||
} else if (strcmp(arg[iarg],"mc") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR, "Illegal fix mdi/qm command");
|
||||
mcflag = 1;
|
||||
delete[] id_mcfix;
|
||||
id_mcfix = utils::strdup(arg[iarg+1]);
|
||||
iarg += 2;
|
||||
|
||||
} else if (strcmp(arg[iarg], "elements") == 0) {
|
||||
const char *symbols[] = {
|
||||
@ -133,6 +127,13 @@ FixMDIQM::FixMDIQM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
|
||||
}
|
||||
iarg += ntypes + 1;
|
||||
|
||||
} else if (strcmp(arg[iarg],"mc") == 0) {
|
||||
if (iarg+2 > narg) error->all(FLERR, "Illegal fix mdi/qm command");
|
||||
mcflag = 1;
|
||||
delete[] id_mcfix;
|
||||
id_mcfix = utils::strdup(arg[iarg+1]);
|
||||
iarg += 2;
|
||||
|
||||
} else
|
||||
error->all(FLERR, "Illegal fix mdi/qm command");
|
||||
}
|
||||
@ -143,16 +144,16 @@ FixMDIQM::FixMDIQM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
|
||||
global_freq = every;
|
||||
extscalar = 1;
|
||||
|
||||
peratom_flag = 1;
|
||||
size_peratom_cols = 3;
|
||||
peratom_freq = every;
|
||||
extvector = 0;
|
||||
|
||||
if (virialflag) {
|
||||
vector_flag = 1;
|
||||
size_vector = 6;
|
||||
extvector = 0;
|
||||
}
|
||||
|
||||
peratom_flag = 1;
|
||||
size_peratom_cols = 3;
|
||||
peratom_freq = every;
|
||||
|
||||
if (addflag) {
|
||||
energy_global_flag = 1;
|
||||
virial_global_flag = 1;
|
||||
@ -202,13 +203,11 @@ FixMDIQM::FixMDIQM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
|
||||
// initialize outputs
|
||||
|
||||
qm_energy = 0.0;
|
||||
if (virialflag) {
|
||||
for (int i = 0; i < 6; i++) {
|
||||
qm_virial[i] = 0.0;
|
||||
virial[i] = 0.0;
|
||||
}
|
||||
sumflag = 0;
|
||||
}
|
||||
|
||||
int nlocal = atom->nlocal;
|
||||
for (int i = 0; i < nlocal; i++)
|
||||
@ -311,7 +310,7 @@ void FixMDIQM::init()
|
||||
if (ierr) error->all(FLERR, "MDI: >NATOMS command check");
|
||||
MPI_Bcast(&natoms_exists, 1, MPI_INT, 0, world);
|
||||
|
||||
ierr = MDI_Check_command_exists("@DEFAULT", ">NATOMS", mdicomm, &celldispl_exists);
|
||||
ierr = MDI_Check_command_exists("@DEFAULT", ">CELL_DISPL", mdicomm, &celldispl_exists);
|
||||
if (ierr) error->all(FLERR, "MDI: >CELL_DISPL command check");
|
||||
MPI_Bcast(&celldispl_exists, 1, MPI_INT, 0, world);
|
||||
|
||||
@ -322,6 +321,10 @@ void FixMDIQM::init()
|
||||
ierr = MDI_Check_command_exists("@DEFAULT", ">TYPES", mdicomm, &types_exists);
|
||||
if (ierr) error->all(FLERR, "MDI: >TYPES command check");
|
||||
MPI_Bcast(&types_exists, 1, MPI_INT, 0, world);
|
||||
|
||||
ierr = MDI_Check_command_exists("@DEFAULT", "<STRESS", mdicomm, &stress_exists);
|
||||
if (ierr) error->all(FLERR, "MDI: <STRESS command check");
|
||||
MPI_Bcast(&stress_exists, 1, MPI_INT, 0, world);
|
||||
}
|
||||
|
||||
// extract pointers to MC variables from id_mcfix
|
||||
@ -339,7 +342,7 @@ void FixMDIQM::init()
|
||||
}
|
||||
|
||||
// determine whether a new vs incremental QM calc is needed
|
||||
// new when first run or when
|
||||
// new if first run or if
|
||||
// atom count or elements/types or box has changed between runs
|
||||
// otherwise incremental = subsequent run of same system
|
||||
|
||||
@ -385,6 +388,7 @@ void FixMDIQM::init()
|
||||
if (eqm[i] != eqm_old[i]) new_system = 1;
|
||||
memory->destroy(eqm_old);
|
||||
}
|
||||
|
||||
} else if (types_exists) {
|
||||
if (new_system) set_tqm();
|
||||
else {
|
||||
@ -558,7 +562,7 @@ void FixMDIQM::post_force(int vflag)
|
||||
// qm_virial_symmetric = fix output for global QM virial
|
||||
// note MDI defines virial tensor as intensive (divided by volume), LAMMPS does not
|
||||
|
||||
if (vflag && virialflag) {
|
||||
if (vflag && virialflag && stress_exists) {
|
||||
ierr = MDI_Send_command("<STRESS", mdicomm);
|
||||
if (ierr) error->all(FLERR, "MDI: <STRESS command");
|
||||
ierr = MDI_Recv(qm_virial, 9, MDI_DOUBLE, mdicomm);
|
||||
@ -689,6 +693,11 @@ void FixMDIQM::reallocate()
|
||||
|
||||
int FixMDIQM::set_nqm()
|
||||
{
|
||||
// require 3*nqm be a small INT, so can MPI_Allreduce xqm
|
||||
|
||||
if (3*atom->natoms > MAXSMALLINT)
|
||||
error->all(FLERR,"Fix mdi/qm has too many atoms");
|
||||
|
||||
int ncount = atom->natoms;
|
||||
nexclude = 0;
|
||||
|
||||
@ -913,11 +922,9 @@ void FixMDIQM::send_natoms()
|
||||
if (natoms_exists) {
|
||||
ierr = MDI_Send_command(">NATOMS", mdicomm);
|
||||
if (ierr) error->all(FLERR, "MDI: >NATOMS command");
|
||||
int n = static_cast<int>(atom->natoms);
|
||||
ierr = MDI_Send(&n, 1, MDI_INT, mdicomm);
|
||||
ierr = MDI_Send(&nqm, 1, MDI_INT, mdicomm);
|
||||
if (ierr) error->all(FLERR, "MDI: >NATOMS data");
|
||||
|
||||
|
||||
} else {
|
||||
ierr = MDI_Send_command("<NATOMS", mdicomm);
|
||||
if (ierr) error->all(FLERR, "MDI: <NATOMS command");
|
||||
@ -926,7 +933,7 @@ void FixMDIQM::send_natoms()
|
||||
if (ierr) error->all(FLERR, "MDI: <NATOMS data");
|
||||
MPI_Bcast(&n, 1, MPI_INT, 0, world);
|
||||
|
||||
if (n != atom->natoms)
|
||||
if (n != nqm)
|
||||
error->all(FLERR, "MDI: Engine has wrong atom count and does not support >NATOMS command");
|
||||
}
|
||||
}
|
||||
@ -952,7 +959,7 @@ void FixMDIQM::send_elements()
|
||||
int ierr = MDI_Send_command(">ELEMENTS", mdicomm);
|
||||
if (ierr) error->all(FLERR, "MDI: >ELEMENTS command");
|
||||
ierr = MDI_Send(eqm, nqm, MDI_INT, mdicomm);
|
||||
if (ierr) error->all(FLERR, "MDI: >ELEMETNS data");
|
||||
if (ierr) error->all(FLERR, "MDI: >ELEMENTS data");
|
||||
}
|
||||
|
||||
/* ----------------------------------------------------------------------
|
||||
|
||||
@ -62,6 +62,7 @@ class FixMDIQM : public Fix {
|
||||
|
||||
MDI_Comm mdicomm;
|
||||
int natoms_exists,celldispl_exists,elements_exists,types_exists;
|
||||
int stress_exists;
|
||||
|
||||
int nmax;
|
||||
|
||||
|
||||
File diff suppressed because it is too large
Load Diff
@ -42,12 +42,14 @@ class FixMDIQMMM : public Fix {
|
||||
void min_post_neighbor() override;
|
||||
void min_pre_force(int) override;
|
||||
void min_post_force(int) override;
|
||||
|
||||
int pack_forward_comm(int, int *, double *, int, int *) override;
|
||||
void unpack_forward_comm(int, int, double *) override;
|
||||
int pack_reverse_comm(int, int, double *) override;
|
||||
void unpack_reverse_comm(int, int *, double *) override;
|
||||
|
||||
double compute_scalar() override;
|
||||
double compute_vector(int) override;
|
||||
double memory_usage() override;
|
||||
|
||||
private:
|
||||
@ -59,49 +61,57 @@ class FixMDIQMMM : public Fix {
|
||||
int *elements;
|
||||
int mode; // QMMM method = DIRECT or POTENTIAL
|
||||
|
||||
int lmpunits; // REAL, METAL, or NATIVE
|
||||
int first_send; // 1 until initial info passed to MDI engine
|
||||
double qm_cell[9],qm_cell_displ[3];
|
||||
|
||||
double qm_energy;
|
||||
double qm_virial[9], qm_virial_symmetric[6];
|
||||
|
||||
MDI_Comm mdicomm;
|
||||
int natoms_exists,celldispl_exists,elements_exists,types_exists;
|
||||
int stress_exists;
|
||||
|
||||
int nmax;
|
||||
|
||||
class Pair *pair_coul; // ptr to instance of pair coul variant
|
||||
|
||||
// data for QM portion
|
||||
// QM atom data structs
|
||||
|
||||
int nqm; // # of QM atoms
|
||||
int nqm_last,max_nqm;
|
||||
|
||||
tagint *qmIDs; // IDs of QM atoms in ascending order
|
||||
double **xqm,**fqm; // QM coords and forces
|
||||
double *qqm; // QM charges
|
||||
int *eqm; // QM atom atomic numbers
|
||||
double *qpotential; // Coulomb potential
|
||||
double **xqm_mine; // same values for QM atoms I own
|
||||
double *qqm_mine;
|
||||
double *qpotential_mine;
|
||||
int *eqm_mine;
|
||||
int *qm2owned; // index of local atom for each QM atom
|
||||
// index = -1 if this proc does not own
|
||||
|
||||
int *eqm,*eqm_mine;
|
||||
int *tqm,*tqm_mine;
|
||||
double **xqm,**xqm_mine;
|
||||
double *qqm,*qqm_mine;
|
||||
double *qpotential,*qpotential_mine;
|
||||
double **fqm;
|
||||
|
||||
double *ecoul; // peratom Coulombic energy from LAMMPS
|
||||
int ncoulmax; // length of ecoul
|
||||
|
||||
// data for MM portion
|
||||
// MM atom data structs
|
||||
|
||||
int nmm; // # of MM atoms
|
||||
int nmm_last,max_nmm;
|
||||
|
||||
tagint *mmIDs; // IDs of MM atoms in ascending order
|
||||
double **xmm,**fmm; // MM coords and forces
|
||||
double *qmm; // MM charges
|
||||
int *emm; // MM atom atomic numbers
|
||||
double **xmm_mine; // same values for MM atoms I own
|
||||
double *qmm_mine;
|
||||
int *emm_mine;
|
||||
int *mm2owned; // index of local atom for each MM atom
|
||||
// index = -1 if this proc does not own
|
||||
|
||||
int *emm,*emm_mine;
|
||||
int *tmm,*tmm_mine;
|
||||
double **xmm,**xmm_mine;
|
||||
double *qmm,*qmm_mine;
|
||||
double **fmm;
|
||||
|
||||
// unit conversion factors
|
||||
|
||||
int lmpunits; // REAL, METAL, or NATIVE
|
||||
|
||||
double lmp2mdi_length, mdi2lmp_length;
|
||||
double lmp2mdi_energy, mdi2lmp_energy;
|
||||
double lmp2mdi_force, mdi2lmp_force;
|
||||
@ -112,22 +122,39 @@ class FixMDIQMMM : public Fix {
|
||||
void post_force_direct(int);
|
||||
void post_force_potential(int);
|
||||
|
||||
void reallocate_qm();
|
||||
void reallocate_mm();
|
||||
|
||||
int set_nqm();
|
||||
int set_nmm();
|
||||
|
||||
void create_qm_list();
|
||||
void create_mm_list();
|
||||
|
||||
void set_qm2owned();
|
||||
void set_mm2owned();
|
||||
|
||||
void set_box();
|
||||
|
||||
void set_xqm();
|
||||
void set_eqm();
|
||||
void set_tqm();
|
||||
void set_qqm();
|
||||
void set_xqm();
|
||||
|
||||
void set_emm();
|
||||
void set_qmm();
|
||||
void set_xmm();
|
||||
void set_emm();
|
||||
void set_tmm();
|
||||
void set_qmm();
|
||||
|
||||
void send_natoms_qm();
|
||||
void send_types_qm();
|
||||
void send_elements_qm();
|
||||
void send_box();
|
||||
void send_natoms_mm();
|
||||
void send_types_mm();
|
||||
void send_elements_mm();
|
||||
void send_charges_mm();
|
||||
|
||||
void unit_conversions();
|
||||
|
||||
};
|
||||
|
||||
Reference in New Issue
Block a user