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Merge branch 'lammps:develop' into fortran-tinkering

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hammondkd
2022-09-09 21:23:26 -05:00
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parent 0214c35c23 fb9c40d936
commit 99c76b84aa
130 changed files with 54742 additions and 2169 deletions
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7
cmake/Modules/Packages/MDI.cmake
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@ -6,10 +6,13 @@ else()
endif() endif()
option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an already installed one" ${DOWNLOAD_MDI_DEFAULT}) option(DOWNLOAD_MDI "Download and compile the MDI library instead of using an already installed one" ${DOWNLOAD_MDI_DEFAULT})
if(DOWNLOAD_MDI) if(DOWNLOAD_MDI)
message(STATUS "MDI download requested - we will build our own") message(STATUS "MDI download requested - we will build our own")
set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.1.tar.gz" CACHE STRING "URL for MDI tarball") set(MDI_URL "https://github.com/MolSSI-MDI/MDI_Library/archive/v1.4.10.tar.gz" CACHE STRING "URL for MDI tarball")
set(MDI_MD5 "f9505fccd4c79301a619f6452dad4ad9" CACHE STRING "MD5 checksum for MDI tarball") set(MDI_MD5 "1c203b7fd462d9934834f643f09f3c06" CACHE STRING "MD5 checksum for MDI tarball")
mark_as_advanced(MDI_URL) mark_as_advanced(MDI_URL)
mark_as_advanced(MDI_MD5) mark_as_advanced(MDI_MD5)
enable_language(C) enable_language(C)

1
doc/src/Commands_all.rst
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@ -61,6 +61,7 @@ An alphabetic list of general LAMMPS commands.
* :doc:`kspace_modify <kspace_modify>` * :doc:`kspace_modify <kspace_modify>`
* :doc:`kspace_style <kspace_style>` * :doc:`kspace_style <kspace_style>`
* :doc:`label <label>` * :doc:`label <label>`
* :doc:`labelmap <labelmap>`
* :doc:`lattice <lattice>` * :doc:`lattice <lattice>`
* :doc:`log <log>` * :doc:`log <log>`
* :doc:`mass <mass>` * :doc:`mass <mass>`

9
doc/src/Developer_utils.rst
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@ -175,6 +175,12 @@ and parsing files or arguments.
.. doxygenfunction:: is_double .. doxygenfunction:: is_double
:project: progguide :project: progguide
.. doxygenfunction:: is_id
:project: progguide
.. doxygenfunction:: is_type
:project: progguide
Potential file functions Potential file functions
^^^^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^^^^
@ -205,6 +211,9 @@ Argument processing
.. doxygenfunction:: expand_args .. doxygenfunction:: expand_args
:project: progguide :project: progguide
.. doxygenfunction:: expand_type
:project: progguide
Convenience functions Convenience functions
^^^^^^^^^^^^^^^^^^^^^ ^^^^^^^^^^^^^^^^^^^^^

40
doc/src/Errors_messages.rst
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@ -5453,6 +5453,11 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
Mass command must set a type from 1-N where N is the number of atom Mass command must set a type from 1-N where N is the number of atom
types. types.
*Invalid label2type() function syntax in variable formula*
The first argument must be a label map kind (atom, bond, angle,
dihedral, or improper) and the second argument must be a valid type
label that has been assigned to a numeric type.
*Invalid use of library file() function* *Invalid use of library file() function*
This function is called through the library interface. This This function is called through the library interface. This
error should not occur. Contact the developers if it does. error should not occur. Contact the developers if it does.
@ -5585,9 +5590,18 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*LJ6 off not supported in pair_style buck/long/coul/long* *LJ6 off not supported in pair_style buck/long/coul/long*
Self-explanatory. Self-explanatory.
*Label map is incomplete: all types must be assigned a unique type label*
For a given type-kind (atom types, bond types, etc.) to be written to
the data file, all associated types must be assigned a type label, and
each type label can be assigned to only one numeric type.
*Label wasn't found in input script* *Label wasn't found in input script*
Self-explanatory. Self-explanatory.
*Labelmap command before simulation box is defined*
The labelmap command cannot be used before a read_data,
read_restart, or create_box command.
*Lattice orient vectors are not orthogonal* *Lattice orient vectors are not orthogonal*
The three specified lattice orientation vectors must be mutually The three specified lattice orientation vectors must be mutually
orthogonal. orthogonal.
@ -5863,6 +5877,12 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
*Must not have multiple fixes change box parameter ...* *Must not have multiple fixes change box parameter ...*
Self-explanatory. Self-explanatory.
*Must read Angle Type Labels before Angles*
An Angle Type Labels section of a data file must come before the Angles section.
*Must read Atom Type Labels before Atoms*
An Atom Type Labels section of a data file must come before the Atoms section.
*Must read Atoms before Angles* *Must read Atoms before Angles*
The Atoms section of a data file must come before an Angles section. The Atoms section of a data file must come before an Angles section.
@ -5893,6 +5913,15 @@ Doc page with :doc:`WARNING messages <Errors_warnings>`
The Atoms section of a data file must come before a Velocities The Atoms section of a data file must come before a Velocities
section. section.
*Must read Bond Type Labels before Bonds*
A Bond Type Labels section of a data file must come before the Bonds section.
*Must read Dihedral Type Labels before Dihedrals*
An Dihedral Type Labels section of a data file must come before the Dihedrals section.
*Must read Improper Type Labels before Impropers*
An Improper Type Labels section of a data file must come before the Impropers section.
*Must re-specify non-restarted pair style (xxx) after read_restart* *Must re-specify non-restarted pair style (xxx) after read_restart*
For pair styles, that do not store their settings in a restart file, For pair styles, that do not store their settings in a restart file,
it must be defined with a new 'pair_style' command after read_restart. it must be defined with a new 'pair_style' command after read_restart.
@ -7849,6 +7878,10 @@ keyword to allow for additional bonds to be formed
Number of local atoms times number of columns must fit in a 32-bit Number of local atoms times number of columns must fit in a 32-bit
integer for dump. integer for dump.
*Topology type exceeds system topology type*
The number of bond, angle, etc types exceeds the system setting. See
the create_box or read_data command for how to specify these values.
*Tree structure in joint connections* *Tree structure in joint connections*
Fix poems cannot (yet) work with coupled bodies whose joints connect Fix poems cannot (yet) work with coupled bodies whose joints connect
the bodies in a tree structure. the bodies in a tree structure.
@ -7873,6 +7906,13 @@ keyword to allow for additional bonds to be formed
*Two groups cannot be the same in fix spring couple* *Two groups cannot be the same in fix spring couple*
Self-explanatory. Self-explanatory.
*The %s type label %s is already in use for type %s*
For a given type-kind (atom types, bond types, etc.), a given type
label can be assigned to only one numeric type.
*Type label string %s for %s type %s is invalid*
See the labelmap command documentation for valid type labels.
*Unable to initialize accelerator for use* *Unable to initialize accelerator for use*
There was a problem initializing an accelerator for the gpu package There was a problem initializing an accelerator for the gpu package

1
doc/src/Howto.rst
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@ -34,6 +34,7 @@ Settings howto
:maxdepth: 1 :maxdepth: 1
Howto_2d Howto_2d
Howto_type_labels
Howto_triclinic Howto_triclinic
Howto_thermostat Howto_thermostat
Howto_barostat Howto_barostat

126
doc/src/Howto_type_labels.rst Normal file
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@ -0,0 +1,126 @@
Type labels
===========
.. versionadded:: TBD
Each atom in LAMMPS has an associated numeric atom type. Similarly,
each bond, angle, dihedral, and improper is assigned a bond type,
angle type, and so on. The primary use of these types is to map
potential (force field) parameters to the interactions of the atom,
bond, angle, dihedral, and improper.
By default, type values are entered as integers from 1 to Ntypes
wherever they appear in LAMMPS input or output files. The total number
Ntypes for each interaction is "locked in" when the simulation box
is created.
A recent addition to LAMMPS is the option to use strings - referred
to as type labels - as an alternative. Using type labels instead of
numeric types can be advantageous in various scenarios. For example,
type labels can make inputs more readable and generic (i.e. usable through
the :doc:`include command <include>` for different systems with different
numerical values assigned to types. This generality also applies to
other inputs like data files read by :doc:`read_data <read_data>` or
molecule template files read by the :doc:`molecule <molecule>`
command. See below for a list of other commands that can use
type labels in different ways.
LAMMPS will *internally* continue to use numeric types, which means
that many previous restrictions still apply. For example, the total
number of types is locked in when creating the simulation box, and
potential parameters for each type must be provided even if not used
by any interactions.
A collection of type labels for all type-kinds (atom types, bond types,
etc.) is stored as a "label map" which is simply a list of numeric types
and their associated type labels. Within a type-kind, each type label
must be unique. It can be assigned to only one numeric type. To read
and write type labels to data files for a given type-kind, *all*
associated numeric types need have a type label assigned. Partial
maps can be saved with the :doc:`labelmap write <labelmap>` command
and read back with the :doc:`include <include>` command.
Valid type labels can contain most ASCII characters, but cannot start
with a number, a '#', or a '*'. Also, labels must not contain whitespace
characters. When using the :doc:`labelmap command <labelmap>` in the
LAMMPS input, if certain characters appear in the type label, such as
the single (') or double (") quote or the '#' character, the label
must be put in either double, single, or triple (""") quotes. Triple
quotes allow for the most generic type label strings, but they require
to have a leading and trailing blank space. When defining type labels
the blanks will be ignored. Example:
.. code-block:: LAMMPS
labelmap angle 1 """ C1'-C2"-C3# """
This command will map the string ```C1'-C2"-C3#``` to the angle type 1.
There are two ways to define label maps. One is via the :doc:`labelmap
<labelmap>` command. The other is via the :doc:`read_data <read_data>`
command. A data file can have sections such as *Atom Type Labels*, *Bond
Type Labels*, etc., which assign type labels to numeric types. The
label map can be written out to data files by the :doc:`write_data
<write_data>` command. This map is also written to and read from
restart files, by the :doc:`write_restart <write_restart>` and
:doc:`read_restart <read_restart>` commands.
----------
Use of type labels in LAMMPS input or output
""""""""""""""""""""""""""""""""""""""""""""
Many LAMMPS input script commands that take a numeric type as an
argument can use the associated type label instead. If a type label
is not defined for a particular numeric type, only its numeric type
can be used.
This example assigns labels to the atom types, and then uses the type
labels to redefine the pair coefficients.
.. code-block:: LAMMPS
pair_coeff 1 2 1.0 1.0 # numeric types
labelmap atom 1 C 2 H
pair_coeff C H 1.0 1.0 # type labels
Adding support for type labels to various commands is an ongoing
project. If an input script command (or a section in a file read by a
command) allows substituting a type label for a numeric type argument,
it will be explicitly mentioned in that command's documentation page.
As a temporary measure, input script commands can take advantage of
variables and how they can be expanded during processing of the input.
The variables can use functions that will translate type label strings
to their respective number as defined in the current label map. See the
:doc:`variable <variable>` command for details.
For example, here is how the pair_coeff command could be used with
type labels if it did not yet support them, either with an explicit
variable command or an implicit variable used in the pair_coeff
command.
.. code-block:: LAMMPS
labelmap atom 1 C 2 H
variable atom1 equal label2type(atom,C)
variable atom2 equal label2type(atom,H)
pair_coeff ${atom1} ${atom2} 1.0 1.0
.. code-block:: LAMMPS
labelmap atom 1 C 2 H
pair_coeff $(label2type(atom,C)) $(label2type(atom,H)) 80.0 1.2
----------
Commands that can use label types
"""""""""""""""""""""""""""""""""
Any workflow that involves reading multiple data files, molecule
templates or a combination of the two can be streamlined by using type
labels instead of numeric types, because types are automatically synced
between the files. The creation of simulation-ready reaction templates
for :doc:`fix bond/react <fix_bond_react>` is much simpler when using
type labels, and results in templates that can be used without
modification in multiple simulations or different systems.

50
doc/src/angle_coeff.rst
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@ -10,7 +10,7 @@ Syntax
angle_coeff N args angle_coeff N args
* N = angle type (see asterisk form below) * N = numeric angle type (see asterisk form below), or type label
* args = coefficients for one or more angle types * args = coefficients for one or more angle types
Examples Examples
@ -22,6 +22,9 @@ Examples
angle_coeff * 5.0 angle_coeff * 5.0
angle_coeff 2*10 5.0 angle_coeff 2*10 5.0
labelmap angle 1 hydroxyl
angle_coeff hydroxyl 300.0 107.0
Description Description
""""""""""" """""""""""
@ -30,18 +33,24 @@ The number and meaning of the coefficients depends on the angle style.
Angle coefficients can also be set in the data file read by the Angle coefficients can also be set in the data file read by the
:doc:`read_data <read_data>` command or in a restart file. :doc:`read_data <read_data>` command or in a restart file.
N can be specified in one of two ways. An explicit numeric value can :math:`N` can be specified in one of two ways. An explicit numeric
be used, as in the first example above. Or a wild-card asterisk can be value can be used, as in the first example above. Or :math:`N` can be a
used to set the coefficients for multiple angle types. This takes the type label, which is an alphanumeric string defined by the
form "\*" or "\*n" or "n\*" or "m\*n". If N = the number of angle types, :doc:`labelmap <labelmap>` command or in a section of a data file read
then an asterisk with no numeric values means all types from 1 to N. A by the :doc:`read_data <read_data>` command.
leading asterisk means all types from 1 to n (inclusive). A trailing
asterisk means all types from n to N (inclusive). A middle asterisk
means all types from m to n (inclusive).
Note that using an :doc:`angle_coeff <angle_coeff>` command can override a previous setting For numeric values only, a wild-card asterisk can be used to set the
for the same angle type. For example, these commands set the coeffs coefficients for multiple angle types. This takes the form "\*" or
for all angle types, then overwrite the coeffs for just angle type 2: "\*n" or "n\*" or "m\*n". If :math:`N` is the number of angle types,
then an asterisk with no numeric values means all types from 1 to
:math:`N`. A leading asterisk means all types from 1 to n (inclusive).
A trailing asterisk means all types from n to :math:`N` (inclusive). A
middle asterisk means all types from m to n (inclusive).
Note that using an :doc:`angle_coeff <angle_coeff>` command can
override a previous setting for the same angle type. For example,
these commands set the coeffs for all angle types, then overwrite the
coeffs for just angle type 2:
.. code-block:: LAMMPS .. code-block:: LAMMPS
@ -49,11 +58,11 @@ for all angle types, then overwrite the coeffs for just angle type 2:
angle_coeff 2 50.0 107.0 angle_coeff 2 50.0 107.0
A line in a data file that specifies angle coefficients uses the exact A line in a data file that specifies angle coefficients uses the exact
same format as the arguments of the :doc:`angle_coeff <angle_coeff>` command in an input same format as the arguments of the :doc:`angle_coeff <angle_coeff>`
script, except that wild-card asterisks should not be used since command in an input script, except that wild-card asterisks should not
coefficients for all N types must be listed in the file. For example, be used since coefficients for all :math:`N` types must be listed in the
under the "Angle Coeffs" section of a data file, the line that file. For example, under the "Angle Coeffs" section of a data file, the
corresponds to the first example above would be listed as line that corresponds to the first example above would be listed as
.. parsed-literal:: .. parsed-literal::
@ -61,15 +70,14 @@ corresponds to the first example above would be listed as
The :doc:`angle_style class2 <angle_class2>` is an exception to this The :doc:`angle_style class2 <angle_class2>` is an exception to this
rule, in that an additional argument is used in the input script to rule, in that an additional argument is used in the input script to
allow specification of the cross-term coefficients. See its allow specification of the cross-term coefficients. See its doc page
doc page for details. for details.
---------- ----------
The list of all angle styles defined in LAMMPS is given on the The list of all angle styles defined in LAMMPS is given on the
:doc:`angle_style <angle_style>` doc page. They are also listed in more :doc:`angle_style <angle_style>` doc page. They are also listed in more
compact form on the :ref:`Commands angle <angle>` doc compact form on the :ref:`Commands angle <angle>` doc page.
page.
On either of those pages, click on the style to display the formula it On either of those pages, click on the style to display the formula it
computes and its coefficients as specified by the associated computes and its coefficients as specified by the associated

30
doc/src/bond_coeff.rst
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@ -10,7 +10,7 @@ Syntax
bond_coeff N args bond_coeff N args
* N = bond type (see asterisk form below) * N = numeric bond type (see asterisk form below), or type label
* args = coefficients for one or more bond types * args = coefficients for one or more bond types
Examples Examples
@ -21,7 +21,10 @@ Examples
bond_coeff 5 80.0 1.2 bond_coeff 5 80.0 1.2
bond_coeff * 30.0 1.5 1.0 1.0 bond_coeff * 30.0 1.5 1.0 1.0
bond_coeff 1*4 30.0 1.5 1.0 1.0 bond_coeff 1*4 30.0 1.5 1.0 1.0
bond_coeff 1 harmonic 200.0 1.0 bond_coeff 1 harmonic 200.0 1.0 (for bond_style hybrid)
labelmap bond 5 carbonyl
bond_coeff carbonyl 80.0 1.2
Description Description
""""""""""" """""""""""
@ -31,14 +34,19 @@ The number and meaning of the coefficients depends on the bond style.
Bond coefficients can also be set in the data file read by the Bond coefficients can also be set in the data file read by the
:doc:`read_data <read_data>` command or in a restart file. :doc:`read_data <read_data>` command or in a restart file.
N can be specified in one of two ways. An explicit numeric value can :math:`N` can be specified in one of several ways. An explicit numeric
be used, as in the first example above. Or a wild-card asterisk can be value can be used, as in the first example above. Or :math:`N` can be a
used to set the coefficients for multiple bond types. This takes the type label, which is an alphanumeric string defined by the
form "\*" or "\*n" or "n\*" or "m\*n". If N = the number of bond types, :doc:`labelmap <labelmap>` command or in a section of a data file read
then an asterisk with no numeric values means all types from 1 to N. A by the :doc:`read_data <read_data>` command.
For numeric values only, a wild-card asterisk can be used to set the
coefficients for multiple bond types. This takes the form "\*" or "\*n"
or "n\*" or "m\*n". If :math:`N` is the number of bond types, then an
asterisk with no numeric values means all types from 1 to :math:`N`. A
leading asterisk means all types from 1 to n (inclusive). A trailing leading asterisk means all types from 1 to n (inclusive). A trailing
asterisk means all types from n to N (inclusive). A middle asterisk asterisk means all types from n to :math:`N` (inclusive). A middle
means all types from m to n (inclusive). asterisk means all types from m to n (inclusive).
Note that using a bond_coeff command can override a previous setting Note that using a bond_coeff command can override a previous setting
for the same bond type. For example, these commands set the coeffs for the same bond type. For example, these commands set the coeffs
@ -52,8 +60,8 @@ for all bond types, then overwrite the coeffs for just bond type 2:
A line in a data file that specifies bond coefficients uses the exact A line in a data file that specifies bond coefficients uses the exact
same format as the arguments of the bond_coeff command in an input same format as the arguments of the bond_coeff command in an input
script, except that wild-card asterisks should not be used since script, except that wild-card asterisks should not be used since
coefficients for all N types must be listed in the file. For example, coefficients for all :math:`N` types must be listed in the file. For
under the "Bond Coeffs" section of a data file, the line that example, under the "Bond Coeffs" section of a data file, the line that
corresponds to the first example above would be listed as corresponds to the first example above would be listed as
.. parsed-literal:: .. parsed-literal::

1
doc/src/commands_list.rst
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@ -56,6 +56,7 @@ Commands
kspace_modify kspace_modify
kspace_style kspace_style
label label
labelmap
lattice lattice
log log
mass mass

37
doc/src/dihedral_coeff.rst
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@ -10,7 +10,7 @@ Syntax
dihedral_coeff N args dihedral_coeff N args
* N = dihedral type (see asterisk form below) * N = numeric dihedral type (see asterisk form below) or alphanumeric type label
* args = coefficients for one or more dihedral types * args = coefficients for one or more dihedral types
Examples Examples
@ -22,26 +22,35 @@ Examples
dihedral_coeff * 80.0 1 3 0.5 dihedral_coeff * 80.0 1 3 0.5
dihedral_coeff 2* 80.0 1 3 0.5 dihedral_coeff 2* 80.0 1 3 0.5
labelmap dihedral 1 backbone
dihedral_coeff backbone 80.0 1 3
Description Description
""""""""""" """""""""""
Specify the dihedral force field coefficients for one or more dihedral types. Specify the dihedral force field coefficients for one or more dihedral
The number and meaning of the coefficients depends on the dihedral style. types. The number and meaning of the coefficients depends on the
Dihedral coefficients can also be set in the data file read by the dihedral style. Dihedral coefficients can also be set in the data file
:doc:`read_data <read_data>` command or in a restart file. read by the :doc:`read_data <read_data>` command or in a restart file.
N can be specified in one of two ways. An explicit numeric value can :math:`N` can be specified in one of two ways. An explicit numeric
be used, as in the first example above. Or a wild-card asterisk can be value can be used, as in the first example above. Or :math:`N` can be
used to set the coefficients for multiple dihedral types. This takes the an alphanumeric type label, which is a string defined by the
form "\*" or "\*n" or "m\*" or "m\*n". If :math:`N` is the number of dihedral :doc:`labelmap <labelmap>` command or in a corresponding section of a
types, then an asterisk with no numeric values means all types from 1 to data file read by the :doc:`read_data <read_data>` command.
:math:`N`. A leading asterisk means all types from 1 to n (inclusive). A
trailing asterisk means all types from m to N (inclusive). A middle asterisk For numeric values only, a wild-card asterisk can be used to set the
means all types from m to n (inclusive). coefficients for multiple dihedral types. This takes the form "\*" or
"\*n" or "n\*" or "m\*n". If :math:`N` is the number of dihedral types,
then an asterisk with no numeric values means all types from 1 to
:math:`N`. A leading asterisk means all types from 1 to n (inclusive).
A trailing asterisk means all types from n to :math:`N` (inclusive). A
middle asterisk means all types from m to n (inclusive).
Note that using a dihedral_coeff command can override a previous setting Note that using a dihedral_coeff command can override a previous setting
for the same dihedral type. For example, these commands set the coeffs for the same dihedral type. For example, these commands set the coeffs
for all dihedral types, then overwrite the coeffs for just dihedral type 2: for all dihedral types, then overwrite the coeffs for just dihedral type
2:
.. code-block:: LAMMPS .. code-block:: LAMMPS

15
doc/src/fix_mdi_qm.rst
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@ -125,13 +125,14 @@ 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 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 specified for each of the ntypes LAMMPS atom types. Ntypes is
typically specified via the create_box command or in the data file typically specified via the create_box command or in the data file
read by the read_data command. If this keyword is not specified, then read by the read_data command.
this fix will send the LAMMPS atom type for each atom to the MDI
engine. If both the LAMMPS driver and the MDI engine are initialized If this keyword is specified, then this fix will send the MDI
so that atom type values are consistent in both codes, then the ">ELEMENTS" command to the engine, to insure the two codes are
*elements* keyword is not needed. Otherwise the keyword can be used consistent in their definition of atomic species. If this keyword is
to insure the two codes are consistent in their definition of atomic not specified, then this fix will send the MDI >TYPES command to the
species. engine. This is fine if both the LAMMPS driver and the MDI engine are
initialized so that the atom type values are consistent in both codes.
---------- ----------

41
doc/src/improper_coeff.rst
View File

@ -10,7 +10,7 @@ Syntax
improper_coeff N args improper_coeff N args
* N = improper type (see asterisk form below) * N = numeric improper type (see asterisk form below), or type label
* args = coefficients for one or more improper types * args = coefficients for one or more improper types
Examples Examples
@ -22,27 +22,34 @@ Examples
improper_coeff * 80.2 -1 2 improper_coeff * 80.2 -1 2
improper_coeff *4 80.2 -1 2 improper_coeff *4 80.2 -1 2
labelmap improper 1 benzene
improper_coeff benzene 300.0 0.0
Description Description
""""""""""" """""""""""
Specify the improper force field coefficients for one or more improper Specify the improper force field coefficients for one or more improper
types. The number and meaning of the coefficients depends on the types. The number and meaning of the coefficients depends on the
improper style. Improper coefficients can also be set in the data improper style. Improper coefficients can also be set in the data file
file read by the :doc:`read_data <read_data>` command or in a restart read by the :doc:`read_data <read_data>` command or in a restart file.
file.
N can be specified in one of two ways. An explicit numeric value can :math:`N` can be specified in one of two ways. An explicit numeric
be used, as in the first example above. Or a wild-card asterisk can be value can be used, as in the first example above. Or :math:`N` can be a
used to set the coefficients for multiple improper types. This takes type label, which is an alphanumeric string defined by the
the form "\*" or "\*n" or "n\*" or "m\*n". If N = the number of improper :doc:`labelmap <labelmap>` command or in a section of a data file read
types, then an asterisk with no numeric values means all types from 1 by the :doc:`read_data <read_data>` command.
to N. A leading asterisk means all types from 1 to n (inclusive). A
trailing asterisk means all types from n to N (inclusive). A middle For numeric values only, a wild-card asterisk can be used to set the
asterisk means all types from m to n (inclusive). coefficients for multiple improper types. This takes the form "\*" or
"\*n" or "n\*" or "m\*n". If :math:`N` = the number of improper types,
then an asterisk with no numeric values means all types from 1 to
:math:`N`. A leading asterisk means all types from 1 to n (inclusive).
A trailing asterisk means all types from n to :math:`N` (inclusive). A
middle asterisk means all types from m to n (inclusive).
Note that using an improper_coeff command can override a previous Note that using an improper_coeff command can override a previous
setting for the same improper type. For example, these commands set setting for the same improper type. For example, these commands set the
the coeffs for all improper types, then overwrite the coeffs for just coeffs for all improper types, then overwrite the coeffs for just
improper type 2: improper type 2:
.. code-block:: LAMMPS .. code-block:: LAMMPS
@ -53,9 +60,9 @@ improper type 2:
A line in a data file that specifies improper coefficients uses the A line in a data file that specifies improper coefficients uses the
exact same format as the arguments of the improper_coeff command in an exact same format as the arguments of the improper_coeff command in an
input script, except that wild-card asterisks should not be used since input script, except that wild-card asterisks should not be used since
coefficients for all N types must be listed in the file. For example, coefficients for all :math:`N` types must be listed in the file. For
under the "Improper Coeffs" section of a data file, the line that example, under the "Improper Coeffs" section of a data file, the line
corresponds to the first example above would be listed as that corresponds to the first example above would be listed as
.. parsed-literal:: .. parsed-literal::

98
doc/src/labelmap.rst Normal file
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@ -0,0 +1,98 @@
.. index:: labelmap
labelmap command
==================
Syntax
""""""
.. code-block:: LAMMPS
labelmap option args
* *option* = *atom* or *bond* or *angle* or *dihedral* or *improper* or *clear* or *write*
.. parsed-literal::
*clear* = no args
*write* arg = filename
*atom* or *bond* or *angle* or *dihedral* or *improper*
args = list of one or more numeric-type/type-label pairs
Examples
""""""""
.. code-block:: LAMMPS
labelmap atom 3 carbon 4 'c3"' 5 "c1'" 6 "c#"
labelmap bond 1 carbonyl 2 nitrile 3 """ c1'-c2" """
labelmap atom $(label2type(atom,carbon)) C # change type label from 'carbon' to 'C'
labelmap clear
labelmap write mymap.include
Description
"""""""""""
.. versionadded:: TBD
Define alphanumeric type labels to associate with one or more numeric
atom, bond, angle, dihedral or improper types. A collection of type
labels for all atom types, bond types, etc. is stored as a label map.
The label map can also be defined by the :doc:`read_data <read_data>`
command when it reads these sections in a data file: Atom Type Labels,
Bond Type Labels, etc. See the :doc:`Howto type labels
<Howto_type_labels>` doc page for a general discussion of how type
labels can be used.
Valid type labels can contain any alphanumeric character, but must not
start with a number, a '#', or a '*' character. They can contain other
standard ASCII characters such as angular or square brackets '<' and '>'
or '[' and ']', parenthesis '(' and ')', dash '-', underscore '_', plus
'+' and equals '=' signs and more. They must not contain blanks or any
other whitespace. Note that type labels must be put in single or double
quotation marks if they contain the '#' character or if they contain a
double (") or single quotation mark ('). If the label contains both
a single and a double quotation mark, then triple quotation (""") must
be used. When enclosing a type label with quotation marks, the
LAMMPS input parser may require adding leading or trailing blanks
around the type label so it can identify the enclosing quotation
marks. Those blanks will be removed when defining the label.
A *labelmap* command can only modify the label map for one type-kind
(atom types, bond types, etc). Any number of numeric-type/type-label
pairs may follow. If a type label already exists for the same numeric
type, it will be overwritten. Type labels must be unique; assigning the
same type label to multiple numeric types within the same type-kind is
not allowed. When reading and writing data files, it is required that
there is a label defined for *every* numeric type within a given
type-kind in order to write out the type label section for that
type-kind.
The *clear* option resets the labelmap and thus discards all previous
settings.
The *write* option takes a filename as argument and writes the current
label mappings to a file as labelmap commands, so the file can be copied
into a new LAMMPS input file or read in using the :doc:`include
<include>` command.
----------
Restrictions
""""""""""""
This command must come after the simulation box is defined by a
:doc:`read_data <read_data>`, :doc:`read_restart <read_restart>`, or
:doc:`create_box <create_box>` command.
Related commands
""""""""""""""""
:doc:`read_data <read_data>`, :doc:`write_data <write_data>`,
:doc:`molecule <molecule>`, :doc:`fix bond/react <fix_bond_react>`
Default
"""""""
none

21
doc/src/mass.rst
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@ -10,7 +10,7 @@ Syntax
mass I value mass I value
* I = atom type (see asterisk form below) * I = atom type (see asterisk form below), or type label
* value = mass * value = mass
Examples Examples
@ -22,6 +22,9 @@ Examples
mass * 62.5 mass * 62.5
mass 2* 62.5 mass 2* 62.5
labelmap atom 1 C
mass C 12.01
Description Description
""""""""""" """""""""""
@ -30,12 +33,16 @@ values can also be set in the :doc:`read_data <read_data>` data file
using the "Masses" keyword. See the :doc:`units <units>` command for using the "Masses" keyword. See the :doc:`units <units>` command for
what mass units to use. what mass units to use.
The I index can be specified in one of two ways. An explicit numeric The I index can be specified in one of several ways. An explicit
value can be used, as in the first example above. Or a wild-card numeric value can be used, as in the first example above. Or I can be
asterisk can be used to set the mass for multiple atom types. This a type label, which is an alphanumeric string defined by the
takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = the number of :doc:`labelmap <labelmap>` command or in a section of a data file read
atom types, then an asterisk with no numeric values means all types by the :doc:`read_data <read_data>` command, and which converts
from 1 to N. A leading asterisk means all types from 1 to n internally to a numeric type. Or a wild-card asterisk can be used to
set the mass for multiple atom types. This takes the form "\*" or
"\*n" or "n\*" or "m\*n", where m and n are numbers. If N = the
number of atom types, then an asterisk with no numeric values means
all types from 1 to N. A leading asterisk means all types from 1 to n
(inclusive). A trailing asterisk means all types from n to N (inclusive). A trailing asterisk means all types from n to N
(inclusive). A middle asterisk means all types from m to n (inclusive). A middle asterisk means all types from m to n
(inclusive). (inclusive).

22
doc/src/mdi.rst
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@ -14,7 +14,7 @@ Syntax
.. parsed-literal:: .. parsed-literal::
*engine* args = zero or more keyword arg pairs *engine* args = zero or more keyword/args pairs
keywords = *elements* keywords = *elements*
*elements* args = N_1 N_2 ... N_ntypes *elements* args = N_1 N_2 ... N_ntypes
N_1,N_2,...N_ntypes = atomic number for each of ntypes LAMMPS atom types N_1,N_2,...N_ntypes = atomic number for each of ntypes LAMMPS atom types
@ -24,7 +24,7 @@ Syntax
keywords = *mdi* or *infile* or *extra* or *command* keywords = *mdi* or *infile* or *extra* or *command*
*mdi* value = args passed to MDI for driver to operate with plugins (required) *mdi* value = args passed to MDI for driver to operate with plugins (required)
*infile* value = filename the engine will read at start-up (optional) *infile* value = filename the engine will read at start-up (optional)
*extra* value = aditional command-line args to pass to engine library when loaded *extra* value = aditional command-line args to pass to engine library when loaded (optional)
*command* value = a LAMMPS input script command to execute (required) *command* value = a LAMMPS input script command to execute (required)
*connect* args = none *connect* args = none
*exit* args = none *exit* args = none
@ -289,11 +289,11 @@ are required. The -name setting can be anything you choose. MDI
drivers and engines can query their names to verify they are values drivers and engines can query their names to verify they are values
they expect. they expect.
The *infile* keyword is also required. It is the name of an input The *infile* keyword is optional. It sets the name of an input script
script which the engine will open and process. MDI will pass it as a which the engine will open and process. MDI will pass it as a
command-line argument to the library when it is launched. The file command-line argument to the library when it is launched. The file
typically contains settings that an MD or QM code will use for its typically contains settings that an MD or QM code will use for its
subsequent calculations. calculations.
The *extra* keyword is optional. It contains additional command-line The *extra* keyword is optional. It contains additional command-line
arguments which MDI will pass to the library when it is launched. arguments which MDI will pass to the library when it is launched.
@ -309,12 +309,12 @@ could specify a filename with multiple LAMMPS commands.
.. note:: .. note::
When the single *command* is complete, LAMMPS will send an MDI When the *command* is complete, LAMMPS will send an MDI EXIT
EXIT command to the plugin engine and the plugin will be removed. command to the plugin engine and the plugin will be removed. The
The "mdi plugin" command will then exit and the next command "mdi plugin" command will then exit and the next command (if any)
(if any) in the LAMMPS input script will be processed. A subsequent in the LAMMPS input script will be processed. A subsequent "mdi
"mdi plugin" command could then load the same library plugin or plugin" command could then load the same or a different MDI
a different one if desired. plugin if desired.
---------- ----------

100
doc/src/molecule.rst
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@ -70,8 +70,9 @@ and underscores.
A single template can contain multiple molecules, listed one per file. A single template can contain multiple molecules, listed one per file.
Some of the commands listed above currently use only the first Some of the commands listed above currently use only the first
molecule in the template, and will issue a warning if the template molecule in the template, and will issue a warning if the template
contains multiple molecules. The :doc:`atom_style template <atom_style>` command allows multiple-molecule templates contains multiple molecules. The :doc:`atom_style template
to define a system with more than one templated molecule. <atom_style>` command allows multiple-molecule templates to define a
system with more than one templated molecule.
Each filename can be followed by optional keywords which are applied Each filename can be followed by optional keywords which are applied
only to the molecule in the file as used in this template. This is to only to the molecule in the file as used in this template. This is to
@ -88,6 +89,12 @@ molecule file. E.g. if *toff* = 2, and the file uses atom types
individual values will be ignored if the molecule template does not individual values will be ignored if the molecule template does not
use that attribute (e.g. no bonds). use that attribute (e.g. no bonds).
.. note::
Offsets are **ignored** on lines using type labels, as the type
labels will determine the actual types directly depending on the
current :doc:`labelmap <labelmap>` settings.
The *scale* keyword scales the size of the molecule. This can be The *scale* keyword scales the size of the molecule. This can be
useful for modeling polydisperse granular rigid bodies. The scale useful for modeling polydisperse granular rigid bodies. The scale
factor is applied to each of these properties in the molecule file, if factor is applied to each of these properties in the molecule file, if
@ -118,14 +125,18 @@ The format of an individual molecule file is similar but
(not identical) to the data file read by the :doc:`read_data <read_data>` (not identical) to the data file read by the :doc:`read_data <read_data>`
commands, and is as follows. commands, and is as follows.
A molecule file has a header and a body. The header appears first. A molecule file has a header and a body. The header appears first. The
The first line of the header is always skipped; it typically contains first line of the header and thus of the molecule file is *always* skipped;
a description of the file. Then lines are read one at a time. Lines it typically contains a description of the file or a comment from the software
can have a trailing comment starting with '#' that is ignored. If the that created the file.
line is blank (only white-space after comment is deleted), it is
Then lines are read one line at a time. Lines can have a trailing
comment starting with '#' that is ignored. There *must* be at least one
blank between any valid content and the comment. If the line is blank
(i.e. contains only white-space after comments are deleted), it is
skipped. If the line contains a header keyword, the corresponding skipped. If the line contains a header keyword, the corresponding
value(s) is read from the line. If it does not contain a header value(s) is/are read from the line. A line that is *not* blank and does
keyword, the line begins the body of the file. *not* contains a header keyword begins the body of the file.
The body of the file contains zero or more sections. The first line The body of the file contains zero or more sections. The first line
of a section has only a keyword. The next line is skipped. The of a section has only a keyword. The next line is skipped. The
@ -173,31 +184,43 @@ These are the allowed section keywords for the body of the file.
* *Special Bond Counts, Special Bonds* = special neighbor info * *Special Bond Counts, Special Bonds* = special neighbor info
* *Shake Flags, Shake Atoms, Shake Bond Types* = SHAKE info * *Shake Flags, Shake Atoms, Shake Bond Types* = SHAKE info
For the Types, Bonds, Angles, Dihedrals, and Impropers sections, each
atom/bond/angle/etc type can be specified either as a number (numeric
type) or as an alphanumeric type label. The latter is only allowed if
type labels have been defined, either by the :doc:`labelmap
<labelmap>` command or in data files read by the :doc:`read_data
<read_data>` command which have sections for Atom Type Labels, Bond
Type Labels, Angle Type Labels, etc. See the :doc:`Howto type labels
<Howto_type_labels>` doc page for the allowed syntax of type labels
and a general discussion of how type labels can be used.
When using type labels, any values specified as *offset* are ignored.
If a Bonds section is specified then the Special Bond Counts and If a Bonds section is specified then the Special Bond Counts and
Special Bonds sections can also be used, if desired, to explicitly Special Bonds sections can also be used, if desired, to explicitly
list the 1-2, 1-3, 1-4 neighbors within the molecule topology (see list the 1-2, 1-3, 1-4 neighbors within the molecule topology (see
details below). This is optional since if these sections are not details below). This is optional since if these sections are not
included, LAMMPS will auto-generate this information. Note that included, LAMMPS will auto-generate this information. Note that
LAMMPS uses this info to properly exclude or weight bonded pairwise LAMMPS uses this info to properly exclude or weight bonded pairwise
interactions between bonded atoms. See the interactions between bonded atoms. See the :doc:`special_bonds
:doc:`special_bonds <special_bonds>` command for more details. One <special_bonds>` command for more details. One reason to list the
reason to list the special bond info explicitly is for the special bond info explicitly is for the :doc:`thermalized Drude
:doc:`thermalized Drude oscillator model <Howto_drude>` which treats the oscillator model <Howto_drude>` which treats the bonds between nuclear
bonds between nuclear cores and Drude electrons in a different manner. cores and Drude electrons in a different manner.
.. note:: .. note::
Whether a section is required depends on how the molecule Whether a section is required depends on how the molecule template
template is used by other LAMMPS commands. For example, to add a is used by other LAMMPS commands. For example, to add a molecule
molecule via the :doc:`fix deposit <fix_deposit>` command, the Coords via the :doc:`fix deposit <fix_deposit>` command, the Coords and
and Types sections are required. To add a rigid body via the :doc:`fix pour <fix_pour>` command, the Bonds (Angles, etc) sections are not Types sections are required. To add a rigid body via the :doc:`fix
pour <fix_pour>` command, the Bonds (Angles, etc) sections are not
required, since the molecule will be treated as a rigid body. Some required, since the molecule will be treated as a rigid body. Some
sections are optional. For example, the :doc:`fix pour <fix_pour>` sections are optional. For example, the :doc:`fix pour <fix_pour>`
command can be used to add "molecules" which are clusters of command can be used to add "molecules" which are clusters of
finite-size granular particles. If the Diameters section is not finite-size granular particles. If the Diameters section is not
specified, each particle in the molecule will have a default diameter specified, each particle in the molecule will have a default
of 1.0. See the doc pages for LAMMPS commands that use molecule diameter of 1.0. See the doc pages for LAMMPS commands that use
templates for more details. molecule templates for more details.
Each section is listed below in alphabetic order. The format of each Each section is listed below in alphabetic order. The format of each
section is described including the number of lines it must contain and section is described including the number of lines it must contain and
@ -222,7 +245,7 @@ order.
* one line per atom * one line per atom
* line syntax: ID type * line syntax: ID type
* type = atom type of atom * type = atom type of atom (1-Natomtype, or type label)
---------- ----------
@ -289,7 +312,7 @@ included, the default mass for each atom is derived from its volume
* one line per bond * one line per bond
* line syntax: ID type atom1 atom2 * line syntax: ID type atom1 atom2
* type = bond type (1-Nbondtype) * type = bond type (1-Nbondtype, or type label)
* atom1,atom2 = IDs of atoms in bond * atom1,atom2 = IDs of atoms in bond
The IDs for the two atoms in each bond should be values The IDs for the two atoms in each bond should be values
@ -301,7 +324,7 @@ from 1 to Natoms, where Natoms = # of atoms in the molecule.
* one line per angle * one line per angle
* line syntax: ID type atom1 atom2 atom3 * line syntax: ID type atom1 atom2 atom3
* type = angle type (1-Nangletype) * type = angle type (1-Nangletype, or type label)
* atom1,atom2,atom3 = IDs of atoms in angle * atom1,atom2,atom3 = IDs of atoms in angle
The IDs for the three atoms in each angle should be values from 1 to The IDs for the three atoms in each angle should be values from 1 to
@ -315,7 +338,7 @@ which the angle is computed) is the atom2 in the list.
* one line per dihedral * one line per dihedral
* line syntax: ID type atom1 atom2 atom3 atom4 * line syntax: ID type atom1 atom2 atom3 atom4
* type = dihedral type (1-Ndihedraltype) * type = dihedral type (1-Ndihedraltype, or type label)
* atom1,atom2,atom3,atom4 = IDs of atoms in dihedral * atom1,atom2,atom3,atom4 = IDs of atoms in dihedral
The IDs for the four atoms in each dihedral should be values from 1 to The IDs for the four atoms in each dihedral should be values from 1 to
@ -328,7 +351,7 @@ ordered linearly within the dihedral.
* one line per improper * one line per improper
* line syntax: ID type atom1 atom2 atom3 atom4 * line syntax: ID type atom1 atom2 atom3 atom4
* type = improper type (1-Nimpropertype) * type = improper type (1-Nimpropertype, or type label)
* atom1,atom2,atom3,atom4 = IDs of atoms in improper * atom1,atom2,atom3,atom4 = IDs of atoms in improper
The IDs for the four atoms in each improper should be values from 1 to The IDs for the four atoms in each improper should be values from 1 to
@ -447,11 +470,15 @@ This section is only needed when molecules created using the template
will be constrained by SHAKE via the "fix shake" command. The other will be constrained by SHAKE via the "fix shake" command. The other
two Shake sections must also appear in the file. two Shake sections must also appear in the file.
The a,b,c values are bond types (from 1 to Nbondtypes) for all bonds The a,b,c values are bond types for all bonds in the SHAKE cluster that
in the SHAKE cluster that this atom belongs to. The number of values this atom belongs to. Bond types may be either numbers (from 1 to Nbondtypes)
that must appear is determined by the shake flag for the atom (see the or bond type labels as defined by the :doc:`labelmap <labelmap>` command
Shake Flags section above). All atoms in a particular cluster should or a "Bond Type Labels" section of a data file.
list their a,b,c values identically.
The number of values that must appear is determined by the shake flag
for the atom (see the Shake Flags section above). All atoms in a
particular cluster should list their a,b,c values identically.
If flag = 0, no a,b,c values are listed on the line, just the If flag = 0, no a,b,c values are listed on the line, just the
(ignored) ID. (ignored) ID.
@ -459,8 +486,9 @@ If flag = 0, no a,b,c values are listed on the line, just the
If flag = 1, a,b,c are listed, where a = bondtype of the bond between If flag = 1, a,b,c are listed, where a = bondtype of the bond between
the central atom and the first non-central atom (value b in the Shake the central atom and the first non-central atom (value b in the Shake
Atoms section), b = bondtype of the bond between the central atom and Atoms section), b = bondtype of the bond between the central atom and
the second non-central atom (value c in the Shake Atoms section), and c = the second non-central atom (value c in the Shake Atoms section), and c
the angle type (1 to Nangletypes) of the angle between the 3 atoms. = the angle type (1 to Nangletypes, or angle type label) of the angle
between the 3 atoms.
If flag = 2, only a is listed, where a = bondtype of the bond between If flag = 2, only a is listed, where a = bondtype of the bond between
the 2 atoms in the cluster. the 2 atoms in the cluster.
@ -473,9 +501,9 @@ and the second non-central atom (value c in the Shake Atoms section).
If flag = 4, a,b,c are listed, where a = bondtype of the bond between If flag = 4, a,b,c are listed, where a = bondtype of the bond between
the central atom and the first non-central atom (value b in the Shake the central atom and the first non-central atom (value b in the Shake
Atoms section), b = bondtype of the bond between the central atom and Atoms section), b = bondtype of the bond between the central atom and
the second non-central atom (value c in the Shake Atoms section), and c = the second non-central atom (value c in the Shake Atoms section), and c
bondtype of the bond between the central atom and the third non-central = bondtype of the bond between the central atom and the third
atom (value d in the Shake Atoms section). non-central atom (value d in the Shake Atoms section).
See the :doc:`fix shake <fix_shake>` page for a further description See the :doc:`fix shake <fix_shake>` page for a further description
of SHAKE clusters. of SHAKE clusters.

49
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@ -10,7 +10,7 @@ Syntax
pair_coeff I J args pair_coeff I J args
* I,J = atom types (see asterisk form below) * I,J = numeric atom types (see asterisk form below), or type labels
* args = coefficients for one or more pairs of atom types * args = coefficients for one or more pairs of atom types
Examples Examples
@ -26,6 +26,10 @@ Examples
pair_coeff * 3 morse.table ENTRY1 pair_coeff * 3 morse.table ENTRY1
pair_coeff 1 2 lj/cut 1.0 1.0 2.5 # (for pair_style hybrid) pair_coeff 1 2 lj/cut 1.0 1.0 2.5 # (for pair_style hybrid)
labelmap atom 1 C
labelmap atom 2 H
pair_coeff C H 1.0 1.0 2.5
Description Description
""""""""""" """""""""""
@ -34,20 +38,27 @@ atom types. The number and meaning of the coefficients depends on the
pair style. Pair coefficients can also be set in the data file read pair style. Pair coefficients can also be set in the data file read
by the :doc:`read_data <read_data>` command or in a restart file. by the :doc:`read_data <read_data>` command or in a restart file.
I and J can be specified in one of two ways. Explicit numeric values I and J can be specified in one of several ways. Explicit numeric
can be used for each, as in the first example above. I <= J is values can be used for each, as in the first example above. Or, one
required. LAMMPS sets the coefficients for the symmetric J,I or both of the types in the I,J pair can be a type label, which is an
interaction to the same values. alphanumeric string defined by the :doc:`labelmap <labelmap>` command
or in a section of a data file read by the :doc:`read_data
<read_data>` command, and which converts internally to a numeric type.
Internally, LAMMPS will set coefficients for the symmetric J,I
interaction to the same values as the I,J interaction.
A wildcard asterisk can be used in place of or in conjunction with the For numeric values only, a wildcard asterisk can be used in place of or
I,J arguments to set the coefficients for multiple pairs of atom in conjunction with the I,J arguments to set the coefficients for
types. This takes the form "\*" or "\*n" or "n\*" or "m\*n". If N = the multiple pairs of atom types. This takes the form "\*" or "\*n" or
number of atom types, then an asterisk with no numeric values means all "n\*" or "m\*n". If :math:`N` is the number of atom types, then an
types from 1 to N. A leading asterisk means all types from 1 to n asterisk with no numeric values means all types from 1 to :math:`N`. A
(inclusive). A trailing asterisk means all types from n to N leading asterisk means all types from 1 to n (inclusive). A trailing
(inclusive). A middle asterisk means all types from m to n asterisk means all types from n to :math:`N` (inclusive). A middle
(inclusive). Note that only type pairs with I <= J are considered; if asterisk means all types from m to n (inclusive). For the asterisk
asterisks imply type pairs where J < I, they are ignored. syntax, only type pairs with I <= J are considered; if asterisks imply
type pairs where J < I, they are ignored. Again internally, LAMMPS will
set the coefficients for the symmetric J,I interactions to the same
values as the I <= J interactions.
Note that a pair_coeff command can override a previous setting for the Note that a pair_coeff command can override a previous setting for the
same I,J pair. For example, these commands set the coeffs for all I,J same I,J pair. For example, these commands set the coeffs for all I,J
@ -63,11 +74,11 @@ same format as the arguments of the pair_coeff command in an input
script, with the exception of the I,J type arguments. In each line of script, with the exception of the I,J type arguments. In each line of
the "Pair Coeffs" section of a data file, only a single type I is the "Pair Coeffs" section of a data file, only a single type I is
specified, which sets the coefficients for type I interacting with specified, which sets the coefficients for type I interacting with
type I. This is because the section has exactly N lines, where N = type I. This is because the section has exactly :math:`N` lines, where
the number of atom types. For this reason, the wild-card asterisk :math:`N` is the number of atom types. For this reason, the wild-card
should also not be used as part of the I argument. Thus in a data asterisk should also not be used as part of the I argument. Thus in a
file, the line corresponding to the first example above would be listed data file, the line corresponding to the first example above would be
as listed as
.. parsed-literal:: .. parsed-literal::

220
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@ -164,6 +164,12 @@ other types already exist. All five offset values must be specified,
but individual values will be ignored if the data file does not use but individual values will be ignored if the data file does not use
that attribute (e.g. no bonds). that attribute (e.g. no bonds).
.. note::
Offsets are **ignored** on lines using type labels, as the type
labels will determine the actual types directly depending on the
current :doc:`labelmap <labelmap>` settings.
The *shift* keyword can be used to specify an (Sx, Sy, Sz) The *shift* keyword can be used to specify an (Sx, Sy, Sz)
displacement applied to the coordinates of each atom. Sz must be 0.0 displacement applied to the coordinates of each atom. Sz must be 0.0
for a 2d simulation. This is a mechanism for adding structured for a 2d simulation. This is a mechanism for adding structured
@ -227,22 +233,27 @@ The file will be read line by line, but there is a limit of 254
characters per line and characters beyond that limit will be ignored. characters per line and characters beyond that limit will be ignored.
A data file has a header and a body. The header appears first. The A data file has a header and a body. The header appears first. The
first line of the header is always skipped; it typically contains a first line of the header and thus of the data file is *always* skipped;
description of the file. Then lines are read one at a time. Lines it typically contains a description of the file or a comment from the
can have a trailing comment starting with '#' that is ignored. If the software that created the file.
line is blank (only white-space after comment is deleted), it is
skipped. If the line contains a header keyword, the corresponding
value(s) is read from the line. If it does not contain a header
keyword, the line begins the body of the file.
The body of the file contains zero or more sections. The first line Then lines are read one line at a time. Lines can have a trailing
of a section has only a keyword. This line can have a trailing comment starting with '#' that is ignored. There *must* be at least one
comment starting with '#' that is either ignored or can be used to blank between any valid content and the comment. If a line is blank
check for a style match, as described below. The next line is (i.e. contains only white-space after comments are deleted), it is
skipped. The remaining lines of the section contain values. The skipped. If the line contains a header keyword, the corresponding
number of lines depends on the section keyword as described below. value(s) is/are read from the line. A line that is *not* blank and does
Zero or more blank lines can be used between sections. Sections can *not* contain a header keyword begins the body of the file.
appear in any order, with a few exceptions as noted below.
The body of the file contains zero or more sections. The first line of
a section has only a keyword. This line can have a trailing comment
starting with '#' that is either ignored or can be used to check for a
style match, as described below. There must be a blank between the
keyword and any comment. The *next* line is *always* skipped. The
remaining lines of the section contain values. The number of lines
depends on the section keyword as described below. Zero or more blank
lines can be used *between* sections. Sections can appear in any order,
with a few exceptions as noted below.
The keyword *fix* can be used one or more times. Each usage specifies The keyword *fix* can be used one or more times. Each usage specifies
a fix that will be used to process a specific portion of the data a fix that will be used to process a specific portion of the data
@ -477,6 +488,7 @@ These are the section keywords for the body of the file.
* *Atoms, Velocities, Masses, Ellipsoids, Lines, Triangles, Bodies* = atom-property sections * *Atoms, Velocities, Masses, Ellipsoids, Lines, Triangles, Bodies* = atom-property sections
* *Bonds, Angles, Dihedrals, Impropers* = molecular topology sections * *Bonds, Angles, Dihedrals, Impropers* = molecular topology sections
* *Atom Type Labels, Bond Type Labels, Angle Type Labels, Dihedral Type Labels, Improper Type Labels* = type label maps
* *Pair Coeffs, PairIJ Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, Improper Coeffs* = force field sections * *Pair Coeffs, PairIJ Coeffs, Bond Coeffs, Angle Coeffs, Dihedral Coeffs, Improper Coeffs* = force field sections
* *BondBond Coeffs, BondAngle Coeffs, MiddleBondTorsion Coeffs, EndBondTorsion Coeffs, AngleTorsion Coeffs, AngleAngleTorsion Coeffs, BondBond13 Coeffs, AngleAngle Coeffs* = class 2 force field sections * *BondBond Coeffs, BondAngle Coeffs, MiddleBondTorsion Coeffs, EndBondTorsion Coeffs, AngleTorsion Coeffs, AngleAngleTorsion Coeffs, BondBond13 Coeffs, AngleAngle Coeffs* = class 2 force field sections
@ -503,7 +515,8 @@ section is described including the number of lines it must contain and
rules (if any) for where it can appear in the data file. rules (if any) for where it can appear in the data file.
Any individual line in the various sections can have a trailing Any individual line in the various sections can have a trailing
comment starting with "#" for annotation purposes. E.g. in the comment starting with "#" for annotation purposes. There must be at least
one blank between valid content and the comment. E.g. in the
Atoms section: Atoms section:
.. parsed-literal:: .. parsed-literal::
@ -536,6 +549,26 @@ input script.
---------- ----------
*Angle Type Labels* section:
* one line per angle type
* line syntax: ID label
.. parsed-literal::
ID = angle type (1-N)
label = alphanumeric type label
Define alphanumeric type labels for each numeric angle type. These
can be used in the Angles section in place of a numeric type, but only
if the this section appears before the Angles section.
See the :doc:`Howto type labels <Howto_type_labels>` doc page for the
allowed syntax of type labels and a general discussion of how type
labels can be used.
----------
*AngleAngle Coeffs* section: *AngleAngle Coeffs* section:
* one line per improper type * one line per improper type
@ -568,7 +601,7 @@ input script.
.. parsed-literal:: .. parsed-literal::
ID = number of angle (1-Nangles) ID = number of angle (1-Nangles)
type = angle type (1-Nangletype) type = angle type (1-Nangletype, or type label)
atom1,atom2,atom3 = IDs of 1st,2nd,3rd atom in angle atom1,atom2,atom3 = IDs of 1st,2nd,3rd atom in angle
example: example:
@ -580,8 +613,15 @@ example:
The 3 atoms are ordered linearly within the angle. Thus the central The 3 atoms are ordered linearly within the angle. Thus the central
atom (around which the angle is computed) is the atom2 in the list. atom (around which the angle is computed) is the atom2 in the list.
E.g. H,O,H for a water molecule. The *Angles* section must appear E.g. H,O,H for a water molecule. The *Angles* section must appear
after the *Atoms* section. All values in this section must be after the *Atoms* section.
integers (1, not 1.0).
All values in this section must be integers (1, not 1.0). However,
the type can be a numeric value or an alphanumeric label. The latter
is only allowed if the type label has been defined by the
:doc:`labelmap <labelmap>` command or an Angle Type Labels section
earlier in the data file. See the :doc:`Howto type labels
<Howto_type_labels>` doc page for the allowed syntax of type labels
and a general discussion of how type labels can be used.
---------- ----------
@ -597,6 +637,26 @@ integers (1, not 1.0).
---------- ----------
*Atom Type Labels* section:
* one line per atom type
* line syntax: ID label
.. parsed-literal::
ID = numeric atom type (1-N)
label = alphanumeric type label
Define alphanumeric type labels for each numeric atom type. These
can be used in the Atoms section in place of a numeric type, but only
if the Atom Type Labels section appears before the Atoms section.
See the :doc:`Howto type labels <Howto_type_labels>` doc page for the
allowed syntax of type labels and a general discussion of how type
labels can be used.
----------
*Atoms* section: *Atoms* section:
* one line per atom * one line per atom
@ -670,7 +730,7 @@ of analysis.
The per-atom values have these meanings and units, listed alphabetically: The per-atom values have these meanings and units, listed alphabetically:
* atom-ID = integer ID of atom * atom-ID = integer ID of atom
* atom-type = type of atom (1-Ntype) * atom-type = type of atom (1-Ntype, or type label)
* bodyflag = 1 for body particles, 0 for point particles * bodyflag = 1 for body particles, 0 for point particles
* bond_nt = bond NT factor for MESONT particles (?? units) * bond_nt = bond NT factor for MESONT particles (?? units)
* buckling = buckling factor for MESONT particles (?? units) * buckling = buckling factor for MESONT particles (?? units)
@ -722,6 +782,13 @@ not used (e.g. an atomic system with no bonds), and you don't care if
unique atom IDs appear in dump files, then the atom-IDs can all be set unique atom IDs appear in dump files, then the atom-IDs can all be set
to 0. to 0.
The atom-type can be a numeric value or an alphanumeric label. The
latter is only allowed if the type label has been defined by the
:doc:`labelmap <labelmap>` command or an Atom Type Labels section
earlier in the data file. See the :doc:`Howto type labels
<Howto_type_labels>` doc page for the allowed syntax of type labels
and a general discussion of how type labels can be used.
The molecule ID is a second identifier attached to an atom. Normally, it The molecule ID is a second identifier attached to an atom. Normally, it
is a number from 1 to N, identifying which molecule the atom belongs is a number from 1 to N, identifying which molecule the atom belongs
to. It can be 0 if it is a non-bonded atom or if you don't care to to. It can be 0 if it is a non-bonded atom or if you don't care to
@ -932,6 +999,26 @@ script.
---------- ----------
*Bond Type Labels* section:
* one line per bond type
* line syntax: ID label
.. parsed-literal::
ID = bond type (1-N)
label = alphanumeric type label
Define alphanumeric type labels for each numeric bond type. These can
be used in the Bonds section in place of a numeric type, but only if
the this section appears before the Angles section.
See the :doc:`Howto type labels <Howto_type_labels>` doc page for the
allowed syntax of type labels and a general discussion of how type
labels can be used.
----------
*BondAngle Coeffs* section: *BondAngle Coeffs* section:
* one line per angle type * one line per angle type
@ -976,7 +1063,7 @@ script.
.. parsed-literal:: .. parsed-literal::
ID = bond number (1-Nbonds) ID = bond number (1-Nbonds)
type = bond type (1-Nbondtype) type = bond type (1-Nbondtype, or type label)
atom1,atom2 = IDs of 1st,2nd atom in bond atom1,atom2 = IDs of 1st,2nd atom in bond
* example: * example:
@ -985,8 +1072,15 @@ script.
12 3 17 29 12 3 17 29
The *Bonds* section must appear after the *Atoms* section. All values The *Bonds* section must appear after the *Atoms* section.
in this section must be integers (1, not 1.0).
All values in this section must be integers (1, not 1.0). However,
the type can be a numeric value or an alphanumeric label. The latter
is only allowed if the type label has been defined by the
:doc:`labelmap <labelmap>` command or a Bond Type Labels section
earlier in the data file. See the :doc:`Howto type labels
<Howto_type_labels>` doc page for the allowed syntax of type labels
and a general discussion of how type labels can be used.
---------- ----------
@ -1014,6 +1108,26 @@ Coefficients can also be set via the
---------- ----------
*Dihedral Type Labels* section:
* one line per dihedral type
* line syntax: ID label
.. parsed-literal::
ID = dihedral type (1-N)
label = alphanumeric type label
Define alphanumeric type labels for each numeric dihedral type. These
can be used in the Dihedrals section in place of a numeric type, but
only if the this section appears before the Dihedrals section.
See the :doc:`Howto type labels <Howto_type_labels>` doc page for the
allowed syntax of type labels and a general discussion of how type
labels can be used.
----------
*Dihedrals* section: *Dihedrals* section:
* one line per dihedral * one line per dihedral
@ -1022,7 +1136,7 @@ Coefficients can also be set via the
.. parsed-literal:: .. parsed-literal::
ID = number of dihedral (1-Ndihedrals) ID = number of dihedral (1-Ndihedrals)
type = dihedral type (1-Ndihedraltype) type = dihedral type (1-Ndihedraltype, or type label)
atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atom in dihedral atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atom in dihedral
* example: * example:
@ -1032,8 +1146,15 @@ Coefficients can also be set via the
12 4 17 29 30 21 12 4 17 29 30 21
The 4 atoms are ordered linearly within the dihedral. The *Dihedrals* The 4 atoms are ordered linearly within the dihedral. The *Dihedrals*
section must appear after the *Atoms* section. All values in this section must appear after the *Atoms* section.
section must be integers (1, not 1.0).
All values in this section must be integers (1, not 1.0). However,
the type can be a numeric value or an alphanumeric label. The latter
is only allowed if the type label has been defined by the
:doc:`labelmap <labelmap>` command or a Dihedral Type Labels section
earlier in the data file. See the :doc:`Howto type labels
<Howto_type_labels>` doc page for the allowed syntax of type labels
and a general discussion of how type labels can be used.
---------- ----------
@ -1115,6 +1236,26 @@ Coefficients can also be set via the
---------- ----------
*Improper Type Labels* section:
* one line per improper type
* line syntax: ID label
.. parsed-literal::
ID = improper type (1-N)
label = alphanumeric type label
Define alphanumeric type labels for each numeric improper type. These
can be used in the Impropers section in place of a numeric type, but
only if the this section appears before the Impropers section.
See the :doc:`Howto type labels <Howto_type_labels>` doc page for the
allowed syntax of type labels and a general discussion of how type
labels can be used.
----------
*Impropers* section: *Impropers* section:
* one line per improper * one line per improper
@ -1123,7 +1264,7 @@ Coefficients can also be set via the
.. parsed-literal:: .. parsed-literal::
ID = number of improper (1-Nimpropers) ID = number of improper (1-Nimpropers)
type = improper type (1-Nimpropertype) type = improper type (1-Nimpropertype, or type label)
atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atom in improper atom1,atom2,atom3,atom4 = IDs of 1st,2nd,3rd,4th atom in improper
* example: * example:
@ -1133,11 +1274,19 @@ Coefficients can also be set via the
12 3 17 29 13 100 12 3 17 29 13 100
The ordering of the 4 atoms determines the definition of the improper The ordering of the 4 atoms determines the definition of the improper
angle used in the formula for each :doc:`improper style <improper_style>`. See the doc pages for individual styles angle used in the formula for each :doc:`improper style
for details. <improper_style>`. See the doc pages for individual styles for
details.
The *Impropers* section must appear after the *Atoms* section. All The *Impropers* section must appear after the *Atoms* section.
values in this section must be integers (1, not 1.0).
All values in this section must be integers (1, not 1.0). However,
the type can be a numeric value or an alphanumeric label. The latter
is only allowed if the type label has been defined by the
:doc:`labelmap <labelmap>` command or a Improper Type Labels section
earlier in the data file. See the :doc:`Howto type labels
<Howto_type_labels>` doc page for the allowed syntax of type labels
and a general discussion of how type labels can be used.
---------- ----------
@ -1181,7 +1330,7 @@ The *Lines* section must appear after the *Atoms* section.
.. parsed-literal:: .. parsed-literal::
ID = atom type (1-N) ID = atom type (1-N or atom type label)
mass = mass value mass = mass value
* example: * example:
@ -1195,6 +1344,13 @@ This defines the mass of each atom type. This can also be set via the
used for atom styles that define a mass for individual atoms - used for atom styles that define a mass for individual atoms -
e.g. :doc:`atom_style sphere <atom_style>`. e.g. :doc:`atom_style sphere <atom_style>`.
Using type labels instead of atom type numbers is only allowed if the
type label has been defined by the :doc:`labelmap <labelmap>` command or
a Atom Type Labels section earlier in the data file. See the
:doc:`Howto type labels <Howto_type_labels>` doc page for the allowed
syntax of type labels and a general discussion of how type labels can be
used.
---------- ----------
*MiddleBondTorsion Coeffs* section: *MiddleBondTorsion Coeffs* section:

17
doc/src/restart.rst
View File

@ -12,7 +12,7 @@ Syntax
restart N root keyword value ... restart N root keyword value ...
restart N file1 file2 keyword value ... restart N file1 file2 keyword value ...
* N = write a restart file every this many timesteps * N = write a restart file on timesteps which are multipls of N
* N can be a variable (see below) * N can be a variable (see below)
* root = filename to which timestep # is appended * root = filename to which timestep # is appended
* file1,file2 = two full filenames, toggle between them when writing file * file1,file2 = two full filenames, toggle between them when writing file
@ -42,13 +42,14 @@ Description
""""""""""" """""""""""
Write out a binary restart file with the current state of the Write out a binary restart file with the current state of the
simulation every so many timesteps, in either or both of two modes, as simulation on timesteps which are a multiple of N. A value of N = 0
a run proceeds. A value of 0 means do not write out any restart means do not write out any restart files, which is the default.
files. The two modes are as follows. If one filename is specified, a Restart files are written in one (or both) of two modes as a run
series of filenames will be created which include the timestep in the proceeds. If one filename is specified, a series of filenames will be
filename. If two filenames are specified, only 2 restart files will created which include the timestep in the filename. If two filenames
be created, with those names. LAMMPS will toggle between the 2 names are specified, only 2 restart files will be created, with those names.
as it writes successive restart files. LAMMPS will toggle between the 2 names as it writes successive restart
files.
Note that you can specify the restart command twice, once with a Note that you can specify the restart command twice, once with a
single filename and once with two filenames. This would allow you, single filename and once with two filenames. This would allow you,

10
doc/src/variable.rst
View File

@ -66,7 +66,7 @@ Syntax
bound(group,dir,region), gyration(group,region), ke(group,reigon), bound(group,dir,region), gyration(group,region), ke(group,reigon),
angmom(group,dim,region), torque(group,dim,region), angmom(group,dim,region), torque(group,dim,region),
inertia(group,dimdim,region), omega(group,dim,region) inertia(group,dimdim,region), omega(group,dim,region)
special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), is_os(name), extract_setting(name) special functions = sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x), is_file(name), is_os(name), extract_setting(name), label2type(kind,label)
feature functions = is_active(category,feature), is_available(category,feature), is_defined(category,id) feature functions = is_active(category,feature), is_available(category,feature), is_defined(category,id)
atom value = id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i] atom value = id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i]
atom vector = id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q atom vector = id, mass, type, mol, x, y, z, vx, vy, vz, fx, fy, fz, q
@ -505,7 +505,7 @@ references, and references to other variables.
+--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Region functions | count(ID,IDR), mass(ID,IDR), charge(ID,IDR), xcm(ID,dim,IDR), vcm(ID,dim,IDR), fcm(ID,dim,IDR), bound(ID,dir,IDR), gyration(ID,IDR), ke(ID,IDR), angmom(ID,dim,IDR), torque(ID,dim,IDR), inertia(ID,dimdim,IDR), omega(ID,dim,IDR) | | Region functions | count(ID,IDR), mass(ID,IDR), charge(ID,IDR), xcm(ID,dim,IDR), vcm(ID,dim,IDR), fcm(ID,dim,IDR), bound(ID,dir,IDR), gyration(ID,IDR), ke(ID,IDR), angmom(ID,dim,IDR), torque(ID,dim,IDR), inertia(ID,dimdim,IDR), omega(ID,dim,IDR) |
+--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Special functions | sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x) | | Special functions | sum(x), min(x), max(x), ave(x), trap(x), slope(x), gmask(x), rmask(x), grmask(x,y), next(x), label2type(kind,label) |
+--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
| Atom values | id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i] | | Atom values | id[i], mass[i], type[i], mol[i], x[i], y[i], z[i], vx[i], vy[i], vz[i], fx[i], fy[i], fz[i], q[i] |
+--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+ +--------------------+-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+
@ -962,6 +962,12 @@ types, bond types and so on. For the full list of available keywords
*name* and their meaning, see the documentation for extract_setting() *name* and their meaning, see the documentation for extract_setting()
via the link in this paragraph. via the link in this paragraph.
The label2type() function converts type labels into numeric types, using label
maps created by the :doc:`labelmap <labelmap>` or :doc:`read_data <read_data>`
commands. The first argument is the label map kind (atom, bond, angle,
dihedral, or improper) and the second argument is the label. The function
returns the corresponding numeric type.
---------- ----------
Feature Functions Feature Functions

47
doc/src/write_data.rst
View File

@ -12,12 +12,14 @@ Syntax
* file = name of data file to write out * file = name of data file to write out
* zero or more keyword/value pairs may be appended * zero or more keyword/value pairs may be appended
* keyword = *pair* or *nocoeff* * keyword = *pair* or *nocoeff* or *nofix* or *nolabelmap*
.. parsed-literal:: .. parsed-literal::
*nocoeff* = do not write out force field info *nocoeff* = do not write out force field info
*nofix* = do not write out extra sections read by fixes *nofix* = do not write out extra sections read by fixes
*nolabelmap* = do not write out type labels
*types* value = *numeric* or *labels*
*pair* value = *ii* or *ij* *pair* value = *ii* or *ij*
*ii* = write one line of pair coefficient info per atom type *ii* = write one line of pair coefficient info per atom type
*ij* = write one line of pair coefficient info per IJ atom type pair *ij* = write one line of pair coefficient info per IJ atom type pair
@ -94,16 +96,39 @@ data file is read.
---------- ----------
The *nocoeff* keyword requests that no force field parameters should Use of the *nocoeff* keyword means no force field parameters are
be written to the data file. This can be very helpful, if one wants written to the data file. This can be helpful, for example, if you
to make significant changes to the force field or if the parameters want to make significant changes to the force field or if the force
are read in separately anyway, e.g. from an include file. field parameters are read in separately, e.g. from an include file.
The *nofix* keyword requests that no extra sections read by fixes Use of the *nofix* keyword means no extra sections read by fixes are
should be written to the data file (see the *fix* option of the written to the data file (see the *fix* option of the :doc:`read_data
:doc:`read_data <read_data>` command for details). For example, this <read_data>` command for details). For example, this option excludes
option excludes sections for user-created per-atom properties sections for user-created per-atom properties from :doc:`fix
from :doc:`fix property/atom <fix_property_atom>`. property/atom <fix_property_atom>`.
The *nolabelmap* and *types* keywords refer to type labels that may be
defined for numeric atom types, bond types, angle types, etc. The
label map can be defined in two ways, either by the :doc:`labelmap
<labelmap>` command or in data files read by the :doc:`read_data
<read_data>` command which have sections for Atom Type Labels, Bond
Type Labels, Angle Type Labels, etc. See the :doc:`Howto type labels
<Howto_type_labels>` doc page for the allowed syntax of type labels
and a general discussion of how type labels can be used.
Use of the *nolabelmap* keyword means that even if type labels exist
for a given type-kind (Atoms, Bonds, Angles, etc.), type labels are
not written to the data file. By default, they are written if they
exist. A type label must be defined for every numeric type (within a
given type-kind) to be written to the data file.
The *types* keyword determines how atom types, bond types, angle
types, etc are written into these data file sections: Atoms, Bonds,
Angles, etc. The default is the *numeric* setting, even if type label
maps exist. If the *labels* setting is used, type labels will be
written to the data file, if the corresponding label map exists. Note
that when using *types labels*, the *nolabelmap* keyword cannot be
used.
The *pair* keyword lets you specify in what format the pair The *pair* keyword lets you specify in what format the pair
coefficient information is written into the data file. If the value coefficient information is written into the data file. If the value
@ -144,4 +169,4 @@ Related commands
Default Default
""""""" """""""
The option defaults are pair = ii. The option defaults are pair = ii and types_style = numeric.

10
doc/utils/sphinx-config/false_positives.txt
View File

@ -61,6 +61,7 @@ ajs
akohlmey akohlmey
Aktulga Aktulga
al al
alabel
alain alain
Alain Alain
Alamos Alamos
@ -287,6 +288,7 @@ bitrates
Bitzek Bitzek
Bjerrum Bjerrum
Bkappa Bkappa
blabel
Blaise Blaise
blanchedalmond blanchedalmond
blocksize blocksize
@ -750,6 +752,7 @@ dissipative
Dissipative Dissipative
distharm distharm
dl dl
dlabel
dlambda dlambda
DLAMMPS DLAMMPS
dll dll
@ -1425,6 +1428,7 @@ ijk
ijkl ijkl
ik ik
Ikeshoji Ikeshoji
ilabel
Ilie Ilie
ilmenau ilmenau
Ilmenau Ilmenau
@ -1714,6 +1718,8 @@ Kusters
Kutta Kutta
Kuznetsov Kuznetsov
kx kx
labelmap
Labelmap
Lachet Lachet
Lackmann Lackmann
Ladd Ladd
@ -1937,6 +1943,8 @@ Manolopoulos
manpages manpages
manybody manybody
MANYBODY MANYBODY
mapID
mapIDs
Maras Maras
Marchetti Marchetti
Marchi Marchi
@ -2258,6 +2266,7 @@ natively
Natoli Natoli
natoms natoms
Natoms Natoms
Natomtype
Nattempt Nattempt
navajowhite navajowhite
Navier Navier
@ -3554,6 +3563,7 @@ typeargs
typedefs typedefs
typeI typeI
typeJ typeJ
typelabel
typeN typeN
typesafe typesafe
Tz Tz

24
examples/QM/LATTE/2uo2.lmp Normal file
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@ -0,0 +1,24 @@
LAMMPS Description
6 atoms
2 atom types
0.0000000000000000 10.800000000000001 xlo xhi
0.0000000000000000 5.4000000000000004 ylo yhi
0.0000000000000000 5.4000000000000004 zlo zhi
3.3065463576978537E-016 3.3065463576978537E-016 3.3065463576978537E-016 xy xz yz
Masses
1 238.05078125000000
2 15.994915008544922
Atoms
1 1 1 0.0 2.70000 8.10000 0.00000
2 1 2 0.0 1.35000 9.45000 1.35000
3 1 2 0.0 4.05000 9.45000 1.35000
4 1 1 0.0 2.70000 10.80000 2.70000
5 1 2 0.0 1.35000 12.15000 4.05000
6 1 2 0.0 4.05000 12.15000 4.05000

27
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@ -0,0 +1,27 @@
LAMMPS Description
9 atoms
2 atom types
0.0000000000000000 16.199999999999999 xlo xhi
0.0000000000000000 5.4000000000000004 ylo yhi
0.0000000000000000 5.4000000000000004 zlo zhi
3.3065463576978537E-016 3.3065463576978537E-016 3.3065463576978537E-016 xy xz yz
Masses
1 238.05078125000000
2 15.994915008544922
Atoms
1 1 1 0.0 2.70000 8.10000 0.00000
2 1 2 0.0 1.35000 9.45000 1.35000
3 1 2 0.0 4.05000 9.45000 1.35000
4 1 1 0.0 2.70000 10.80000 2.70000
5 1 2 0.0 1.35000 12.15000 4.05000
6 1 2 0.0 4.05000 12.15000 4.05000
7 1 1 0.0 2.70000 13.50000 5.40000
8 1 2 0.0 1.35000 14.85000 6.75000
9 1 2 0.0 4.05000 14.85000 6.75000

30
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@ -0,0 +1,30 @@
LAMMPS Description
12 atoms
2 atom types
0.0000000000000000 10.800000000000001 xlo xhi
0.0000000000000000 10.800000000000001 ylo yhi
0.0000000000000000 5.4000000000000004 zlo zhi
6.6130927153957075E-016 3.3065463576978537E-016 3.3065463576978537E-016 xy xz yz
Masses
1 238.05078125000000
2 15.994915008544922
Atoms
1 1 1 0.0 2.70000 8.10000 0.00000
2 1 2 0.0 1.35000 9.45000 1.35000
3 1 2 0.0 4.05000 9.45000 1.35000
4 1 1 0.0 5.40000 8.10000 2.70000
5 1 2 0.0 4.05000 9.45000 4.05000
6 1 2 0.0 6.75000 9.45000 4.05000
7 1 1 0.0 2.70000 10.80000 2.70000
8 1 2 0.0 1.35000 12.15000 4.05000
9 1 2 0.0 4.05000 12.15000 4.05000
10 1 1 0.0 5.40000 10.80000 5.40000
11 1 2 0.0 4.05000 12.15000 6.75000
12 1 2 0.0 6.75000 12.15000 6.75000

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@ -0,0 +1,149 @@
LATTE is a semi-empirical tight-binding quantum code, developed
primarily at Los Alamos National Labs.
See these links:
https://www.osti.gov/biblio/1526907-los-alamos-transferable-tight-binding-energetics-latte-version
https://github.com/lanl/LATTE
LAMMPS has 2 ways of working with LATTE:
(1) Via its LATTE package and the fix latte command
must run LAMMPS on a single processor, it calls LATTE as a library
(2) Via its MDI package and the code-coupling MDI library
(a) can run LAMMPS and LATTE as stand-alone codes
LAMMPS can be run on any number of procs
LATTE must run on a single proc, but can use OpenMP
(b) can run LAMMPS with LATTE as a plug-in library
must run LAMMPS on a single processor
Examples for use case (1) are in the examples/latte dir. Use case (2)
is illustrated in this dir.
NOTE: If you compare MDI runs in this dir to similar fix latte runs in
examples/latte, the answers for energy and virial will be differnt.
This is b/c the version of LATTE used by the fix latte command within
the LATTE package is older than the version of LATTE used here.
------------------
Building 3 codes needed to run these examples
(1) Download and build MDI
% git clone git@github.com:MolSSI-MDI/MDI_Library.git mdi
% cd mdi
% mkdir build; cd build
% cmake .. # includes support for all langauges (incl Fortran, Python)
% make
(2) Download and build LATTE with MDI support
% git clone git@github.com:lanl/LATTE.git latte
% cd latte
% git checkout skimLATTE-progress # goto branch with MDI support
% cp makefiles/makefile.CHOICES.mdi makefile.CHOICES # so can now edit
% edit makefile.CHOICES settings to have these settings:
MAKELIB = OFF, SHARED = ON, MDI = ON
MDI_PATH must point to CMake build of MDI in (1),
e.g. /home/sjplimp/mdi/build/MDI_Library
comment out 2 LIB lines with CUDA-CUDART_LIBRARY
% make clean
% make # creates liblatte.so and LATTE_DOUBLE with support for MDI
(3) Build LAMMPS with its MDI package
also with the MOLECULE package for these example scripts
Build with CMake (NOTE: do not use traditional make for this use case)
% cd lammps
% mkdir build; cd build
% cmake -D PKG_MDI=yes -D PKG_MOLECULE=yes ../cmake
% make # creates lmp
(4) Copy LAMMPS and LATTE executables into this dir
Copy the LAMMPS executable into this dir as lmp_mpi.
Copy the LATTE executable LATTE_DOUBLE into this dir.
The run commands below assume you have done this.
(5) Insure LD_LIBRARY_PATH includes the dir where MDI was built in (1)
with its libmdi.so file, e.g. mdi/build/MDI_Library. This is needed
so when LATTE_DOUBLE runs as an executable it will able to find
libmdi.so.
------------------
Notes on LATTE usage
You must run this version of LATTE on a single MPI processor.
However, you can use OpenMP with LATTE. To do this you need to build
LATTE with OpenMP support by editing the makefile.CHOICES file to
include -fopenmp with FFLAGS and LINKFLAGS. Also -lapack and -lblas
need to be added to LIB, and those libraries must be available on your
system. For best performance you should also build LATTE with its
PROGRESS and BML libraries. Building those libs is more complex,
see details here:
https://github.com/lanl/LATTE_SUPER/tree/allMachines/Laptop
At run time, you need to also first set an environment variable for
the number of OpenMP threads to use, e.g.
% export OMP_NUM_THREADS=12
By default LATTE reads the latte.in file for its parameters. That
file specifies other files LATTE will read. With MDI, the driver code
(e.g. LAMMPS) can use the >FNAME command to specify an alternate
filename to use instead of latte.in.
By default LATTE writes out a log.latte file with info about its
calculations. An "OUTFILE= logfile" setting in latte.in can rename
this file.
---------
Run example #1: AIMD
* Run with MPI: 1 proc each
mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" \
-in in.aimd -log log.aimd.lammps.mpi : \
-np 1 LATTE_DOUBLE -mdi "-name LATTE -role ENGINE -method MPI"
* Run with MPI: 2 procs for LAMMPS, 1 for LATTE
mpirun -np 2 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" \
-in in.aimd -log log.aimd.lammps.mpi : \
-np 1 LATTE_DOUBLE -mdi "-name LATTE -role ENGINE -method MPI"
* Run in plugin mode: 1 proc
lmp_mpi -mdi \
"-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/latte/git" \
-in in.aimd.plugin -log log.aimd.lammps.plugin
NOTE: The -plugin_path needs to point to where LATTE was built in step
(2).
---------
Run example #2: sequence of configurations
* Run with MPI: 1 proc each
mpirun -np 1 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" \
-in in.series -log log.series.lammps.mpi : \
-np 1 LATTE_DOUBLE -mdi "-name LATTE -role ENGINE -method MPI"
* Run with MPI: 2 procs for LAMMPS, 1 for LATTE
mpirun -np 2 lmp_mpi -mdi "-name LMP -role DRIVER -method MPI" \
-in in.series -log log.series.lammps.mpi : \
-np 1 LATTE_DOUBLE -mdi "-name LATTE -role ENGINE -method MPI"
* Run in plugin mode: 1 proc
lmp_mpi -mdi \
"-name LMP -role DRIVER -method LINK -plugin_path /home/sjplimp/latte/git" \
-in in.series.plugin -log log.series.lammps.plugin
NOTE: The -plugin_path needs to point to where LATTE was built in step
(2).

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ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z vx vy vz fx fy fz
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2 2 1.35 4.05 1.35 8.2897 4.55901 5.97376 2.35473 2.21578e-14 7.40069e-15
3 2 4.05 4.05 1.35 1.7742 6.51885 0.385522 -2.35473 2.97071e-15 -2.01341e-14
4 1 2.7 1.65327e-16 2.7 -0.325605 -1.03244 0.724324 -2.90278e-14 6.77422e-15 2.86766e-15
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6 2 4.05 1.35 4.05 1.30688 0.784281 -1.73922 -2.35473 -1.38761e-14 1.09382e-14
ITEM: TIMESTEP
1
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z vx vy vz fx fy fz
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2 2 1.35212 4.05114 1.35149 8.64389 4.55886 5.97363 2.34251 -0.00209926 -0.00172976
3 2 4.0504 4.05163 1.3501 1.41949 6.51866 0.385561 -2.34936 -0.00247497 0.00051716
4 1 2.69992 -0.00025811 2.70018 -0.325581 -1.03243 0.724334 0.00481137 0.00249244 0.00195665
5 2 1.35065 1.34963 4.0494 2.78199 -1.49112 -2.4159 2.3517 -0.00043711 0.000874754
6 2 4.05028 1.3502 4.04957 0.951796 0.784184 -1.73923 -2.35436 -0.00128625 -0.00020256
ITEM: TIMESTEP
2
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z vx vy vz fx fy fz
1 1 2.6997 2.70017 -0.000436214 -0.601396 0.335673 -0.872449 0.00939888 0.00756163 -0.00288164
2 2 1.35432 4.05228 1.35299 8.99615 4.55837 5.97323 2.32921 -0.00431846 -0.00355855
3 2 4.05071 4.05326 1.35019 1.06567 6.5181 0.385678 -2.34304 -0.00494314 0.00103532
4 1 2.69984 -0.000516214 2.70036 -0.325507 -1.03239 0.724364 0.00976944 0.00512657 0.00403686
5 2 1.35139 1.34925 4.04879 3.13634 -1.49122 -2.4157 2.34776 -0.000851489 0.00177498
6 2 4.05048 1.35039 4.04913 0.596838 0.783892 -1.73928 -2.3531 -0.00257512 -0.000406965
ITEM: TIMESTEP
3
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z vx vy vz fx fy fz
1 1 2.69955 2.70025 -0.00065433 -0.601277 0.335769 -0.872486 0.0141006 0.0112702 -0.00439552
2 2 1.35661 4.05342 1.35448 9.34633 4.55754 5.97255 2.31482 -0.00666433 -0.00549143
3 2 4.05093 4.05489 1.35029 0.712875 6.51717 0.385873 -2.33577 -0.00740896 0.00154764
4 1 2.69976 -0.000774304 2.70054 -0.325382 -1.03232 0.724417 0.0148831 0.00790884 0.00624833
5 2 1.35222 1.34888 4.04819 3.49003 -1.49137 -2.41536 2.3429 -0.0012407 0.00270313
6 2 4.05058 1.35059 4.0487 0.242138 0.783407 -1.73935 -2.35094 -0.00386511 -0.000612161
ITEM: TIMESTEP
4
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z vx vy vz fx fy fz
1 1 2.6994 2.70034 -0.000872457 -0.60111 0.335902 -0.872539 0.0188131 0.0149318 -0.00595718
2 2 1.359 4.05456 1.35597 9.69425 4.55635 5.97156 2.29933 -0.00914346 -0.00753331
3 2 4.05107 4.05652 1.35039 0.361248 6.51586 0.386144 -2.32753 -0.00987687 0.00204727
4 1 2.69967 -0.00103238 2.70072 -0.325204 -1.03223 0.724492 0.020161 0.0108455 0.00859866
5 2 1.35314 1.34851 4.04758 3.84292 -1.49159 -2.41488 2.33711 -0.00160232 0.00366164
6 2 4.0506 1.35078 4.04826 -0.112168 0.782727 -1.73946 -2.34789 -0.00515472 -0.000817084
ITEM: TIMESTEP
5
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z vx vy vz fx fy fz
1 1 2.69925 2.70042 -0.0010906 -0.600896 0.336071 -0.872607 0.0235434 0.0185473 -0.00756588
2 2 1.36146 4.0557 1.35747 10.0397 4.55478 5.97026 2.2827 -0.0117623 -0.00968894
3 2 4.05111 4.05815 1.35048 0.0109366 6.51419 0.386489 -2.31832 -0.0123511 0.00252727
4 1 2.69959 -0.00129042 2.70091 -0.324972 -1.0321 0.724592 0.0256115 0.0139425 0.0110953
5 2 1.35414 1.34814 4.04698 4.19487 -1.49186 -2.41425 2.33039 -0.00193394 0.0046529
6 2 4.05052 1.35098 4.04783 -0.465946 0.781852 -1.7396 -2.34393 -0.00644244 -0.00102066
ITEM: TIMESTEP
6
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z vx vy vz fx fy fz
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2 2 1.36401 4.05684 1.35896 10.3827 4.55279 5.96863 2.26494 -0.0145272 -0.0119629
3 2 4.05107 4.05978 1.35058 -0.337913 6.51214 0.386904 -2.30814 -0.0148362 0.00298071
4 1 2.69951 -0.00154843 2.70109 -0.324684 -1.03194 0.724717 0.0312427 0.0172058 0.0137455
5 2 1.35523 1.34776 4.04638 4.54573 -1.49217 -2.41347 2.32273 -0.00223319 0.00567932
6 2 4.05036 1.35117 4.04739 -0.819058 0.780784 -1.73977 -2.33906 -0.00772673 -0.00122181
ITEM: TIMESTEP
7
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z vx vy vz fx fy fz
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2 2 1.36665 4.05797 1.36045 10.7228 4.55038 5.96665 2.24601 -0.0174443 -0.0143597
3 2 4.05094 4.0614 1.35068 -0.685154 6.50971 0.387385 -2.29698 -0.0173365 0.00340068
4 1 2.69943 -0.00180639 2.70127 -0.324338 -1.03175 0.724871 0.0370626 0.020641 0.0165564
5 2 1.35641 1.34739 4.04577 4.89536 -1.49253 -2.41254 2.31411 -0.0024977 0.00674323
6 2 4.05012 1.35137 4.04696 -1.17137 0.779522 -1.73997 -2.33329 -0.00900604 -0.00141944
ITEM: TIMESTEP
8
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS xy xz yz pp pp pp
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0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z vx vy vz fx fy fz
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3 2 4.05073 4.06303 1.35077 -1.03064 6.50691 0.387927 -2.28482 -0.0198564 0.00378025
4 1 2.69935 -0.0020643 2.70145 -0.323932 -1.03153 0.725054 0.0430788 0.0242538 0.0195348
5 2 1.35768 1.34702 4.04517 5.24362 -1.49292 -2.41144 2.30452 -0.0027252 0.00784692
6 2 4.04978 1.35156 4.04652 -1.52274 0.778068 -1.7402 -2.32659 -0.0102788 -0.00161245
ITEM: TIMESTEP
9
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z vx vy vz fx fy fz
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3 2 4.05043 4.06466 1.35087 -1.37421 6.50372 0.388522 -2.27166 -0.0224003 0.00411244
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ITEM: TIMESTEP
10
ITEM: NUMBER OF ATOMS
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ITEM: BOX BOUNDS xy xz yz pp pp pp
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0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z vx vy vz fx fy fz
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ITEM: TIMESTEP
11
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS xy xz yz pp pp pp
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0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z vx vy vz fx fy fz
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6 2 4.05 1.35 4.05 -2.79365 0.684734 0.684734
7 1 2.7 2.7 0 -1.30843e-13 0.760572 0.760572
8 2 1.35 4.05 1.35 0.682428 -0.329901 -0.329901
9 2 4.05 4.05 1.35 -0.682428 -0.329901 -0.329901

21
examples/QM/LATTE/dump.8Sep22.series.mpi.2.4uo2 Normal file
View File

@ -0,0 +1,21 @@
ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
12
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 6.6130927153957075e-16
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z fx fy fz
1 1 2.7 8.1 0 -0.433947 2.16479 1.55466
2 2 1.35 9.45 1.35 1.64718 -0.119006 0.375837
3 2 4.05 9.45 1.35 0.999862 -1.02573 0.037629
4 1 5.4 8.1 2.7 0.433947 2.16479 1.55466
5 2 4.05 9.45 4.05 -0.999862 -1.02573 0.037629
6 2 6.75 9.45 4.05 -1.64718 -0.119006 0.375837
7 1 2.7 1.65327e-16 2.7 -0.211437 1.63064 -0.0728897
8 2 1.35 1.35 4.05 0.461807 -1.3955 -1.94959
9 2 4.05 1.35 4.05 0.708573 -1.2552 0.0543549
10 1 5.4 0 0 0.211437 1.63064 -0.0728897
11 2 4.05 1.35 1.35 -0.708573 -1.2552 0.0543549
12 2 6.75 1.35 1.35 -0.461807 -1.3955 -1.94959

15
examples/QM/LATTE/dump.8Sep22.series.plugin.2uo2 Normal file
View File

@ -0,0 +1,15 @@
ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
6
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z fx fy fz
1 1 2.7 2.7 0 -2.27066e-14 -1.33391e-14 2.31141e-14
2 2 1.35 4.05 1.35 2.35473 2.21578e-14 7.40069e-15
3 2 4.05 4.05 1.35 -2.35473 2.97071e-15 -2.01341e-14
4 1 2.7 1.65327e-16 2.7 -2.90278e-14 6.77422e-15 2.86766e-15
5 2 1.35 1.35 4.05 2.35473 5.79901e-15 -1.19594e-14
6 2 4.05 1.35 4.05 -2.35473 -1.38761e-14 1.09382e-14

18
examples/QM/LATTE/dump.8Sep22.series.plugin.3uo2 Normal file
View File

@ -0,0 +1,18 @@
ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
9
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.6199999999999999e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z fx fy fz
1 1 2.7 2.7 0 -1.27436e-13 0.760572 0.760572
2 2 1.35 4.05 1.35 0.682428 -0.329901 -0.329901
3 2 4.05 4.05 1.35 -0.682428 -0.329901 -0.329901
4 1 2.7 1.65327e-16 2.7 -8.06311e-14 -1.57101 -1.57101
5 2 1.35 1.35 4.05 2.79365 0.684734 0.684734
6 2 4.05 1.35 4.05 -2.79365 0.684734 0.684734
7 1 2.7 2.7 0 -1.30843e-13 0.760572 0.760572
8 2 1.35 4.05 1.35 0.682428 -0.329901 -0.329901
9 2 4.05 4.05 1.35 -0.682428 -0.329901 -0.329901

21
examples/QM/LATTE/dump.8Sep22.series.plugin.4uo2 Normal file
View File

@ -0,0 +1,21 @@
ITEM: TIMESTEP
0
ITEM: NUMBER OF ATOMS
12
ITEM: BOX BOUNDS xy xz yz pp pp pp
0.0000000000000000e+00 1.0800000000000001e+01 6.6130927153957075e-16
0.0000000000000000e+00 1.0800000000000001e+01 3.3065463576978537e-16
0.0000000000000000e+00 5.4000000000000004e+00 3.3065463576978537e-16
ITEM: ATOMS id type x y z fx fy fz
1 1 2.7 8.1 0 -0.433947 2.16479 1.55466
2 2 1.35 9.45 1.35 1.64718 -0.119006 0.375837
3 2 4.05 9.45 1.35 0.999862 -1.02573 0.037629
4 1 5.4 8.1 2.7 0.433947 2.16479 1.55466
5 2 4.05 9.45 4.05 -0.999862 -1.02573 0.037629
6 2 6.75 9.45 4.05 -1.64718 -0.119006 0.375837
7 1 2.7 1.65327e-16 2.7 -0.211437 1.63064 -0.0728897
8 2 1.35 1.35 4.05 0.461807 -1.3955 -1.94959
9 2 4.05 1.35 4.05 0.708573 -1.2552 0.0543549
10 1 5.4 0 0 0.211437 1.63064 -0.0728897
11 2 4.05 1.35 1.35 -0.708573 -1.2552 0.0543549
12 2 6.75 1.35 1.35 -0.461807 -1.3955 -1.94959

15
examples/QM/LATTE/electrons.dat Normal file
View File

@ -0,0 +1,15 @@
Noelem= 2
Element basis Numel Es Ep Ed Ef Mass HubbardU Wss Wpp Wdd Wff
U sdf 6.0 -4.08 0.0 0.816 -0.586 238.05078 9.0 0.0 0.0 0.0 0.0
O sp 6.0 -23.77 -8.85 0.0 0.0 15.994915 12.2 0.0 0.0 0.0 0.0
W spd 6.0 -4.52 0.53 -2.91 0.0 183.84 7.048 0.0 0.0 0.0 0.0
Mo sd 6.0 -3.29 0.0 -1.98 0.0 95.95 6.48 0.0 0.0 0.0 0.0
S sp 6.0 -14.00 -3.97 0.0 0.0 32.06 8.28 0.0 -0.4278 0.0 0.0
N sp 5.000000 -18.543798 -7.862407 0.000000 0.000000 14.006700 17.053958 0.000000 -0.6934 0.000000 0.000000
H s 1.000000 -6.237968 0.000000 0.000000 0.000000 1.007900 13.684855 -2.23400 0.000000 0.000000 0.000000
C sp 4.000000 -13.736556 -4.748938 0.000000 0.000000 12.010000 10.522540 0.000000 -0.618100 0.000000 0.000000
O sp 6.000000 -23.833752 -9.645001 0.000000 0.000000 15.999400 14.443874 0.000000 -0.757650 0.000000 0.000000

26
examples/QM/LATTE/in.aimd Normal file
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@ -0,0 +1,26 @@
# AIMD test of two UO2 molecules with LATTE in MDI stand-alone mode
units metal
atom_style full
atom_modify sort 0 0.0
read_data 2uo2.lmp
velocity all create 300.0 87287 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
timestep 0.00025
fix 1 all nve
fix 2 all mdi/qm virial yes elements 92 8
thermo_style custom step temp pe etotal press
thermo 1
dump 1 all custom 1 dump.aimd.mpi &
id type x y z vx vy vz fx fy fz
run 20

27
examples/QM/LATTE/in.aimd.plugin Normal file
View File

@ -0,0 +1,27 @@
# AIMD test of two UO2 molecules with LATTE in MDI plugin mode
units metal
atom_style full
atom_modify sort 0 0.0
read_data 2uo2.lmp
velocity all create 300.0 87287 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
timestep 0.00025
fix 1 all nve
fix 2 all mdi/qm virial yes elements 92 8
thermo_style custom step temp pe etotal press
thermo 1
dump 1 all custom 1 dump.aimd.plugin &
id type x y z vx vy vz fx fy fz
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" &
command "run 20"

37
examples/QM/LATTE/in.series Normal file
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@ -0,0 +1,37 @@
# Series of single-point calcs of 2,3,4 UO2 molecules
# with LATTE in MDI stand-alone mode
variable files index 2uo2 3uo2 4uo2
mdi connect
label LOOP
units metal
atom_style full
atom_modify sort 0 0.0
read_data ${files}.lmp
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
timestep 0.001
fix 1 all mdi/qm virial yes elements 92 8 connect no
thermo_style custom step temp pe etotal press
thermo 1
run 0
write_dump all custom dump.series.mpi.${files} &
id type x y z fx fy fz modify sort id
clear
next files
jump SELF LOOP
mdi exit

32
examples/QM/LATTE/in.series.plugin Normal file
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@ -0,0 +1,32 @@
# Series of single-point calcs of 2,3,4 UO2 molecules
# with LATTE in MDI plugin mode
variable files index 2uo2 3uo2 4uo2
label LOOP
units metal
atom_style full
atom_modify sort 0 0.0
read_data ${files}.lmp
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
fix 1 all mdi/qm virial yes elements 92 8
thermo_style custom step temp pe etotal press
thermo 1
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" &
command "run 0"
write_dump all custom dump.series.plugin.${files} &
id type x y z fx fy fz modify sort id
clear
next files
jump SELF LOOP

67
examples/QM/LATTE/latte.in Executable file
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@ -0,0 +1,67 @@
#General controls
CONTROL{
XCONTROL= 1
BASISTYPE= NONORTHO
PARAMPATH= './'
SCLTYPE= TABLE
DEBUGON= 0
FERMIM= 6
CGORLIB= 1 CGTOL= 1.0e-6
KBT= 1.0
NORECS= 5
ENTROPYKIND= 1
PPOTON= 2 VDWON= 0
SPINON= 0 SPINTOL= 1.0e-4
ELECTRO= 1 ELECMETH= 0 ELEC_ETOL= 0.001 ELEC_QTOL= 1.0e-12
COULACC= 1.0e-6 COULCUT= -500.0 COULR1= 500.0
MAXSCF= 250
BREAKTOL= 1.0E-12 MINSP2ITER= 22 SP2CONV= REL
FULLQCONV= 1 QITER= 0
QMIX= 0.05 SPINMIX= 0.05 MDMIX= 0.05
#QMIX= 0.25 SPINMIX= 0.25 MDMIX= 0.25
ORDERNMOL= 0
SPARSEON= 0 THRESHOLDON= 1 NUMTHRESH= 1.0e-6 FILLINSTOP= 100 BLKSZ= 4
MSPARSE= 3000
LCNON= 0 LCNITER= 4 CHTOL= 0.01
SKIN= 1.0
RELAX= 0 RELAXTYPE= SD MAXITER= 100 RLXFTOL= 0.001
MDON= 1
PBCON= 1
RESTART= 0
CHARGE= 0
XBO= 1
XBODISON= 1
XBODISORDER= 5
NGPU= 2
KON= 0
COMPFORCE= 1
DOSFIT= 0 INTS2FIT= 1 BETA= 1000.0 NFITSTEP= 5000 QFIT= 0 MCSIGMA= 0.2
PPFITON= 0
ALLFITON= 0
PPSTEP= 500 BISTEP= 500 PP2FIT= 2 BINT2FIT= 6
PPBETA= 1000.0 PPSIGMA= 0.01 PPNMOL= 10 PPNGEOM= 200
PARREP= 0
ER= 1.0
#DOKERNEL= T
}
MDCONTROL{
MAXITER= 2000
UDNEIGH= 1
DT= 0.5
TEMPERATURE= 1.0e-10 RNDIST= GAUSSIAN SEEDINIT= UNIFORM
DUMPFREQ= 250
RSFREQ= 500
WRTFREQ= 1
TOINITTEMP5= 1
THERMPER= 500
THERMRUN= 50000
NVTON= 0 NPTON= 0 AVEPER= 1000 FRICTION= 1000.0 SEED= 54
PTARGET= 0.0 NPTTYPE= ISO
SHOCKON= 0
SHOCKSTART= 100000
SHOCKDIR= 1
UPARTICLE= 500.0 USHOCK= -4590.0 C0= 1300.0
MDADAPT= 0
GETHUG= 0 E0= -795.725 V0= 896.984864 P0= 0.083149
}

102
examples/QM/LATTE/log.8Sep22.aimd.lammps.mpi.1 Normal file
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@ -0,0 +1,102 @@
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# AIMD test of two UO2 molecules with LATTE in MDI stand-alone mode
units metal
atom_style full
atom_modify sort 0 0.0
read_data 2uo2.lmp
Reading data file ...
triclinic box = (0 0 0) to (10.8 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
1 by 1 by 1 MPI processor grid
reading atoms ...
6 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.003 seconds
velocity all create 300.0 87287 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
timestep 0.00025
fix 1 all nve
fix 2 all mdi/qm virial yes elements 92 8
thermo_style custom step temp pe etotal press
thermo 1
dump 1 all custom 1 dump.aimd.mpi id type x y z vx vy vz fx fy fz
run 20
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 10.8, bins = 1 1 1
0 neighbor lists, perpetual/occasional/extra = 0 0 0
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 6.489 | 6.489 | 6.489 Mbytes
Step Temp PotEng TotEng Press
0 300 -50.539035 -50.345145 -120197.6
1 307.57345 -50.544722 -50.345937 -120123.27
2 316.3757 -50.551342 -50.346868 -120035.12
3 326.39203 -50.558885 -50.347938 -119933.11
4 337.60559 -50.567341 -50.349146 -119817.17
5 349.99734 -50.576697 -50.350493 -119687.24
6 363.54606 -50.586939 -50.351979 -119543.23
7 378.22834 -50.598054 -50.353605 -119385.07
8 394.0186 -50.610024 -50.355369 -119212.67
9 410.88903 -50.622831 -50.357273 -119025.94
10 428.80963 -50.636457 -50.359317 -118824.77
11 447.74819 -50.65088 -50.3615 -118609.06
12 467.67027 -50.666079 -50.363823 -118378.7
13 488.53922 -50.68203 -50.366287 -118133.58
14 510.31617 -50.698708 -50.36889 -117873.58
15 532.96002 -50.716086 -50.371633 -117598.57
16 556.42747 -50.734137 -50.374517 -117308.44
17 580.67298 -50.75283 -50.377541 -117003.05
18 605.64879 -50.772136 -50.380705 -116682.27
19 631.30497 -50.792023 -50.38401 -116345.95
20 657.58937 -50.812455 -50.387454 -115993.97
Loop time of 3.40001 on 1 procs for 20 steps with 6 atoms
Performance: 0.127 ns/day, 188.889 hours/ns, 5.882 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 1.2223e-05 | 1.2223e-05 | 1.2223e-05 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 6.0971e-05 | 6.0971e-05 | 6.0971e-05 | 0.0 | 0.00
Output | 0.0009257 | 0.0009257 | 0.0009257 | 0.0 | 0.03
Modify | 3.3989 | 3.3989 | 3.3989 | 0.0 | 99.97
Other | | 6.824e-05 | | | 0.00
Nlocal: 6 ave 6 max 6 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2 ave 2 max 2 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:03

102
examples/QM/LATTE/log.8Sep22.aimd.lammps.mpi.2 Normal file
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@ -0,0 +1,102 @@
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# AIMD test of two UO2 molecules with LATTE in MDI stand-alone mode
units metal
atom_style full
atom_modify sort 0 0.0
read_data 2uo2.lmp
Reading data file ...
triclinic box = (0 0 0) to (10.8 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
2 by 1 by 1 MPI processor grid
reading atoms ...
6 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.005 seconds
velocity all create 300.0 87287 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
timestep 0.00025
fix 1 all nve
fix 2 all mdi/qm virial yes elements 92 8
thermo_style custom step temp pe etotal press
thermo 1
dump 1 all custom 1 dump.aimd.mpi id type x y z vx vy vz fx fy fz
run 20
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 10.8, bins = 1 1 1
0 neighbor lists, perpetual/occasional/extra = 0 0 0
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 5.485 | 5.987 | 6.489 Mbytes
Step Temp PotEng TotEng Press
0 300 -50.539035 -50.345145 -120197.6
1 307.57345 -50.544722 -50.345937 -120123.27
2 316.3757 -50.551342 -50.346868 -120035.12
3 326.39203 -50.558885 -50.347938 -119933.11
4 337.60559 -50.567341 -50.349146 -119817.17
5 349.99734 -50.576697 -50.350493 -119687.24
6 363.54606 -50.586939 -50.351979 -119543.23
7 378.22834 -50.598054 -50.353605 -119385.07
8 394.0186 -50.610024 -50.355369 -119212.67
9 410.88903 -50.622831 -50.357273 -119025.94
10 428.80963 -50.636457 -50.359317 -118824.77
11 447.74819 -50.65088 -50.3615 -118609.06
12 467.67027 -50.666079 -50.363823 -118378.7
13 488.53922 -50.68203 -50.366287 -118133.58
14 510.31617 -50.698708 -50.36889 -117873.58
15 532.96002 -50.716086 -50.371633 -117598.57
16 556.42747 -50.734137 -50.374517 -117308.44
17 580.67298 -50.75283 -50.377541 -117003.05
18 605.64879 -50.772136 -50.380705 -116682.27
19 631.30497 -50.792023 -50.38401 -116345.95
20 657.58937 -50.812455 -50.387454 -115993.97
Loop time of 25.2055 on 2 procs for 20 steps with 6 atoms
Performance: 0.017 ns/day, 1400.306 hours/ns, 0.793 timesteps/s
99.9% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 1.746e-05 | 2.5213e-05 | 3.2966e-05 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 4.3862e-05 | 5.4267e-05 | 6.4671e-05 | 0.0 | 0.00
Output | 0.001642 | 0.0018189 | 0.0019957 | 0.4 | 0.01
Modify | 25.203 | 25.203 | 25.203 | 0.0 | 99.99
Other | | 0.000307 | | | 0.00
Nlocal: 3 ave 6 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 1 ave 2 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:26

103
examples/QM/LATTE/log.8Sep22.aimd.lammps.plugin Normal file
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@ -0,0 +1,103 @@
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# AIMD test of two UO2 molecules with LATTE in MDI plugin mode
units metal
atom_style full
atom_modify sort 0 0.0
read_data 2uo2.lmp
Reading data file ...
triclinic box = (0 0 0) to (10.8 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
1 by 1 by 1 MPI processor grid
reading atoms ...
6 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.004 seconds
velocity all create 300.0 87287 loop geom
neighbor 1.0 bin
neigh_modify every 1 delay 0 check yes
timestep 0.00025
fix 1 all nve
fix 2 all mdi/qm virial yes elements 92 8
thermo_style custom step temp pe etotal press
thermo 1
dump 1 all custom 1 dump.aimd.plugin id type x y z vx vy vz fx fy fz
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" command "run 20"
run 20
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 10.8, bins = 1 1 1
0 neighbor lists, perpetual/occasional/extra = 0 0 0
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 6.489 | 6.489 | 6.489 Mbytes
Step Temp PotEng TotEng Press
0 300 -50.539035 -50.345145 -120197.6
1 307.57345 -50.544722 -50.345937 -120123.27
2 316.3757 -50.551342 -50.346868 -120035.12
3 326.39203 -50.558885 -50.347938 -119933.11
4 337.60559 -50.567341 -50.349146 -119817.17
5 349.99734 -50.576697 -50.350493 -119687.24
6 363.54606 -50.586939 -50.351979 -119543.23
7 378.22834 -50.598054 -50.353605 -119385.07
8 394.0186 -50.610024 -50.355369 -119212.67
9 410.88903 -50.622831 -50.357273 -119025.94
10 428.80963 -50.636457 -50.359317 -118824.77
11 447.74819 -50.65088 -50.3615 -118609.06
12 467.67027 -50.666079 -50.363823 -118378.7
13 488.53922 -50.68203 -50.366287 -118133.58
14 510.31617 -50.698708 -50.36889 -117873.58
15 532.96002 -50.716086 -50.371633 -117598.57
16 556.42747 -50.734137 -50.374517 -117308.44
17 580.67298 -50.75283 -50.377541 -117003.05
18 605.64879 -50.772136 -50.380705 -116682.27
19 631.30497 -50.792023 -50.38401 -116345.95
20 657.58937 -50.812455 -50.387454 -115993.97
Loop time of 2.74435 on 1 procs for 20 steps with 6 atoms
Performance: 0.157 ns/day, 152.464 hours/ns, 7.288 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 1.299e-05 | 1.299e-05 | 1.299e-05 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 7.9198e-05 | 7.9198e-05 | 7.9198e-05 | 0.0 | 0.00
Output | 0.001118 | 0.001118 | 0.001118 | 0.0 | 0.04
Modify | 2.743 | 2.743 | 2.743 | 0.0 | 99.95
Other | | 0.0001456 | | | 0.01
Nlocal: 6 ave 6 max 6 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2 ave 2 max 2 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
Total wall time: 0:00:03

12604
examples/QM/LATTE/log.8Sep22.aimd.latte.1 Normal file
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12604
examples/QM/LATTE/log.8Sep22.aimd.latte.2 Normal file
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12604
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263
examples/QM/LATTE/log.8Sep22.series.lammps.mpi.1 Normal file
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@ -0,0 +1,263 @@
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Series of single-point calcs of 2,3,4 UO2 molecules
# with LATTE in MDI stand-alone mode
variable files index 2uo2 3uo2 4uo2
mdi connect
label LOOP
units metal
atom_style full
atom_modify sort 0 0.0
read_data ${files}.lmp
read_data 2uo2.lmp
Reading data file ...
triclinic box = (0 0 0) to (10.8 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
1 by 1 by 1 MPI processor grid
reading atoms ...
6 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.003 seconds
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
timestep 0.001
fix 1 all mdi/qm virial yes elements 92 8 connect no
thermo_style custom step temp pe etotal press
thermo 1
run 0
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 10.8, bins = 1 1 1
0 neighbor lists, perpetual/occasional/extra = 0 0 0
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes
Step Temp PotEng TotEng Press
0 0 -50.539035 -50.539035 -120855.2
Loop time of 1.397e-06 on 1 procs for 0 steps with 6 atoms
71.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.397e-06 | | |100.00
Nlocal: 6 ave 6 max 6 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2 ave 2 max 2 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
write_dump all custom dump.series.mpi.${files} id type x y z fx fy fz modify sort id
write_dump all custom dump.series.mpi.2uo2 id type x y z fx fy fz modify sort id
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
next files
jump SELF LOOP
units metal
atom_style full
atom_modify sort 0 0.0
read_data ${files}.lmp
read_data 3uo2.lmp
Reading data file ...
triclinic box = (0 0 0) to (16.2 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
1 by 1 by 1 MPI processor grid
reading atoms ...
9 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.002 seconds
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
timestep 0.001
fix 1 all mdi/qm virial yes elements 92 8 connect no
thermo_style custom step temp pe etotal press
thermo 1
run 0
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 16.2, bins = 1 1 1
0 neighbor lists, perpetual/occasional/extra = 0 0 0
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes
Step Temp PotEng TotEng Press
0 0 -78.155679 -78.155679 -99931.431
Loop time of 1.117e-06 on 1 procs for 0 steps with 9 atoms
89.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.117e-06 | | |100.00
Nlocal: 9 ave 9 max 9 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
write_dump all custom dump.series.mpi.${files} id type x y z fx fy fz modify sort id
write_dump all custom dump.series.mpi.3uo2 id type x y z fx fy fz modify sort id
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
next files
jump SELF LOOP
units metal
atom_style full
atom_modify sort 0 0.0
read_data ${files}.lmp
read_data 4uo2.lmp
Reading data file ...
triclinic box = (0 0 0) to (10.8 10.8 5.4) with tilt (6.6130927e-16 3.3065464e-16 3.3065464e-16)
1 by 1 by 1 MPI processor grid
reading atoms ...
12 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.001 seconds
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
timestep 0.001
fix 1 all mdi/qm virial yes elements 92 8 connect no
thermo_style custom step temp pe etotal press
thermo 1
run 0
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 10.8, bins = 1 1 1
0 neighbor lists, perpetual/occasional/extra = 0 0 0
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes
Step Temp PotEng TotEng Press
0 0 -102.35713 -102.35713 -31036.168
Loop time of 1.466e-06 on 1 procs for 0 steps with 12 atoms
136.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.466e-06 | | |100.00
Nlocal: 12 ave 12 max 12 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5 ave 5 max 5 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
write_dump all custom dump.series.mpi.${files} id type x y z fx fy fz modify sort id
write_dump all custom dump.series.mpi.4uo2 id type x y z fx fy fz modify sort id
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
next files
jump SELF LOOP
mdi exit
Total wall time: 0:00:02

263
examples/QM/LATTE/log.8Sep22.series.lammps.mpi.2 Normal file
View File

@ -0,0 +1,263 @@
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Series of single-point calcs of 2,3,4 UO2 molecules
# with LATTE in MDI stand-alone mode
variable files index 2uo2 3uo2 4uo2
mdi connect
label LOOP
units metal
atom_style full
atom_modify sort 0 0.0
read_data ${files}.lmp
read_data 2uo2.lmp
Reading data file ...
triclinic box = (0 0 0) to (10.8 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
2 by 1 by 1 MPI processor grid
reading atoms ...
6 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.004 seconds
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
timestep 0.001
fix 1 all mdi/qm virial yes elements 92 8 connect no
thermo_style custom step temp pe etotal press
thermo 1
run 0
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 10.8, bins = 1 1 1
0 neighbor lists, perpetual/occasional/extra = 0 0 0
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 5.234 | 5.236 | 5.238 Mbytes
Step Temp PotEng TotEng Press
0 0 -50.539035 -50.539035 -120855.2
Loop time of 1.956e-06 on 2 procs for 0 steps with 6 atoms
127.8% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.956e-06 | | |100.00
Nlocal: 3 ave 6 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 1 ave 2 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
write_dump all custom dump.series.mpi.${files} id type x y z fx fy fz modify sort id
write_dump all custom dump.series.mpi.2uo2 id type x y z fx fy fz modify sort id
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
next files
jump SELF LOOP
units metal
atom_style full
atom_modify sort 0 0.0
read_data ${files}.lmp
read_data 3uo2.lmp
Reading data file ...
triclinic box = (0 0 0) to (16.2 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
2 by 1 by 1 MPI processor grid
reading atoms ...
9 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.001 seconds
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
timestep 0.001
fix 1 all mdi/qm virial yes elements 92 8 connect no
thermo_style custom step temp pe etotal press
thermo 1
run 0
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 16.2, bins = 1 1 1
0 neighbor lists, perpetual/occasional/extra = 0 0 0
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 5.234 | 5.236 | 5.238 Mbytes
Step Temp PotEng TotEng Press
0 0 -78.155679 -78.155679 -99931.431
Loop time of 2.375e-06 on 2 procs for 0 steps with 9 atoms
147.4% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.375e-06 | | |100.00
Nlocal: 4.5 ave 9 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 1.5 ave 3 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
write_dump all custom dump.series.mpi.${files} id type x y z fx fy fz modify sort id
write_dump all custom dump.series.mpi.3uo2 id type x y z fx fy fz modify sort id
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
next files
jump SELF LOOP
units metal
atom_style full
atom_modify sort 0 0.0
read_data ${files}.lmp
read_data 4uo2.lmp
Reading data file ...
triclinic box = (0 0 0) to (10.8 10.8 5.4) with tilt (6.6130927e-16 3.3065464e-16 3.3065464e-16)
1 by 2 by 1 MPI processor grid
reading atoms ...
12 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.002 seconds
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
timestep 0.001
fix 1 all mdi/qm virial yes elements 92 8 connect no
thermo_style custom step temp pe etotal press
thermo 1
run 0
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 10.8, bins = 1 1 1
0 neighbor lists, perpetual/occasional/extra = 0 0 0
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes
Step Temp PotEng TotEng Press
0 0 -102.35713 -102.35713 -31036.168
Loop time of 2.4445e-06 on 2 procs for 0 steps with 12 atoms
122.7% CPU use with 2 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 2.444e-06 | | |100.00
Nlocal: 6 ave 6 max 6 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Nghost: 2.5 ave 4 max 1 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
write_dump all custom dump.series.mpi.${files} id type x y z fx fy fz modify sort id
write_dump all custom dump.series.mpi.4uo2 id type x y z fx fy fz modify sort id
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
next files
jump SELF LOOP
mdi exit
Total wall time: 0:00:08

256
examples/QM/LATTE/log.8Sep22.series.lammps.plugin Normal file
View File

@ -0,0 +1,256 @@
LAMMPS (23 Jun 2022)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# Series of single-point calcs of 2,3,4 UO2 molecules
# with LATTE in MDI plugin mode
variable files index 2uo2 3uo2 4uo2
label LOOP
units metal
atom_style full
atom_modify sort 0 0.0
read_data ${files}.lmp
read_data 2uo2.lmp
Reading data file ...
triclinic box = (0 0 0) to (10.8 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
1 by 1 by 1 MPI processor grid
reading atoms ...
6 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.004 seconds
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
fix 1 all mdi/qm virial yes elements 92 8
thermo_style custom step temp pe etotal press
thermo 1
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" command "run 0"
run 0
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 10.8, bins = 1 1 1
0 neighbor lists, perpetual/occasional/extra = 0 0 0
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes
Step Temp PotEng TotEng Press
0 0 -50.539035 -50.539035 -120855.2
Loop time of 1.396e-06 on 1 procs for 0 steps with 6 atoms
143.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.396e-06 | | |100.00
Nlocal: 6 ave 6 max 6 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2 ave 2 max 2 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
write_dump all custom dump.series.plugin.${files} id type x y z fx fy fz modify sort id
write_dump all custom dump.series.plugin.2uo2 id type x y z fx fy fz modify sort id
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
next files
jump SELF LOOP
units metal
atom_style full
atom_modify sort 0 0.0
read_data ${files}.lmp
read_data 3uo2.lmp
Reading data file ...
triclinic box = (0 0 0) to (16.2 5.4 5.4) with tilt (3.3065464e-16 3.3065464e-16 3.3065464e-16)
1 by 1 by 1 MPI processor grid
reading atoms ...
9 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.002 seconds
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
fix 1 all mdi/qm virial yes elements 92 8
thermo_style custom step temp pe etotal press
thermo 1
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" command "run 0"
run 0
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 16.2, bins = 1 1 1
0 neighbor lists, perpetual/occasional/extra = 0 0 0
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes
Step Temp PotEng TotEng Press
0 0 -78.155679 -78.155679 -99931.431
Loop time of 1.117e-06 on 1 procs for 0 steps with 9 atoms
89.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.117e-06 | | |100.00
Nlocal: 9 ave 9 max 9 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
write_dump all custom dump.series.plugin.${files} id type x y z fx fy fz modify sort id
write_dump all custom dump.series.plugin.3uo2 id type x y z fx fy fz modify sort id
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
next files
jump SELF LOOP
units metal
atom_style full
atom_modify sort 0 0.0
read_data ${files}.lmp
read_data 4uo2.lmp
Reading data file ...
triclinic box = (0 0 0) to (10.8 10.8 5.4) with tilt (6.6130927e-16 3.3065464e-16 3.3065464e-16)
1 by 1 by 1 MPI processor grid
reading atoms ...
12 atoms
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
0 = max # of 1-2 neighbors
0 = max # of 1-3 neighbors
0 = max # of 1-4 neighbors
1 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.001 seconds
neighbor 0.3 bin
neigh_modify every 1 delay 0 check yes
fix 1 all mdi/qm virial yes elements 92 8
thermo_style custom step temp pe etotal press
thermo 1
mdi plugin latte_mdi mdi "-role ENGINE -name LATTE -method LINK" command "run 0"
run 0
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 0
ghost atom cutoff = 0
binsize = 10.8, bins = 1 1 1
0 neighbor lists, perpetual/occasional/extra = 0 0 0
WARNING: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost. (src/comm_brick.cpp:210)
Per MPI rank memory allocation (min/avg/max) = 5.238 | 5.238 | 5.238 Mbytes
Step Temp PotEng TotEng Press
0 0 -102.35713 -102.35713 -31036.168
Loop time of 1.048e-06 on 1 procs for 0 steps with 12 atoms
190.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0 | 0 | 0 | 0.0 | 0.00
Bond | 0 | 0 | 0 | 0.0 | 0.00
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0 | 0 | 0 | 0.0 | 0.00
Output | 0 | 0 | 0 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 1.048e-06 | | |100.00
Nlocal: 12 ave 12 max 12 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 5 ave 5 max 5 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 0
Neighbor list builds = 0
Dangerous builds = 0
write_dump all custom dump.series.plugin.${files} id type x y z fx fy fz modify sort id
write_dump all custom dump.series.plugin.4uo2 id type x y z fx fy fz modify sort id
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
next files
jump SELF LOOP
Total wall time: 0:00:01

3209
examples/QM/LATTE/log.8Sep22.series.latte.1 Normal file
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examples/QM/LATTE/log.8Sep22.series.latte.2 Normal file
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178
examples/QM/LATTE/ppots.dftb Normal file
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@ -0,0 +1,178 @@
3
U O
101
1.0000000000000000 53.452052832272599
1.0520000000000000 48.423668742582244
1.1040000000000001 43.721445018814535
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3.2880000000000003 -0.28169770300137842
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3.4440000000000000 -0.11101397528126161
3.4960000000000004 -5.8190073505363524E-002
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3.6000000000000001 3.4657543064533058E-002
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4.0160000000000000 0.19730443479147558
4.0679999999999996 0.19913820516436204
4.1200000000000001 0.19804725060311840
4.1719999999999997 0.19438729303370450
4.2240000000000002 0.18851405438207983
4.2759999999999998 0.18078325657420447
4.3280000000000003 0.17155062153603778
4.3799999999999999 0.16117187119353987
4.4320000000000004 0.15000272747267010
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4.5359999999999996 0.12671614759965491
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4.6400000000000006 0.10450791010072910
4.6920000000000002 9.4401608127654982E-002
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4.7960000000000003 7.6186266463431560E-002
4.8480000000000008 6.8030778812237541E-002
4.9000000000000004 6.0479114641625663E-002
4.9520000000000000 5.3508049971573365E-002
5.0040000000000004 4.7094360822058187E-002
5.0560000000000000 4.1214823213057958E-002
5.1080000000000005 3.5846213164550077E-002
5.1600000000000001 3.0965306696512353E-002
5.2119999999999997 2.6548879828922314E-002
5.2640000000000002 2.2573708581757501E-002
5.3159999999999998 1.9016568974995669E-002
5.3680000000000003 1.5854237028614312E-002
5.4199999999999999 1.3063488762591162E-002
5.4719999999999995 1.0621100196903764E-002
5.5240000000000000 8.5038473515297100E-003
5.5760000000000005 6.6885062464466568E-003
5.6280000000000001 5.1518529016322447E-003
5.6799999999999997 3.8706633370640541E-003
5.7320000000000002 2.8217135727196876E-003
5.7840000000000007 1.9817796285767830E-003
5.8360000000000003 1.3276375246129659E-003
5.8879999999999999 8.3606328080583568E-004
5.9400000000000004 4.8383291713300426E-004
5.9920000000000009 2.4772245357209625E-004
6.0440000000000005 1.0450791010072858E-004
6.0960000000000001 3.0965306696512431E-005
6.1480000000000006 3.8706633370639547E-006
6.2000000000000002 0.0000000000000000
O O
20
0.59999999999999998 29923.073152218909
0.70000000000000007 4662.8666204588562
0.80000000000000004 849.06541460837946
0.90000000000000002 174.94775568214448
1.0000000000000000 39.499570511324919
1.1000000000000001 9.4630438308109763
1.2000000000000002 2.3294935751104737
1.3000000000000003 0.57058726754144162
1.4000000000000001 0.13466360499250576
1.5000000000000002 2.9654028763683022E-002
1.6000000000000001 5.9001110666872716E-003
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1.8000000000000003 1.5149315970664778E-004
1.9000000000000001 1.8332630772941197E-005
2.0000000000000000 1.7625863466525047E-006
2.1000000000000001 1.3037897449239816E-007
2.2000000000000002 7.1851191723432173E-009
2.3000000000000003 2.8567178835137876E-010
2.4000000000000004 7.9349720447872060E-012
2.5000000000000004 1.4910967552225071E-013
U U
50
0.10000000000000001 74348.981230147430
0.20000000000000001 40311.628875481227
0.30000000000000004 22512.215747793147
0.40000000000000002 12931.185562052075
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0.80000000000000004 1814.8199558215895
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1.0000000000000000 776.63138285251296
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5.0000000000000000 7.4970692168027886E-005

21
examples/QM/README Normal file
View File

@ -0,0 +1,21 @@
Each of the directories shows how to use LAMMPS in tandem with a
specific quantum code
LATTE = semi-empirical tight-binding code from LANL
https://www.osti.gov/biblio/1526907-los-alamos-transferable-tight-binding-energetics-latte-version
https://github.com/lanl/LATTE
To be added later (as of Aug 2022):
Quantum Espresso (QE) = DFT code for materials modeling
https://www.quantum-espresso.org/
DFT-FE = real-space DFT code from U Michigan
https://github.com/dftfeDevelopers/dftfe
INQ = DFT code from LLNL
https://github.com/LLNL/inq
NWChem = computational chemistry code from PNNL
focus here is on DFT portion of NWChem
https://www.nwchem-sw.org

3
examples/README
View File

@ -189,6 +189,9 @@ corresponding doc page in the manual for more info. See the
https://docs.lammps.org/Build_package.html page for more info about https://docs.lammps.org/Build_package.html page for more info about
installing and building packages. installing and building packages.
The QM directory has examples of how to use LAMMPS in tandem with
several quantum codes.
The TIP4P directory has an example for testing forces computed on a The TIP4P directory has an example for testing forces computed on a
GPU. GPU.

64
examples/mdi/README
View File

@ -2,15 +2,17 @@ These are examples that work the MDI package in LAMMPS which uses the
MolSSI MDI library for coupling codes together and communicating MolSSI MDI library for coupling codes together and communicating
between them with MDI messages. between them with MDI messages.
Within the MDI context, one code is the driver and another code is There are more examples of using LAMMPS with quantum codes via MDI in
the engine. The 2 codes can be written in any language; C++ (LAMMPS) the examples/QM directory.
and Python are illustrated here. The 2 codes can each be stand-alone
codes, in which case they can be run on different numbers of processors. Within the MDI context, one code is the driver and another code is the
The 2 engine. The 2 codes can be written in any language; C++ (LAMMPS) and
codes can communicate either via TCP (sockets) or via MPI. For the Python are illustrated here. The 2 codes can each be stand-alone
TCP case, the driver and engine need to be launched separately, codes, in which case they can be run on different numbers of
e.g. in 2 windows on your desktop machine. For the MPI case, a single processors. The 2 codes can communicate either via TCP (sockets) or
mpirun command launches both codes. via MPI. For the TCP case, the driver and engine need to be launched
separately, e.g. in 2 windows on your desktop machine. For the MPI
case, a single mpirun command launches both codes.
Alternatively the engine code can be a plugin library which the driver Alternatively the engine code can be a plugin library which the driver
code loads, in which case the driver and engine run on the same code loads, in which case the driver and engine run on the same
@ -19,17 +21,39 @@ processors.
LAMMPS supports operating in all these MDI modes. It can be an engine LAMMPS supports operating in all these MDI modes. It can be an engine
operating either as a stand-alone code or as a plugin. It can also be operating either as a stand-alone code or as a plugin. It can also be
a driver and couple to an engine that is either a stand-alone code or a driver and couple to an engine that is either a stand-alone code or
a plugin. Examples for all these use cases are in this directory. a plugin.
The Run.sh file shows how run in all the modes. Type "sh Run.sh"
to try them all out.
To use LAMMPS as a plugin engine, you must build it as a shared Examples for all these use cases, using LAMMPS as a driver and as an
library. Something like this with make, which also builds the normal engine are in this directory. The Run.sh file shows how run in all
LAMMPS executable lmp_mpi: the modes. Type "sh Run.sh" to try them all out.
cd src Examples for using LAMMPS as a driver with the tight-binding code
make yes-mdi LATTE are in the examples/QM/LATTE sub-directory. See its README file
make mode=shlib mpi for more info.
-------------------------------------------------
Here is how to build LAMMPS with MDI support. Both as an executable
and a shared library. The former is needed to use LAMMPS as an MDI
driver or as an MDI engine in stand-alone mode. The latter is needed
to use LAMMPS as an MDI engine in plugin mode.
Build via regular make:
% cd lammps/src
% make lib-mdi args="-m mpi" # download, install MDI in lib/mdi w/ MPI support
% make yes-mdi # include MDI package in LAMMPS build
% make mode=shlib mpi # creates lmp_mpi and liblammps.so
Build via CMake:
cd lammps
mkdir build; cd build
cmake -D PKG_MDI=yes -D BUILD_SHARED_LIBS=yes ../cmake
make # creates lmp and liblammps.so
Both of these build procedures build LAMMPS both as an executable
(lmp_mpi) and as a shared library (liblammps.so).
------------------------------------------------- -------------------------------------------------
@ -39,9 +63,9 @@ Python/mpi4py are using same the same version of MPI.
You will also need MDI installed in your Python. You cannot use the You will also need MDI installed in your Python. You cannot use the
LAMMPS build of the MDI library for this, b/c LAMMPS builds MDI as a LAMMPS build of the MDI library for this, b/c LAMMPS builds MDI as a
static library, not shared, which Python requires. static library, while Python requires a shared library.
You can install MDI in your Python via conda: Instead you can install MDI in your Python via conda:
% conda install -c conda-forge pymdi=1.4.1 % conda install -c conda-forge pymdi=1.4.1

21
lib/gpu/geryon/nvd_device.h
View File

@ -316,6 +316,9 @@ class UCL_Device {
std::vector<CUstream> _cq; std::vector<CUstream> _cq;
CUdevice _cu_device; CUdevice _cu_device;
CUcontext _context; CUcontext _context;
#if GERYON_NVD_PRIMARY_CONTEXT
CUcontext _old_context;
#endif
}; };
// Grabs the properties for all devices // Grabs the properties for all devices
@ -391,8 +394,14 @@ int UCL_Device::set_platform(const int pid) {
int UCL_Device::set(int num) { int UCL_Device::set(int num) {
clear(); clear();
_device=_properties[num].device_id; _device=_properties[num].device_id;
#if GERYON_NVD_PRIMARY_CONTEXT
CU_SAFE_CALL_NS(cuCtxGetCurrent(&_old_context));
CU_SAFE_CALL_NS(cuDeviceGet(&_cu_device,_device));
CUresult err=cuDevicePrimaryCtxRetain(&_context,_cu_device);
#else
CU_SAFE_CALL_NS(cuDeviceGet(&_cu_device,_device)); CU_SAFE_CALL_NS(cuDeviceGet(&_cu_device,_device));
CUresult err=cuCtxCreate(&_context,0,_cu_device); CUresult err=cuCtxCreate(&_context,0,_cu_device);
#endif
if (err!=CUDA_SUCCESS) { if (err!=CUDA_SUCCESS) {
#ifndef UCL_NO_EXIT #ifndef UCL_NO_EXIT
std::cerr << "UCL Error: Could not access accelerator number " << num std::cerr << "UCL Error: Could not access accelerator number " << num
@ -401,13 +410,23 @@ int UCL_Device::set(int num) {
#endif #endif
return UCL_ERROR; return UCL_ERROR;
} }
#if GERYON_NVD_PRIMARY_CONTEXT
if (_context != _old_context) {
CU_SAFE_CALL_NS(cuCtxSetCurrent(_context));
}
#endif
return UCL_SUCCESS; return UCL_SUCCESS;
} }
void UCL_Device::clear() { void UCL_Device::clear() {
if (_device>-1) { if (_device>-1) {
for (int i=1; i<num_queues(); i++) pop_command_queue(); for (int i=1; i<num_queues(); i++) pop_command_queue();
cuCtxDestroy(_context); #if GERYON_NVD_PRIMARY_CONTEXT
CU_SAFE_CALL_NS(cuCtxSetCurrent(_old_context));
CU_SAFE_CALL_NS(cuDevicePrimaryCtxRelease(_cu_device));
#else
cuCtxDestroy(_context));
#endif
} }
_device=-1; _device=-1;
} }

7
lib/gpu/geryon/nvd_macros.h
View File

@ -7,6 +7,13 @@
#define CUDA_INT_TYPE size_t #define CUDA_INT_TYPE size_t
// Use the primary context for GPU access to enable compatibility with tools
// like OpenMPI accessing the GPU through the runtime interface.
// Set to 0 to revert to old behavior
#ifndef GERYON_NVD_PRIMARY_CONTEXT
#define GERYON_NVD_PRIMARY_CONTEXT 1
#endif
#ifdef MPI_GERYON #ifdef MPI_GERYON
#include "mpi.h" #include "mpi.h"
#define NVD_GERYON_EXIT do { \ #define NVD_GERYON_EXIT do { \

8
lib/mdi/Install.py
View File

@ -27,19 +27,17 @@ specify -m and optionally -e, order does not matter
Examples: Examples:
make lib-poems args="-m serial" # build POEMS lib with same settings as in the serial Makefile in src make lib-mdi args="-m mpi" # build MDI lib with same settings as in the mpi Makefile in src
make lib-colvars args="-m mpi" # build COLVARS lib with same settings as in the mpi Makefile in src
make lib-meam args="-m ifort" # build MEAM lib with custom Makefile.ifort (using Intel Fortran)
""" """
# settings # settings
version = "1.4.1" version = "1.4.10"
url = "https://github.com/MolSSI-MDI/MDI_Library/archive/v%s.tar.gz" % version url = "https://github.com/MolSSI-MDI/MDI_Library/archive/v%s.tar.gz" % version
# known checksums for different MDI versions. used to validate the download. # known checksums for different MDI versions. used to validate the download.
checksums = { \ checksums = { \
'1.4.1' : 'f9505fccd4c79301a619f6452dad4ad9', \ '1.4.10' : '1c203b7fd462d9934834f643f09f3c06', \
} }
# print error message or help # print error message or help

40
src/DIELECTRIC/atom_vec_dielectric.cpp
View File

@ -15,6 +15,10 @@
#include "atom.h" #include "atom.h"
#include "citeme.h" #include "citeme.h"
#include "error.h"
#include "force.h"
#include "pair.h"
#include "pair_hybrid.h"
#include <cmath> #include <cmath>
@ -87,6 +91,42 @@ AtomVecDielectric::AtomVecDielectric(LAMMPS *_lmp) : AtomVec(_lmp)
bond_per_atom = angle_per_atom = dihedral_per_atom = improper_per_atom = 0; bond_per_atom = angle_per_atom = dihedral_per_atom = improper_per_atom = 0;
} }
/* ---------------------------------------------------------------------- */
void AtomVecDielectric::init()
{
AtomVec::init();
// since atom style dielectric modifies the charge q, it will produce incorrect results
// with pair styles using coulomb without dielectric support.
std::string pair_style(force->pair_style);
if ((pair_style != "none") && (pair_style != "zero") && !utils::strmatch(force->pair_style,"/dielectric")) {
bool mismatch = false;
if (utils::strmatch(force->pair_style,"^reaxff")) mismatch = true;
if (utils::strmatch(force->pair_style,"^comb")) mismatch = true;
if (utils::strmatch(force->pair_style,"coul")) mismatch = true;
if (utils::strmatch(force->pair_style,"tip4p")) mismatch = true;
if (utils::strmatch(force->pair_style,"dipole")) mismatch = true;
if (utils::strmatch(force->pair_style,"^hybrid")) {
auto hybrid = dynamic_cast<PairHybrid *>(force->pair);
if (hybrid) {
for (int i = 0; i < hybrid->nstyles; i++) {
if (utils::strmatch(hybrid->keywords[i],"^reaxff")) mismatch = true;
if (utils::strmatch(hybrid->keywords[i],"^comb")) mismatch = true;
if (utils::strmatch(hybrid->keywords[i],"coul")) mismatch = true;
if (utils::strmatch(hybrid->keywords[i],"tip4p")) mismatch = true;
if (utils::strmatch(hybrid->keywords[i],"dipole")) mismatch = true;
}
}
}
if (mismatch)
error->all(FLERR, "Pair style {} is not compatible with atom style {}",
pair_style, atom->get_style());
}
}
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
set local copies of all grow ptrs used by this class, except defaults set local copies of all grow ptrs used by this class, except defaults
needed in replicate when 2 atom classes exist and it calls pack_restart() needed in replicate when 2 atom classes exist and it calls pack_restart()

1
src/DIELECTRIC/atom_vec_dielectric.h
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@ -31,6 +31,7 @@ class AtomVecDielectric : public AtomVec {
public: public:
AtomVecDielectric(class LAMMPS *); AtomVecDielectric(class LAMMPS *);
void init() override;
void grow_pointers() override; void grow_pointers() override;
void create_atom_post(int) override; void create_atom_post(int) override;
void data_atom_post(int) override; void data_atom_post(int) override;

1
src/DIELECTRIC/pair_coul_cut_dielectric.cpp
View File

@ -38,6 +38,7 @@ static constexpr double EPSILON = 1.0e-6;
PairCoulCutDielectric::PairCoulCutDielectric(LAMMPS *_lmp) : PairCoulCut(_lmp), efield(nullptr) PairCoulCutDielectric::PairCoulCutDielectric(LAMMPS *_lmp) : PairCoulCut(_lmp), efield(nullptr)
{ {
nmax = 0; nmax = 0;
no_virial_fdotr_compute = 1;
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */

1
src/DIELECTRIC/pair_coul_long_dielectric.cpp
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@ -41,6 +41,7 @@ PairCoulLongDielectric::PairCoulLongDielectric(LAMMPS *_lmp) :
{ {
nmax = 0; nmax = 0;
single_enable = 0; single_enable = 0;
no_virial_fdotr_compute = 1;
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */

4
src/DIELECTRIC/pair_lj_cut_coul_cut_dielectric.cpp
View File

@ -40,6 +40,7 @@ PairLJCutCoulCutDielectric::PairLJCutCoulCutDielectric(LAMMPS *_lmp) : PairLJCut
efield = nullptr; efield = nullptr;
epot = nullptr; epot = nullptr;
nmax = 0; nmax = 0;
no_virial_fdotr_compute = 1;
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
@ -93,15 +94,16 @@ void PairLJCutCoulCutDielectric::compute(int eflag, int vflag)
for (ii = 0; ii < inum; ii++) { for (ii = 0; ii < inum; ii++) {
i = ilist[ii]; i = ilist[ii];
qtmp = q[i]; qtmp = q[i];
etmp = eps[i];
xtmp = x[i][0]; xtmp = x[i][0];
ytmp = x[i][1]; ytmp = x[i][1];
ztmp = x[i][2]; ztmp = x[i][2];
etmp = eps[i];
itype = type[i]; itype = type[i];
jlist = firstneigh[i]; jlist = firstneigh[i];
jnum = numneigh[i]; jnum = numneigh[i];
// self term Eq. (55) for I_{ii} and Eq. (52) and in Barros et al // self term Eq. (55) for I_{ii} and Eq. (52) and in Barros et al
double curvature_threshold = sqrt(area[i]); double curvature_threshold = sqrt(area[i]);
if (curvature[i] < curvature_threshold) { if (curvature[i] < curvature_threshold) {
double sf = curvature[i] / (4.0 * MY_PIS * curvature_threshold) * area[i] * q[i]; double sf = curvature[i] / (4.0 * MY_PIS * curvature_threshold) * area[i] * q[i];

1
src/DIELECTRIC/pair_lj_cut_coul_debye_dielectric.cpp
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@ -40,6 +40,7 @@ PairLJCutCoulDebyeDielectric::PairLJCutCoulDebyeDielectric(LAMMPS *_lmp) : PairL
efield = nullptr; efield = nullptr;
epot = nullptr; epot = nullptr;
nmax = 0; nmax = 0;
no_virial_fdotr_compute = 1;
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */

1
src/DIELECTRIC/pair_lj_cut_coul_long_dielectric.cpp
View File

@ -45,6 +45,7 @@ PairLJCutCoulLongDielectric::PairLJCutCoulLongDielectric(LAMMPS *_lmp) : PairLJC
efield = nullptr; efield = nullptr;
epot = nullptr; epot = nullptr;
nmax = 0; nmax = 0;
no_virial_fdotr_compute = 1;
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */

1
src/DIELECTRIC/pair_lj_cut_coul_msm_dielectric.cpp
View File

@ -47,6 +47,7 @@ PairLJCutCoulMSMDielectric::PairLJCutCoulMSMDielectric(LAMMPS *_lmp) : PairLJCut
nmax = 0; nmax = 0;
ftmp = nullptr; ftmp = nullptr;
efield = nullptr; efield = nullptr;
no_virial_fdotr_compute = 1;
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */

1
src/DIELECTRIC/pair_lj_long_coul_long_dielectric.cpp
View File

@ -45,6 +45,7 @@ PairLJLongCoulLongDielectric::PairLJLongCoulLongDielectric(LAMMPS *_lmp) : PairL
efield = nullptr; efield = nullptr;
epot = nullptr; epot = nullptr;
nmax = 0; nmax = 0;
no_virial_fdotr_compute = 1;
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------

78
src/MDI/fix_mdi_qm.cpp
View File

@ -33,8 +33,7 @@ FixMDIQM::FixMDIQM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
{ {
// check requirements for LAMMPS to work with MDI as an engine // check requirements for LAMMPS to work with MDI as an engine
if (atom->tag_enable == 0) if (atom->tag_enable == 0) error->all(FLERR, "Cannot use MDI engine without atom IDs");
error->all(FLERR, "Cannot use MDI engine without atom IDs");
if (atom->natoms && atom->tag_consecutive() == 0) if (atom->natoms && atom->tag_consecutive() == 0)
error->all(FLERR, "MDI engine requires consecutive atom IDs"); error->all(FLERR, "MDI engine requires consecutive atom IDs");
@ -57,15 +56,21 @@ FixMDIQM::FixMDIQM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
while (iarg < narg) { while (iarg < narg) {
if (strcmp(arg[iarg], "virial") == 0) { if (strcmp(arg[iarg], "virial") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal fix mdi/qm command"); if (iarg + 2 > narg) error->all(FLERR, "Illegal fix mdi/qm command");
if (strcmp(arg[iarg+1],"yes") == 0) virialflag = 1; if (strcmp(arg[iarg + 1], "yes") == 0)
else if (strcmp(arg[iarg+1],"no") == 0) virialflag = 0; virialflag = 1;
else error->all(FLERR,"Illegal fix mdi/qm command"); else if (strcmp(arg[iarg + 1], "no") == 0)
virialflag = 0;
else
error->all(FLERR, "Illegal fix mdi/qm command");
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg], "add") == 0) { } else if (strcmp(arg[iarg], "add") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal fix mdi/qm command"); if (iarg + 2 > narg) error->all(FLERR, "Illegal fix mdi/qm command");
if (strcmp(arg[iarg+1],"yes") == 0) addflag = 1; if (strcmp(arg[iarg + 1], "yes") == 0)
else if (strcmp(arg[iarg+1],"no") == 0) addflag = 0; addflag = 1;
else error->all(FLERR,"Illegal fix mdi/qm command"); else if (strcmp(arg[iarg + 1], "no") == 0)
addflag = 0;
else
error->all(FLERR, "Illegal fix mdi/qm command");
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg], "every") == 0) { } else if (strcmp(arg[iarg], "every") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal fix mdi/qm command"); if (iarg + 2 > narg) error->all(FLERR, "Illegal fix mdi/qm command");
@ -74,9 +79,12 @@ FixMDIQM::FixMDIQM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg], "connect") == 0) { } else if (strcmp(arg[iarg], "connect") == 0) {
if (iarg + 2 > narg) error->all(FLERR, "Illegal fix mdi/qm command"); if (iarg + 2 > narg) error->all(FLERR, "Illegal fix mdi/qm command");
if (strcmp(arg[iarg+1],"yes") == 0) connectflag = 1; if (strcmp(arg[iarg + 1], "yes") == 0)
else if (strcmp(arg[iarg+1],"no") == 0) connectflag = 0; connectflag = 1;
else error->all(FLERR,"Illegal fix mdi/qm command"); else if (strcmp(arg[iarg + 1], "no") == 0)
connectflag = 0;
else
error->all(FLERR, "Illegal fix mdi/qm command");
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg], "elements") == 0) { } else if (strcmp(arg[iarg], "elements") == 0) {
int ntypes = atom->ntypes; int ntypes = atom->ntypes;
@ -89,7 +97,8 @@ FixMDIQM::FixMDIQM(LAMMPS *lmp, int narg, char **arg) : Fix(lmp, narg, arg)
error->all(FLERR, "Illegal fix mdi/qm command"); error->all(FLERR, "Illegal fix mdi/qm command");
} }
iarg += ntypes + 1; iarg += ntypes + 1;
} else error->all(FLERR,"Illegal fix mdi/qm command"); } else
error->all(FLERR, "Illegal fix mdi/qm command");
} }
// fix output settings are based on optional keywords // fix output settings are based on optional keywords
@ -217,8 +226,7 @@ void FixMDIQM::init()
plugin = 1; plugin = 1;
int method; int method;
MDI_Get_method(&method, mdicomm); MDI_Get_method(&method, mdicomm);
if (method != MDI_PLUGIN) if (method != MDI_PLUGIN) error->all(FLERR, "MDI internal error for plugin engine");
error->all(FLERR, "MDI internal error for plugin engine");
} }
// connection should have been already made by "mdi connect" command // connection should have been already made by "mdi connect" command
@ -237,6 +245,7 @@ void FixMDIQM::init()
} }
// send natoms, atom types or elements, and simulation box to engine // send natoms, atom types or elements, and simulation box to engine
// confirm engine count of NATOMS is correct
// this will trigger setup of a new system // this will trigger setup of a new system
// subsequent calls in post_force() will be for same system until new init() // subsequent calls in post_force() will be for same system until new init()
@ -245,36 +254,41 @@ void FixMDIQM::init()
int natoms_exists; int natoms_exists;
int ierr = MDI_Check_command_exists("@DEFAULT", ">NATOMS", mdicomm, &natoms_exists); int ierr = MDI_Check_command_exists("@DEFAULT", ">NATOMS", mdicomm, &natoms_exists);
if (ierr) error->all(FLERR, "MDI: >NATOMS command check"); if (ierr) error->all(FLERR, "MDI: >NATOMS command check");
if ( natoms_exists ) { MPI_Bcast(&natoms_exists, 1, MPI_INT, 0, world);
if (natoms_exists) {
ierr = MDI_Send_command(">NATOMS", mdicomm); ierr = MDI_Send_command(">NATOMS", mdicomm);
if (ierr) error->all(FLERR, "MDI: >NATOMS command"); if (ierr) error->all(FLERR, "MDI: >NATOMS command");
int n = static_cast<int>(atom->natoms); int n = static_cast<int>(atom->natoms);
ierr = MDI_Send(&n, 1, MDI_INT, mdicomm); ierr = MDI_Send(&n, 1, MDI_INT, mdicomm);
if (ierr) error->all(FLERR, "MDI: >NATOMS data"); if (ierr) error->all(FLERR, "MDI: >NATOMS data");
} else { // confirm that the engine's NATOMS is correct } else {
ierr = MDI_Send_command("<NATOMS", mdicomm); ierr = MDI_Send_command("<NATOMS", mdicomm);
if (ierr) error->all(FLERR, "MDI: <NATOMS command"); if (ierr) error->all(FLERR, "MDI: <NATOMS command");
int n; int n;
ierr = MDI_Recv(&n, 1, MDI_INT, mdicomm); ierr = MDI_Recv(&n, 1, MDI_INT, mdicomm);
if (ierr) error->all(FLERR, "MDI: <NATOMS data"); if (ierr) error->all(FLERR, "MDI: <NATOMS data");
if ( n != atom->natoms ) error->all(FLERR, "MDI: Engine has the wrong number of atoms, and does not support the >NATOMS command."); MPI_Bcast(&n, 1, MPI_INT, 0, world);
if (n != atom->natoms)
error->all(FLERR, "MDI: Engine has wrong atom count and does not support >NATOMS command");
} }
int elements_exists; int elements_exists;
int types_exists; int types_exists;
ierr = MDI_Check_command_exists("@DEFAULT", ">ELEMENTS", mdicomm, &elements_exists); ierr = MDI_Check_command_exists("@DEFAULT", ">ELEMENTS", mdicomm, &elements_exists);
if (ierr) error->all(FLERR, "MDI: >ELEMENTS command check"); if (ierr) error->all(FLERR, "MDI: >ELEMENTS command check");
MPI_Bcast(&elements_exists, 1, MPI_INT, 0, world);
ierr = MDI_Check_command_exists("@DEFAULT", ">TYPES", mdicomm, &types_exists); ierr = MDI_Check_command_exists("@DEFAULT", ">TYPES", mdicomm, &types_exists);
if (ierr) error->all(FLERR, "MDI: >TYPES command check"); if (ierr) error->all(FLERR, "MDI: >TYPES command check");
if ( elements && elements_exists ) { MPI_Bcast(&types_exists, 1, MPI_INT, 0, world);
if (elements && elements_exists)
send_elements(); send_elements();
} else if ( types_exists ) { else if (types_exists)
send_types(); send_types();
}
send_box(); send_box();
} }
@ -301,8 +315,7 @@ void FixMDIQM::post_force(int vflag)
// if simulation box dynamically changes, send current box to MDI engine // if simulation box dynamically changes, send current box to MDI engine
if (domain->box_change_size || domain->box_change_shape) if (domain->box_change_size || domain->box_change_shape) send_box();
send_box();
// gather all coords, ordered by atomID // gather all coords, ordered by atomID
@ -358,7 +371,6 @@ void FixMDIQM::post_force(int vflag)
fqm[i][2] = buf3[3 * index + 2] * mdi2lmp_force; fqm[i][2] = buf3[3 * index + 2] * mdi2lmp_force;
} }
// optionally add forces to owned atoms // optionally add forces to owned atoms
// use atomID of local atoms to index into ordered buf3 // use atomID of local atoms to index into ordered buf3
@ -372,7 +384,8 @@ void FixMDIQM::post_force(int vflag)
} }
} }
// optionally request stress tensor from MDI engine, convert to virial // optionally request stress tensor from MDI engine, convert to 6-value virial
// MDI defines virial tensor as intensive (divided by volume), LAMMPS does not
// qm_virial = fix output for global QM virial // qm_virial = fix output for global QM virial
if (virialflag) { if (virialflag) {
@ -402,8 +415,7 @@ void FixMDIQM::post_force(int vflag)
volume = domain->xprd * domain->yprd; volume = domain->xprd * domain->yprd;
else if (domain->dimension == 3) else if (domain->dimension == 3)
volume = domain->xprd * domain->yprd * domain->zprd; volume = domain->xprd * domain->yprd * domain->zprd;
for (int i = 0; i < 6; i++) for (int i = 0; i < 6; i++) virial[i] = qm_virial_symmetric[i] * volume / nprocs;
virial[i] = qm_virial_symmetric[i]*volume/nprocs;
} }
} }
@ -447,8 +459,7 @@ void FixMDIQM::reallocate()
if (atom->natoms > maxbuf) { if (atom->natoms > maxbuf) {
bigint nsize = atom->natoms * 3; bigint nsize = atom->natoms * 3;
if (nsize > MAXSMALLINT) if (nsize > MAXSMALLINT) error->all(FLERR, "Natoms too large to use with fix mdi/qm");
error->all(FLERR, "Natoms too large to use with fix mdi/qm");
maxbuf = static_cast<int>(atom->natoms); maxbuf = static_cast<int>(atom->natoms);
memory->destroy(ibuf1); memory->destroy(ibuf1);
@ -530,6 +541,8 @@ void FixMDIQM::send_box()
int celldispl_exists; int celldispl_exists;
int ierr = MDI_Check_command_exists("@DEFAULT", ">NATOMS", mdicomm, &celldispl_exists); int ierr = MDI_Check_command_exists("@DEFAULT", ">NATOMS", mdicomm, &celldispl_exists);
if (ierr) error->all(FLERR, "MDI: >CELL_DISPL command check"); if (ierr) error->all(FLERR, "MDI: >CELL_DISPL command check");
MPI_Bcast(&celldispl_exists, 1, MPI_INT, 0, world);
if (celldispl_exists) { if (celldispl_exists) {
ierr = MDI_Send_command(">CELL_DISPL", mdicomm); ierr = MDI_Send_command(">CELL_DISPL", mdicomm);
if (ierr) error->all(FLERR, "MDI: >CELL_DISPL command"); if (ierr) error->all(FLERR, "MDI: >CELL_DISPL command");
@ -608,18 +621,17 @@ void FixMDIQM::unit_conversions()
mdi2lmp_force = angstrom_to_bohr / ev_to_hartree; mdi2lmp_force = angstrom_to_bohr / ev_to_hartree;
} }
// pressure or stress units = force/area = energy/volume // stress units = force/area = energy/volume
mdi2lmp_pressure = 1.0; mdi2lmp_pressure = 1.0;
lmp2mdi_pressure = 1.0; lmp2mdi_pressure = 1.0;
if (lmpunits == REAL) { if (lmpunits == REAL) {
lmp2mdi_pressure = (kelvin_to_hartree / force->boltz) / lmp2mdi_pressure = (kelvin_to_hartree / force->boltz) /
(angstrom_to_bohr * angstrom_to_bohr * angstrom_to_bohr) / force->nktv2p; (angstrom_to_bohr * angstrom_to_bohr * angstrom_to_bohr);
mdi2lmp_pressure = 1.0 / lmp2mdi_pressure; mdi2lmp_pressure = 1.0 / lmp2mdi_pressure;
} else if (lmpunits == METAL) { } else if (lmpunits == METAL) {
lmp2mdi_pressure = lmp2mdi_pressure = ev_to_hartree / (angstrom_to_bohr * angstrom_to_bohr * angstrom_to_bohr);
ev_to_hartree / (angstrom_to_bohr * angstrom_to_bohr * angstrom_to_bohr) / force->nktv2p;
mdi2lmp_pressure = 1.0 / lmp2mdi_pressure; mdi2lmp_pressure = 1.0 / lmp2mdi_pressure;
} }
} }

48
src/MDI/library_mdi.cpp
View File

@ -23,12 +23,8 @@
#define LAMMPS_LIB_MPI 1 #define LAMMPS_LIB_MPI 1
#include "library.h" #include "library.h"
#include "mdi_engine.h"
#include <cstring> #include <cstring>
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
/** Initialize an instance of LAMMPS as an MDI plugin /** Initialize an instance of LAMMPS as an MDI plugin
@ -52,15 +48,16 @@ command-line argument, which must be provided by the MDI driver.
* \param class_obj pointer to an instance of an mdi/engine fix cast to ``void *``. * \param class_obj pointer to an instance of an mdi/engine fix cast to ``void *``.
* \return 0 on no error. */ * \return 0 on no error. */
int MDI_Plugin_init_lammps() int MDI_Plugin_init_lammps(void *plugin_state)
{ {
// initialize MDI // initialize MDI
int mdi_argc; int mdi_argc;
char **mdi_argv; char **mdi_argv;
if (MDI_Set_plugin_state(plugin_state)) MPI_Abort(MPI_COMM_WORLD, 1);
if (MDI_Plugin_get_argc(&mdi_argc)) MPI_Abort(MPI_COMM_WORLD, 1); if (MDI_Plugin_get_argc(&mdi_argc)) MPI_Abort(MPI_COMM_WORLD, 1);
if (MDI_Plugin_get_argv(&mdi_argv)) MPI_Abort(MPI_COMM_WORLD, 1); if (MDI_Plugin_get_argv(&mdi_argv)) MPI_Abort(MPI_COMM_WORLD, 1);
if (MDI_Init(&mdi_argc, &mdi_argv)) MPI_Abort(MPI_COMM_WORLD, 1);
// get the MPI intra-communicator for this code // get the MPI intra-communicator for this code
@ -90,14 +87,23 @@ int MDI_Plugin_init_lammps()
if (!found_filename) MPI_Abort(MPI_COMM_WORLD, 1); if (!found_filename) MPI_Abort(MPI_COMM_WORLD, 1);
// create and run a LAMMPS instance // create and run a LAMMPS instance
// lammps_open() expects a first arg (not used) which is executable name // need to add an initial pseudo arg to mdi_argc & mdi_argv
// same as if called from main.cpp // b/c lammps_open() expects first arg to be an executable name
// same as if it were called from main.cpp
int mdi_argc_extra = mdi_argc + 1;
char **mdi_argv_extra = new char *[mdi_argc_extra];
mdi_argv_extra[0] = (char *) "MDI_plugin_engine";
for (int i = 0; i < mdi_argc; i++) mdi_argv_extra[i + 1] = mdi_argv[i];
void *lmp = nullptr; void *lmp = nullptr;
if (lammps_config_has_mpi_support() > 0) if (lammps_config_has_mpi_support() > 0)
lmp = lammps_open(mdi_argc + 1, &mdi_argv[-1], mpi_world_comm, nullptr); lmp = lammps_open(mdi_argc_extra, mdi_argv_extra, mpi_world_comm, nullptr);
else else
lmp = lammps_open_no_mpi(mdi_argc + 1, &mdi_argv[-1], nullptr); lmp = lammps_open_no_mpi(mdi_argc_extra, mdi_argv_extra, nullptr);
delete[] mdi_argv_extra;
// process the specified input script // process the specified input script
// must contain "mdi engine" command // must contain "mdi engine" command
@ -110,25 +116,3 @@ int MDI_Plugin_init_lammps()
return 0; return 0;
} }
/* ---------------------------------------------------------------------- */
/** Execute an MDI command
*
\verbatim embed:rst
This function is called by the MolSSI Driver Interface Library (MDI)
when LAMMPS is run as a plugin, and should not otherwise be used.
The function executes a single command from an external MDI driver.
\endverbatim
* \param command string buffer corresponding to the command to be executed
* \param comm MDI communicator that can be used to communicated with the driver.
* \param class_obj pointer to an instance of an mdi/engine fix cast to ``void *``.
* \return 0 on no error, 1 on error. */
int lammps_execute_mdi_command(const char *command, MDI_Comm comm, void *class_obj)
{
auto mdi_engine = (MDIEngine *) class_obj;
return mdi_engine->execute_command(command, comm);
}

7
src/MDI/library_mdi.h
View File

@ -14,13 +14,12 @@
#ifndef LAMMPS_LIBRARY_MDI_H #ifndef LAMMPS_LIBRARY_MDI_H
#define LAMMPS_LIBRARY_MDI_H #define LAMMPS_LIBRARY_MDI_H
/* C style library calls to LAMMPS when a LAMMPS shared library is /* C style library call to LAMMPS when a LAMMPS shared library is
* used as a plugin through MolSSI Driver Interface (MDI). */ * used as a plugin through MolSSI Driver Interface (MDI) */
#include <mdi.h> #include <mdi.h>
extern "C" { extern "C" {
int MDI_Plugin_init_lammps(); int MDI_Plugin_init_lammps(void *plugin_state);
int lammps_execute_mdi_command(const char *, MDI_Comm, void *);
} }
#endif #endif

9
src/MDI/mdi_command.cpp
View File

@ -53,7 +53,8 @@ void MDICommand::command(int narg, char **arg)
MDI_Accept_communicator(&mdicomm); MDI_Accept_communicator(&mdicomm);
if (mdicomm == MDI_COMM_NULL) if (mdicomm == MDI_COMM_NULL)
error->all(FLERR, "MDI unable to connect to stand-alone engine"); error->all(FLERR, "MDI unable to connect to stand-alone engine");
} else error->all(FLERR, "Cannot use mdi connect with plugin engine"); } else
error->all(FLERR, "Cannot use mdi connect with plugin engine");
int nbytes = sizeof(MDI_Comm); int nbytes = sizeof(MDI_Comm);
char *ptrcomm = (char *) memory->smalloc(nbytes, "mdi:mdicomm"); char *ptrcomm = (char *) memory->smalloc(nbytes, "mdi:mdicomm");
@ -63,8 +64,7 @@ void MDICommand::command(int narg, char **arg)
} else if (strcmp(arg[0], "exit") == 0) { } else if (strcmp(arg[0], "exit") == 0) {
if (lmp->mdicomm == nullptr) if (lmp->mdicomm == nullptr) error->all(FLERR, "MDI cannot send exit to unconnected engine");
error->all(FLERR,"MDI cannot send exit to unconnected engine");
MDI_Comm mdicomm; MDI_Comm mdicomm;
int nbytes = sizeof(MDI_Comm); int nbytes = sizeof(MDI_Comm);
@ -77,5 +77,6 @@ void MDICommand::command(int narg, char **arg)
memory->sfree(ptrcomm); memory->sfree(ptrcomm);
lmp->mdicomm = nullptr; lmp->mdicomm = nullptr;
} else error->all(FLERR, "Illegal mdi command"); } else
error->all(FLERR, "Illegal mdi command");
} }

46
src/MDI/mdi_engine.cpp
View File

@ -91,7 +91,8 @@ MDIEngine::MDIEngine(LAMMPS *_lmp, int narg, char ** arg) : Pointers(_lmp)
error->all(FLERR, "Illegal mdi engine command"); error->all(FLERR, "Illegal mdi engine command");
} }
iarg += ntypes + 1; iarg += ntypes + 1;
} else error->all(FLERR,"Illegal mdi engine command"); } else
error->all(FLERR, "Illegal mdi engine command");
} }
// error check an MDI element does not map to multiple atom types // error check an MDI element does not map to multiple atom types
@ -184,10 +185,10 @@ MDIEngine::MDIEngine(LAMMPS *_lmp, int narg, char ** arg) : Pointers(_lmp)
mdi_commands(); mdi_commands();
// register the execute_command function with MDI // register a callback function with MDI used when engine runs in plugin mode
// only used when engine runs in plugin mode // execute_command_plugin_wrapper() must be a static method
MDI_Set_execute_command_func(lammps_execute_mdi_command, this); MDI_Set_execute_command_func(execute_command_plugin_wrapper, this);
// one-time operation to establish a connection with the driver // one-time operation to establish a connection with the driver
@ -291,11 +292,22 @@ void MDIEngine::engine_node(const char *node)
node_match = true; node_match = true;
} }
/* ----------------------------------------------------------------------
wrapper function on execute_command()
invoked as callback by MDI when engine operates in plugin mode
this is a static method in mdi_engine.h
---------------------------------------------------------------------- */
int MDIEngine::execute_command_plugin_wrapper(const char *command, MDI_Comm comm, void *class_obj)
{
auto mdi_engine = (MDIEngine *) class_obj;
return mdi_engine->execute_command(command, comm);
}
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
process a single driver command process a single driver command
called by engine_node() in loop called by engine_node() in loop when engine runs as stand-alone code
also called by MDI itself via lib::lammps_execute_mdi_command() called by execute_command_plugin_wrapper() when engine runs as plugin lib
when LAMMPS is running as a plugin
---------------------------------------------------------------------- */ ---------------------------------------------------------------------- */
int MDIEngine::execute_command(const char *command, MDI_Comm mdicomm) int MDIEngine::execute_command(const char *command, MDI_Comm mdicomm)
@ -334,8 +346,7 @@ int MDIEngine::execute_command(const char *command, MDI_Comm mdicomm)
receive_coords(); receive_coords();
} else if (strcmp(command, ">ELEMENTS") == 0) { } else if (strcmp(command, ">ELEMENTS") == 0) {
if (!elements) if (!elements) error->all(FLERR, "MDI engine command did not define element list");
error->all(FLERR,"MDI engine command did not define element list");
receive_elements(); receive_elements();
} else if (strcmp(command, ">FORCES") == 0) { } else if (strcmp(command, ">FORCES") == 0) {
@ -1148,9 +1159,16 @@ void MDIEngine::receive_cell()
for (int icell = 0; icell < 9; icell++) sys_cell[icell] *= mdi2lmp_length; for (int icell = 0; icell < 9; icell++) sys_cell[icell] *= mdi2lmp_length;
// error check that edge vectors match LAMMPS triclinic requirement // error check that edge vectors match LAMMPS triclinic requirement
// 3,7,6 = xy, yz, xz tilt factors
if (sys_cell[1] != 0.0 || sys_cell[2] != 0.0 || sys_cell[5] != 0.0) if (sys_cell[1] != 0.0 || sys_cell[2] != 0.0 || sys_cell[5] != 0.0)
error->all(FLERR, "MDI: Received cell edges are not LAMMPS compatible"); error->all(FLERR, "MDI: Received cell edges are not an upper triangular matrix");
if (sys_cell[3] != 0.0 || sys_cell[7] != 0.0 || sys_cell[6] != 0.0)
if (!domain->triclinic)
error->all(FLERR,
"MDI: Received cell edges are for a triclinic box, "
"but LAMMPS is using an orthogonal box");
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
@ -1227,8 +1245,7 @@ void MDIEngine::receive_elements()
break; break;
} }
} }
if (itype > ntypes) if (itype > ntypes) error->all(FLERR, "MDI element not found in element list");
error->all(FLERR,"MDI element not found in element list");
} }
} }
@ -1493,6 +1510,9 @@ void MDIEngine::send_pe()
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
<STRESS command <STRESS command
send 9-component stress tensor (no kinetic energy term) send 9-component stress tensor (no kinetic energy term)
should be intensive quantity (divided by volume in pressure compute)
MDI stress tensor units are energy/volume,
so conversion factor includes nktv2p to convert pressure back to virial
---------------------------------------------------------------------- */ ---------------------------------------------------------------------- */
void MDIEngine::send_stress() void MDIEngine::send_stress()
@ -1837,6 +1857,8 @@ void MDIEngine::unit_conversions()
} }
// pressure or stress units = force/area = energy/volume // pressure or stress units = force/area = energy/volume
// MDI energy/volume = Hartree/Bohr^3,
// so need to remove LAMMPS nktv2p from pressure
mdi2lmp_pressure = 1.0; mdi2lmp_pressure = 1.0;
lmp2mdi_pressure = 1.0; lmp2mdi_pressure = 1.0;

8
src/MDI/mdi_engine.h
View File

@ -22,8 +22,6 @@ namespace LAMMPS_NS {
class MDIEngine : protected Pointers { class MDIEngine : protected Pointers {
public: public:
MDIEngine(class LAMMPS *, int, char **); MDIEngine(class LAMMPS *, int, char **);
int execute_command(const char *command, MDI_Comm mdicomm);
void engine_node(const char *node); void engine_node(const char *node);
private: private:
@ -87,9 +85,13 @@ class MDIEngine : protected Pointers {
class Irregular *irregular; // irregular comm if new COORDS class Irregular *irregular; // irregular comm if new COORDS
// are highly displaced // are highly displaced
// static method for MDI to callback to, when LAMMPS used as plugin engine
static int execute_command_plugin_wrapper(const char *, MDI_Comm, void *);
// class methods // class methods
void mdi_engine(int, char **); int execute_command(const char *, MDI_Comm);
void mdi_commands(); void mdi_commands();
void mdi_md(); void mdi_md();

21
src/MDI/mdi_plugin.cpp
View File

@ -72,18 +72,23 @@ MDIPlugin::MDIPlugin(LAMMPS *_lmp, int narg, char **arg) : Pointers(_lmp)
// error checks // error checks
if (!mdi_arg || !infile_arg || !lammps_command) if (!mdi_arg || !lammps_command)
error->all(FLERR, "MDI plugin must specify mdi, infile, command keywords"); error->all(FLERR, "MDI plugin must specify mdi and command keywords");
// build full plugin_args string for args to plugin library // build full plugin_args string for args to plugin library
int n = strlen(mdi_arg) + strlen(infile_arg) + strlen(extra_arg) + 16; int n = strlen(mdi_arg) + 16;
if (infile_arg) n += strlen(infile_arg);
if (extra_arg) n += strlen(extra_arg);
auto plugin_args = new char[n]; auto plugin_args = new char[n];
plugin_args[0] = 0; plugin_args[0] = 0;
strcat(plugin_args, "-mdi \""); strcat(plugin_args, "-mdi \"");
strcat(plugin_args, mdi_arg); strcat(plugin_args, mdi_arg);
strcat(plugin_args, "\" -in "); strcat(plugin_args, "\"");
if (infile_arg) {
strcat(plugin_args, " -in ");
strcat(plugin_args, infile_arg); strcat(plugin_args, infile_arg);
}
if (extra_arg) { if (extra_arg) {
strcat(plugin_args, " "); strcat(plugin_args, " ");
strcat(plugin_args, extra_arg); strcat(plugin_args, extra_arg);
@ -91,7 +96,8 @@ MDIPlugin::MDIPlugin(LAMMPS *_lmp, int narg, char **arg) : Pointers(_lmp)
// launch the MDI plugin library // launch the MDI plugin library
// path for lib was specified in -mdi command-line arg when LAMMPS started // path for lib was specified in -mdi command-line arg when LAMMPS started
// this calls back to plugin_wrapper, which must issue MDI EXIT at end // this calls back to plugin_wrapper(), which issues MDI EXIT at end & returns
// plugin_wrapper() must be a static method
MDI_Launch_plugin(plugin_name, plugin_args, &world, plugin_wrapper, (void *) this); MDI_Launch_plugin(plugin_name, plugin_args, &world, plugin_wrapper, (void *) this);
@ -99,8 +105,9 @@ MDIPlugin::MDIPlugin(LAMMPS *_lmp, int narg, char **arg) : Pointers(_lmp)
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
callback function from MDI_Launch_plugin() wrapper on entire interaction of LAMMPS as a driver with the plugin engine
this function wraps entire interaction of LAMMPS driver with the plugin invoked as a callback by MDI once plugin library engine is launched
this is a static method in mdi_plugin.h
---------------------------------------------------------------------- */ ---------------------------------------------------------------------- */
int MDIPlugin::plugin_wrapper(void * /*pmpicomm*/, MDI_Comm mdicomm, void *vptr) int MDIPlugin::plugin_wrapper(void * /*pmpicomm*/, MDI_Comm mdicomm, void *vptr)

3
src/MDI/mdi_plugin.h
View File

@ -26,6 +26,9 @@ class MDIPlugin : protected Pointers {
private: private:
char *lammps_command; char *lammps_command;
// static method for MDI to callback to
// when LAMMPS is a driver which launches a plugin engine
static int plugin_wrapper(void *, MDI_Comm, void *); static int plugin_wrapper(void *, MDI_Comm, void *);
}; };

28
src/OPENMP/pair_lj_cut_coul_cut_dielectric_omp.cpp
View File

@ -23,6 +23,7 @@
#include "math_const.h" #include "math_const.h"
#include "memory.h" #include "memory.h"
#include "neigh_list.h" #include "neigh_list.h"
#include "suffix.h"
#include <cmath> #include <cmath>
@ -37,6 +38,7 @@ static constexpr double EPSILON = 1.0e-6;
PairLJCutCoulCutDielectricOMP::PairLJCutCoulCutDielectricOMP(LAMMPS *_lmp) : PairLJCutCoulCutDielectricOMP::PairLJCutCoulCutDielectricOMP(LAMMPS *_lmp) :
PairLJCutCoulCutDielectric(_lmp), ThrOMP(_lmp, THR_PAIR) PairLJCutCoulCutDielectric(_lmp), ThrOMP(_lmp, THR_PAIR)
{ {
suffix_flag |= Suffix::OMP;
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
@ -99,7 +101,7 @@ void PairLJCutCoulCutDielectricOMP::eval(int iifrom, int iito, ThrData *const th
{ {
int i, j, ii, jj, jnum, itype, jtype; int i, j, ii, jj, jnum, itype, jtype;
double qtmp, etmp, xtmp, ytmp, ztmp, delx, dely, delz, evdwl, ecoul; double qtmp, etmp, xtmp, ytmp, ztmp, delx, dely, delz, evdwl, ecoul;
double fpair_i, fpair_j; double fpair_i;
double rsq, r2inv, r6inv, forcecoul, forcelj, factor_coul, factor_lj; double rsq, r2inv, r6inv, forcecoul, forcelj, factor_coul, factor_lj;
double efield_i, epot_i; double efield_i, epot_i;
int *ilist, *jlist, *numneigh, **firstneigh; int *ilist, *jlist, *numneigh, **firstneigh;
@ -130,10 +132,10 @@ void PairLJCutCoulCutDielectricOMP::eval(int iifrom, int iito, ThrData *const th
i = ilist[ii]; i = ilist[ii];
qtmp = q[i]; qtmp = q[i];
etmp = eps[i];
xtmp = x[i].x; xtmp = x[i].x;
ytmp = x[i].y; ytmp = x[i].y;
ztmp = x[i].z; ztmp = x[i].z;
etmp = eps[i];
itype = type[i]; itype = type[i];
jlist = firstneigh[i]; jlist = firstneigh[i];
jnum = numneigh[i]; jnum = numneigh[i];
@ -141,6 +143,7 @@ void PairLJCutCoulCutDielectricOMP::eval(int iifrom, int iito, ThrData *const th
extmp = eytmp = eztmp = 0.0; extmp = eytmp = eztmp = 0.0;
// self term Eq. (55) for I_{ii} and Eq. (52) and in Barros et al // self term Eq. (55) for I_{ii} and Eq. (52) and in Barros et al
double curvature_threshold = sqrt(area[i]); double curvature_threshold = sqrt(area[i]);
if (curvature[i] < curvature_threshold) { if (curvature[i] < curvature_threshold) {
double sf = curvature[i] / (4.0 * MY_PIS * curvature_threshold) * area[i] * q[i]; double sf = curvature[i] / (4.0 * MY_PIS * curvature_threshold) * area[i] * q[i];
@ -151,7 +154,7 @@ void PairLJCutCoulCutDielectricOMP::eval(int iifrom, int iito, ThrData *const th
efield[i][0] = efield[i][1] = efield[i][2] = 0; efield[i][0] = efield[i][1] = efield[i][2] = 0;
} }
epot[i] = 0; epot[i] = 0.0;
for (jj = 0; jj < jnum; jj++) { for (jj = 0; jj < jnum; jj++) {
j = jlist[jj]; j = jlist[jj];
@ -167,9 +170,10 @@ void PairLJCutCoulCutDielectricOMP::eval(int iifrom, int iito, ThrData *const th
if (rsq < cutsq[itype][jtype]) { if (rsq < cutsq[itype][jtype]) {
r2inv = 1.0 / rsq; r2inv = 1.0 / rsq;
const double rinv = sqrt(r2inv);
if (rsq < cut_coulsq[itype][jtype] && rsq > EPSILON) { if (rsq < cut_coulsq[itype][jtype] && rsq > EPSILON) {
efield_i = qqrd2e * q[j] * sqrt(r2inv); efield_i = qqrd2e * q[j] * rinv;
forcecoul = qtmp * efield_i; forcecoul = qtmp * efield_i;
epot_i = efield_i; epot_i = efield_i;
} else } else
@ -182,7 +186,6 @@ void PairLJCutCoulCutDielectricOMP::eval(int iifrom, int iito, ThrData *const th
forcelj = 0.0; forcelj = 0.0;
fpair_i = (factor_coul * etmp * forcecoul + factor_lj * forcelj) * r2inv; fpair_i = (factor_coul * etmp * forcecoul + factor_lj * forcelj) * r2inv;
fxtmp += delx * fpair_i; fxtmp += delx * fpair_i;
fytmp += dely * fpair_i; fytmp += dely * fpair_i;
fztmp += delz * fpair_i; fztmp += delz * fpair_i;
@ -193,29 +196,18 @@ void PairLJCutCoulCutDielectricOMP::eval(int iifrom, int iito, ThrData *const th
eztmp += delz * efield_i; eztmp += delz * efield_i;
epot[i] += epot_i; epot[i] += epot_i;
if (NEWTON_PAIR || j >= nlocal) {
fpair_j = (factor_coul * eps[j] * forcecoul + factor_lj * forcelj) * r2inv;
f[j].x -= delx * fpair_j;
f[j].y -= dely * fpair_j;
f[j].z -= delz * fpair_j;
}
if (EFLAG) { if (EFLAG) {
if (rsq < cut_coulsq[itype][jtype]) { if (rsq < cut_coulsq[itype][jtype]) {
ecoul = factor_coul * qqrd2e * qtmp * q[j] * (etmp + eps[j]) * sqrt(r2inv); ecoul = factor_coul * qqrd2e * qtmp * q[j] * 0.5 * (etmp + eps[j]) * rinv;
} else } else
ecoul = 0.0; ecoul = 0.0;
ecoul *= 0.5;
if (rsq < cut_ljsq[itype][jtype]) { if (rsq < cut_ljsq[itype][jtype]) {
evdwl = r6inv * (lj3[itype][jtype] * r6inv - lj4[itype][jtype]) - offset[itype][jtype]; evdwl = r6inv * (lj3[itype][jtype] * r6inv - lj4[itype][jtype]) - offset[itype][jtype];
evdwl *= factor_lj; evdwl *= factor_lj;
} else } else
evdwl = 0.0; evdwl = 0.0;
} }
if (EVFLAG) ev_tally_full_thr(this, i, evdwl, ecoul, fpair_i, delx, dely, delz, thr);
if (EVFLAG)
ev_tally_thr(this, i, j, nlocal, NEWTON_PAIR, evdwl, ecoul, fpair_i, delx, dely, delz,
thr);
} }
} }
f[i].x += fxtmp; f[i].x += fxtmp;

19
src/OPENMP/pair_lj_cut_coul_debye_dielectric_omp.cpp
View File

@ -23,6 +23,7 @@
#include "math_const.h" #include "math_const.h"
#include "memory.h" #include "memory.h"
#include "neigh_list.h" #include "neigh_list.h"
#include "suffix.h"
#include <cmath> #include <cmath>
@ -37,6 +38,7 @@ static constexpr double EPSILON = 1.0e-6;
PairLJCutCoulDebyeDielectricOMP::PairLJCutCoulDebyeDielectricOMP(LAMMPS *_lmp) : PairLJCutCoulDebyeDielectricOMP::PairLJCutCoulDebyeDielectricOMP(LAMMPS *_lmp) :
PairLJCutCoulDebyeDielectric(_lmp), ThrOMP(_lmp, THR_PAIR) PairLJCutCoulDebyeDielectric(_lmp), ThrOMP(_lmp, THR_PAIR)
{ {
suffix_flag |= Suffix::OMP;
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
@ -99,7 +101,7 @@ void PairLJCutCoulDebyeDielectricOMP::eval(int iifrom, int iito, ThrData *const
{ {
int i, j, ii, jj, jnum, itype, jtype; int i, j, ii, jj, jnum, itype, jtype;
double qtmp, etmp, xtmp, ytmp, ztmp, delx, dely, delz, evdwl, ecoul; double qtmp, etmp, xtmp, ytmp, ztmp, delx, dely, delz, evdwl, ecoul;
double fpair_i, fpair_j; double fpair_i;
double rsq, r2inv, r6inv, forcecoul, forcelj, factor_coul, factor_lj, efield_i, epot_i; double rsq, r2inv, r6inv, forcecoul, forcelj, factor_coul, factor_lj, efield_i, epot_i;
double r, rinv, screening; double r, rinv, screening;
int *ilist, *jlist, *numneigh, **firstneigh; int *ilist, *jlist, *numneigh, **firstneigh;
@ -185,7 +187,6 @@ void PairLJCutCoulDebyeDielectricOMP::eval(int iifrom, int iito, ThrData *const
forcelj = 0.0; forcelj = 0.0;
fpair_i = (factor_coul * etmp * forcecoul + factor_lj * forcelj) * r2inv; fpair_i = (factor_coul * etmp * forcecoul + factor_lj * forcelj) * r2inv;
fxtmp += delx * fpair_i; fxtmp += delx * fpair_i;
fytmp += dely * fpair_i; fytmp += dely * fpair_i;
fztmp += delz * fpair_i; fztmp += delz * fpair_i;
@ -196,19 +197,11 @@ void PairLJCutCoulDebyeDielectricOMP::eval(int iifrom, int iito, ThrData *const
eztmp += delz * efield_i; eztmp += delz * efield_i;
epot[i] += epot_i; epot[i] += epot_i;
if (NEWTON_PAIR || j >= nlocal) {
fpair_j = (factor_coul * eps[j] * forcecoul + factor_lj * forcelj) * r2inv;
f[j].x -= delx * fpair_j;
f[j].y -= dely * fpair_j;
f[j].z -= delz * fpair_j;
}
if (EFLAG) { if (EFLAG) {
if (rsq < cut_coulsq[itype][jtype]) { if (rsq < cut_coulsq[itype][jtype]) {
ecoul = factor_coul * qqrd2e * qtmp * q[j] * (etmp + eps[j]) * rinv * screening; ecoul = factor_coul * qqrd2e * qtmp * q[j] * 0.5 * (etmp + eps[j]) * rinv * screening;
} else } else
ecoul = 0.0; ecoul = 0.0;
ecoul *= 0.5;
if (rsq < cut_ljsq[itype][jtype]) { if (rsq < cut_ljsq[itype][jtype]) {
evdwl = r6inv * (lj3[itype][jtype] * r6inv - lj4[itype][jtype]) - offset[itype][jtype]; evdwl = r6inv * (lj3[itype][jtype] * r6inv - lj4[itype][jtype]) - offset[itype][jtype];
evdwl *= factor_lj; evdwl *= factor_lj;
@ -216,9 +209,7 @@ void PairLJCutCoulDebyeDielectricOMP::eval(int iifrom, int iito, ThrData *const
evdwl = 0.0; evdwl = 0.0;
} }
if (EVFLAG) if (EVFLAG) ev_tally_full_thr(this, i, evdwl, ecoul, fpair_i, delx, dely, delz, thr);
ev_tally_thr(this, i, j, nlocal, NEWTON_PAIR, evdwl, ecoul, fpair_i, delx, dely, delz,
thr);
} }
} }
f[i].x += fxtmp; f[i].x += fxtmp;

6
src/OPENMP/pair_lj_cut_coul_long_dielectric_omp.cpp
View File

@ -24,6 +24,7 @@
#include "math_const.h" #include "math_const.h"
#include "memory.h" #include "memory.h"
#include "neigh_list.h" #include "neigh_list.h"
#include "suffix.h"
#include <cmath> #include <cmath>
@ -39,6 +40,7 @@ static constexpr double EPSILON = 1.0e-6;
PairLJCutCoulLongDielectricOMP::PairLJCutCoulLongDielectricOMP(LAMMPS *_lmp) : PairLJCutCoulLongDielectricOMP::PairLJCutCoulLongDielectricOMP(LAMMPS *_lmp) :
PairLJCutCoulLongDielectric(_lmp), ThrOMP(_lmp, THR_PAIR) PairLJCutCoulLongDielectric(_lmp), ThrOMP(_lmp, THR_PAIR)
{ {
suffix_flag |= Suffix::OMP;
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
@ -229,10 +231,10 @@ void PairLJCutCoulLongDielectricOMP::eval(int iifrom, int iito, ThrData *const t
if (EFLAG) { if (EFLAG) {
if (rsq < cut_coulsq) { if (rsq < cut_coulsq) {
if (!ncoultablebits || rsq <= tabinnersq) if (!ncoultablebits || rsq <= tabinnersq)
ecoul = prefactor * (etmp + eps[j]) * erfc; ecoul = prefactor * 0.5 * (etmp + eps[j]) * erfc;
else { else {
table = etable[itable] + fraction * detable[itable]; table = etable[itable] + fraction * detable[itable];
ecoul = qtmp * q[j] * (etmp + eps[j]) * table; ecoul = qtmp * q[j] * 0.5 * (etmp + eps[j]) * table;
} }
if (factor_coul < 1.0) ecoul -= (1.0 - factor_coul) * prefactor; if (factor_coul < 1.0) ecoul -= (1.0 - factor_coul) * prefactor;
} else } else

5
src/OPENMP/thr_omp.cpp
View File

@ -597,9 +597,8 @@ void ThrOMP::ev_tally_full_thr(Pair * const pair, const int i, const double evdw
const double ecoul, const double fpair, const double delx, const double ecoul, const double fpair, const double delx,
const double dely, const double delz, ThrData * const thr) const double dely, const double delz, ThrData * const thr)
{ {
if (pair->eflag_either) if (pair->eflag_either)
e_tally_thr(pair, i, i+1, i, 0, evdwl, ecoul, thr); e_tally_thr(pair, i, /*j*/ i+1, /*nlocal*/ i+1, /*newton_pair*/ 0, evdwl, ecoul, thr);
if (pair->vflag_either) { if (pair->vflag_either) {
double v[6]; double v[6];
@ -610,7 +609,7 @@ void ThrOMP::ev_tally_full_thr(Pair * const pair, const int i, const double evdw
v[4] = delx*delz*fpair; v[4] = delx*delz*fpair;
v[5] = dely*delz*fpair; v[5] = dely*delz*fpair;
v_tally_thr(pair, i, i+1, i, 0, v, thr); v_tally_thr(pair, i, /*j*/ i+1, /*nlocal*/ i+1, /*newton_pair*/ 0, v, thr);
} }
if (pair->num_tally_compute > 0) { if (pair->num_tally_compute > 0) {

389
src/atom.cpp
View File

@ -24,6 +24,7 @@
#include "force.h" #include "force.h"
#include "group.h" #include "group.h"
#include "input.h" #include "input.h"
#include "label_map.h"
#include "math_const.h" #include "math_const.h"
#include "memory.h" #include "memory.h"
#include "modify.h" #include "modify.h"
@ -48,14 +49,15 @@ using namespace MathConst;
#define DELTA 1 #define DELTA 1
#define EPSILON 1.0e-6 #define EPSILON 1.0e-6
#define MAXLINE 256
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
one instance per AtomVec style in style_atom.h one instance per AtomVec style in style_atom.h
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
template <typename T> static AtomVec *avec_creator(LAMMPS *lmp) template <typename T> static AtomVec *avec_creator(LAMMPS *_lmp)
{ {
return new T(lmp); return new T(_lmp);
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
@ -85,9 +87,9 @@ are updated by the AtomVec class as needed.
* instances of classes derived from the AtomVec base * instances of classes derived from the AtomVec base
* class, which correspond to the selected atom style. * class, which correspond to the selected atom style.
* *
* \param lmp pointer to the base LAMMPS class */ * \param _lmp pointer to the base LAMMPS class */
Atom::Atom(LAMMPS *lmp) : Pointers(lmp) Atom::Atom(LAMMPS *_lmp) : Pointers(_lmp)
{ {
natoms = 0; natoms = 0;
nlocal = nghost = nmax = 0; nlocal = nghost = nmax = 0;
@ -222,6 +224,10 @@ Atom::Atom(LAMMPS *lmp) : Pointers(lmp)
nmolecule = 0; nmolecule = 0;
molecules = nullptr; molecules = nullptr;
// type labels
lmap = nullptr;
// custom atom arrays // custom atom arrays
nivector = ndvector = niarray = ndarray = 0; nivector = ndvector = niarray = ndarray = 0;
@ -339,6 +345,10 @@ Atom::~Atom()
for (int i = 0; i < nmolecule; i++) delete molecules[i]; for (int i = 0; i < nmolecule; i++) delete molecules[i];
memory->sfree(molecules); memory->sfree(molecules);
// delete label map
delete lmap;
// delete per-type arrays // delete per-type arrays
delete[] mass; delete[] mass;
@ -616,6 +626,7 @@ void Atom::set_atomflag_defaults()
// 3rd customization section: customize by adding new flag // 3rd customization section: customize by adding new flag
// identical list as 2nd customization in atom.h // identical list as 2nd customization in atom.h
labelmapflag = 0;
sphere_flag = ellipsoid_flag = line_flag = tri_flag = body_flag = 0; sphere_flag = ellipsoid_flag = line_flag = tri_flag = body_flag = 0;
quat_flag = 0; quat_flag = 0;
peri_flag = electron_flag = 0; peri_flag = electron_flag = 0;
@ -1032,24 +1043,34 @@ void Atom::deallocate_topology()
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset, void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
int type_offset, int shiftflag, double *shift) int type_offset, int shiftflag, double *shift,
int labelflag, int *ilabel)
{ {
int xptr,iptr; int xptr,iptr;
imageint imagedata; imageint imagedata;
double xdata[3],lamda[3]; double xdata[3],lamda[3];
double *coord; double *coord;
char *next; char *next;
std::string typestr;
auto location = "Atoms section of data file";
// use the first line to detect and validate the number of words/tokens per line // use the first line to detect and validate the number of words/tokens per line
next = strchr(buf,'\n'); next = strchr(buf,'\n');
if (!next) error->all(FLERR, "Missing data in Atoms section of data file"); if (!next) error->all(FLERR, "Missing data in {}", location);
*next = '\0'; *next = '\0';
int nwords = utils::trim_and_count_words(buf); auto values = Tokenizer(buf).as_vector();
*next = '\n'; int nwords = values.size();
for (std::size_t i = 0; i < values.size(); ++i) {
if (utils::strmatch(values[i], "^#")) {
nwords = i;
break;
}
}
if ((nwords != avec->size_data_atom) && (nwords != avec->size_data_atom + 3)) if ((nwords != avec->size_data_atom) && (nwords != avec->size_data_atom + 3))
error->all(FLERR,"Incorrect atom format in data file: {}", utils::trim(buf)); error->all(FLERR,"Incorrect format in {}: {}", location, utils::trim(buf));
*next = '\n';
// set bounds for my proc // set bounds for my proc
// if periodic and I am lo/hi proc, adjust bounds by EPSILON // if periodic and I am lo/hi proc, adjust bounds by EPSILON
// insures all data atoms will be owned even with round-off // insures all data atoms will be owned even with round-off
@ -1120,13 +1141,15 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
for (int i = 0; i < n; i++) { for (int i = 0; i < n; i++) {
next = strchr(buf,'\n'); next = strchr(buf,'\n');
if (!next) error->all(FLERR, "Missing data in Atoms section of data file"); if (!next) error->all(FLERR, "Missing data in {}", location);
*next = '\0'; *next = '\0';
auto values = Tokenizer(utils::trim_comment(buf)).as_vector(); auto values = Tokenizer(buf).as_vector();
if (values.size() == 0) { int nvalues = values.size();
if ((nvalues == 0) || (utils::strmatch(values[0],"^#.*"))) {
// skip over empty or comment lines // skip over empty or comment lines
} else if ((int)values.size() != nwords) { } else if ((nvalues < nwords) ||
error->all(FLERR, "Incorrect atom format in data file: {}", utils::trim(buf)); ((nvalues > nwords) && (!utils::strmatch(values[nwords],"^#")))) {
error->all(FLERR, "Incorrect format in {}: {}", location, utils::trim(buf));
} else { } else {
int imx = 0, imy = 0, imz = 0; int imx = 0, imy = 0, imz = 0;
if (imageflag) { if (imageflag) {
@ -1161,14 +1184,36 @@ void Atom::data_atoms(int n, char *buf, tagint id_offset, tagint mol_offset,
if (coord[0] >= sublo[0] && coord[0] < subhi[0] && if (coord[0] >= sublo[0] && coord[0] < subhi[0] &&
coord[1] >= sublo[1] && coord[1] < subhi[1] && coord[1] >= sublo[1] && coord[1] < subhi[1] &&
coord[2] >= sublo[2] && coord[2] < subhi[2]) { coord[2] >= sublo[2] && coord[2] < subhi[2]) {
avec->data_atom(xdata,imagedata,values); avec->data_atom(xdata,imagedata,values,typestr);
typestr = utils::utf8_subst(typestr);
if (id_offset) tag[nlocal-1] += id_offset; if (id_offset) tag[nlocal-1] += id_offset;
if (mol_offset) molecule[nlocal-1] += mol_offset; if (mol_offset) molecule[nlocal-1] += mol_offset;
if (type_offset) {
type[nlocal-1] += type_offset; switch (utils::is_type(typestr)) {
if (type[nlocal-1] > ntypes) case 0: { // numeric
error->one(FLERR,"Invalid atom type in Atoms section of data file"); int itype = utils::inumeric(FLERR, typestr, true, lmp) + type_offset;
if ((itype < 1) || (itype > ntypes))
error->one(FLERR, "Invalid atom type {} in {}: {}", itype, location,
utils::trim(buf));
type[nlocal - 1] = itype;
if (labelflag) type[nlocal - 1] = ilabel[itype - 1];
break;
} }
case 1: { // type label
if (!atom->labelmapflag)
error->one(FLERR, "Invalid line in {}: {}", location, utils::trim(buf));
type[nlocal - 1] = lmap->find(typestr, Atom::ATOM);
if (type[nlocal - 1] == -1)
error->one(FLERR, "Invalid line in {}: {}", location, utils::trim(buf));
break;
}
default: // invalid
error->one(FLERR, "Invalid line in {}: {}", location, utils::trim(buf));
break;
}
if (type[nlocal-1] <= 0 || type[nlocal-1] > ntypes)
error->one(FLERR,"Invalid atom type {} in {}", location, typestr);
} }
} }
buf = next + 1; buf = next + 1;
@ -1217,41 +1262,64 @@ void Atom::data_vels(int n, char *buf, tagint id_offset)
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset, void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset,
int type_offset) int type_offset, int labelflag, int *ilabel)
{ {
int m,itype; int m,itype;
tagint atom1,atom2; tagint atom1,atom2;
char *next; char *next;
std::string typestr;
int newton_bond = force->newton_bond; int newton_bond = force->newton_bond;
auto location = "Bonds section of data file"; auto location = "Bonds section of data file";
for (int i = 0; i < n; i++) { for (int i = 0; i < n; i++) {
next = strchr(buf,'\n'); next = strchr(buf,'\n');
if (!next) error->all(FLERR, "Missing data in Bonds section of data file"); if (!next) error->all(FLERR, "Missing data in {}", location);
*next = '\0'; *next = '\0';
ValueTokenizer values(utils::trim_comment(buf)); auto values = Tokenizer(buf).as_vector();
// skip over empty of comment lines int nwords = values.size();
if (values.has_next()) { for (std::size_t i = 0; i < values.size(); ++i) {
try { if (utils::strmatch(values[i], "^#")) {
values.next_int(); nwords = i;
itype = values.next_int(); break;
atom1 = values.next_tagint();
atom2 = values.next_tagint();
if (values.has_next()) throw TokenizerException("Too many tokens","");
} catch (TokenizerException &e) {
error->one(FLERR,"{} in {}: {}", e.what(), location, utils::trim(buf));
} }
}
// skip over empty or comment lines
// Bonds line is: number(ignored), bond type, atomID 1, atomID 2
if (nwords > 0) {
if (nwords != 4) error->all(FLERR, "Incorrect format in {}: {}", location, utils::trim(buf));
typestr = utils::utf8_subst(values[1]);
atom1 = utils::tnumeric(FLERR, values[2], false, lmp);
atom2 = utils::tnumeric(FLERR, values[3], false, lmp);
if (id_offset) { if (id_offset) {
atom1 += id_offset; atom1 += id_offset;
atom2 += id_offset; atom2 += id_offset;
} }
itype += type_offset;
switch (utils::is_type(typestr)) {
case 0: { // numeric
itype = utils::inumeric(FLERR, typestr, false, lmp) + type_offset;
if ((itype < 1) || (itype > nbondtypes))
error->all(FLERR, "Invalid bond type {} in {}: {}", itype, location, utils::trim(buf));
if (labelflag) itype = ilabel[itype - 1];
break;
}
case 1: { // type label
if (!atom->labelmapflag) error->all(FLERR, "Invalid {}: {}", location, utils::trim(buf));
itype = lmap->find(typestr, Atom::BOND);
if (itype == -1) error->all(FLERR, "Invalid {}: {}", location, utils::trim(buf));
break;
}
default: // invalid
error->one(FLERR, "Invalid {}: {}", location, utils::trim(buf));
break;
}
if ((atom1 <= 0) || (atom1 > map_tag_max) || if ((atom1 <= 0) || (atom1 > map_tag_max) ||
(atom2 <= 0) || (atom2 > map_tag_max) || (atom1 == atom2)) (atom2 <= 0) || (atom2 > map_tag_max) || (atom1 == atom2))
error->one(FLERR,"Invalid atom ID in {}: {}", location, utils::trim(buf)); error->all(FLERR,"Invalid atom ID in {}: {}", location, utils::trim(buf));
if (itype <= 0 || itype > nbondtypes) if ((itype <= 0) || (itype > nbondtypes))
error->one(FLERR,"Invalid bond type in {}: {}", location, utils::trim(buf)); error->all(FLERR,"Invalid bond type {} in {}: {}", itype, location, utils::trim(buf));
if ((m = map(atom1)) >= 0) { if ((m = map(atom1)) >= 0) {
if (count) count[m]++; if (count) count[m]++;
else { else {
@ -1285,37 +1353,60 @@ void Atom::data_bonds(int n, char *buf, int *count, tagint id_offset,
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
void Atom::data_angles(int n, char *buf, int *count, tagint id_offset, void Atom::data_angles(int n, char *buf, int *count, tagint id_offset,
int type_offset) int type_offset, int labelflag, int *ilabel)
{ {
int m,itype; int m,itype;
tagint atom1,atom2,atom3; tagint atom1,atom2,atom3;
char *next; char *next;
std::string typestr;
int newton_bond = force->newton_bond; int newton_bond = force->newton_bond;
auto location = "Angles section of data file"; auto location = "Angles section of data file";
for (int i = 0; i < n; i++) { for (int i = 0; i < n; i++) {
next = strchr(buf,'\n'); next = strchr(buf,'\n');
if (!next) error->all(FLERR, "Missing data in Angles section of data file"); if (!next) error->all(FLERR, "Missing data in {}", location);
*next = '\0'; *next = '\0';
ValueTokenizer values(utils::trim_comment(buf)); auto values = Tokenizer(buf).as_vector();
// skip over empty or comment lines int nwords = values.size();
if (values.has_next()) { for (std::size_t i = 0; i < values.size(); ++i) {
try { if (utils::strmatch(values[i], "^#")) {
values.next_int(); nwords = i;
itype = values.next_int(); break;
atom1 = values.next_tagint();
atom2 = values.next_tagint();
atom3 = values.next_tagint();
if (values.has_next()) throw TokenizerException("Too many tokens","");
} catch (TokenizerException &e) {
error->one(FLERR,"{} in {}: {}", e.what(), location, utils::trim(buf));
} }
}
// skip over empty or comment lines
// Angles line is: number(ignored), angle type, atomID 1, atomID 2, atomID 3
if (nwords > 0) {
if (nwords != 5) error->all(FLERR, "Incorrect format in {}: {}", location, utils::trim(buf));
typestr = utils::utf8_subst(values[1]);
atom1 = utils::tnumeric(FLERR, values[2], false, lmp);
atom2 = utils::tnumeric(FLERR, values[3], false, lmp);
atom3 = utils::tnumeric(FLERR, values[4], false, lmp);
if (id_offset) { if (id_offset) {
atom1 += id_offset; atom1 += id_offset;
atom2 += id_offset; atom2 += id_offset;
atom3 += id_offset; atom3 += id_offset;
} }
itype += type_offset;
switch (utils::is_type(typestr)) {
case 0: { // numeric
itype = utils::inumeric(FLERR, typestr, false, lmp) + type_offset;
if ((itype < 1) || (itype > nangletypes))
error->all(FLERR, "Invalid angle type {} in {}: {}", itype, location, utils::trim(buf));
if (labelflag) itype = ilabel[itype - 1];
break;
}
case 1: { // type label
if (!atom->labelmapflag) error->all(FLERR, "Invalid {}: {}", location, utils::trim(buf));
itype = lmap->find(typestr, Atom::ANGLE);
if (itype == -1) error->all(FLERR, "Invalid {}: {}", location, utils::trim(buf));
break;
}
default: // invalid
error->one(FLERR, "Invalid {}: {}", location, utils::trim(buf));
break;
}
if ((atom1 <= 0) || (atom1 > map_tag_max) || if ((atom1 <= 0) || (atom1 > map_tag_max) ||
(atom2 <= 0) || (atom2 > map_tag_max) || (atom2 <= 0) || (atom2 > map_tag_max) ||
@ -1323,7 +1414,7 @@ void Atom::data_angles(int n, char *buf, int *count, tagint id_offset,
(atom1 == atom2) || (atom1 == atom3) || (atom2 == atom3)) (atom1 == atom2) || (atom1 == atom3) || (atom2 == atom3))
error->one(FLERR,"Invalid atom ID in {}: {}", location, utils::trim(buf)); error->one(FLERR,"Invalid atom ID in {}: {}", location, utils::trim(buf));
if (itype <= 0 || itype > nangletypes) if (itype <= 0 || itype > nangletypes)
error->one(FLERR,"Invalid angle type in {}: {}", location, utils::trim(buf)); error->one(FLERR,"Invalid angle type {} in {}: {}", itype, location, utils::trim(buf));
if ((m = map(atom2)) >= 0) { if ((m = map(atom2)) >= 0) {
if (count) count[m]++; if (count) count[m]++;
else { else {
@ -1369,39 +1460,63 @@ void Atom::data_angles(int n, char *buf, int *count, tagint id_offset,
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset, void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset,
int type_offset) int type_offset, int labelflag, int *ilabel)
{ {
int m,itype; int m,itype;
tagint atom1,atom2,atom3,atom4; tagint atom1,atom2,atom3,atom4;
char *next; char *next;
std::string typestr;
int newton_bond = force->newton_bond; int newton_bond = force->newton_bond;
auto location = "Dihedrals section of data file"; auto location = "Dihedrals section of data file";
for (int i = 0; i < n; i++) { for (int i = 0; i < n; i++) {
next = strchr(buf,'\n'); next = strchr(buf,'\n');
if (!next) error->all(FLERR, "Missing data in Dihedrals section of data file"); if (!next) error->all(FLERR, "Missing data in {}", location);
*next = '\0'; *next = '\0';
ValueTokenizer values(utils::trim_comment(buf)); auto values = Tokenizer(buf).as_vector();
// skip over empty or comment lines int nwords = values.size();
if (values.has_next()) { for (std::size_t i = 0; i < values.size(); ++i) {
try { if (utils::strmatch(values[i], "^#")) {
values.next_int(); nwords = i;
itype = values.next_int(); break;
atom1 = values.next_tagint();
atom2 = values.next_tagint();
atom3 = values.next_tagint();
atom4 = values.next_tagint();
if (values.has_next()) throw TokenizerException("Too many tokens","");
} catch (TokenizerException &e) {
error->one(FLERR,"{} in {}: {}", e.what(), location, utils::trim(buf));
} }
}
// skip over empty or comment lines
// Dihedrals line is: number(ignored), bond type, atomID 1, atomID 2, atomID 3, atomID 4
if (nwords > 0) {
if (nwords != 6) error->all(FLERR, "Incorrect format in {}: {}", location, utils::trim(buf));
typestr = utils::utf8_subst(values[1]);
atom1 = utils::tnumeric(FLERR, values[2], false, lmp);
atom2 = utils::tnumeric(FLERR, values[3], false, lmp);
atom3 = utils::tnumeric(FLERR, values[4], false, lmp);
atom4 = utils::tnumeric(FLERR, values[5], false, lmp);
if (id_offset) { if (id_offset) {
atom1 += id_offset; atom1 += id_offset;
atom2 += id_offset; atom2 += id_offset;
atom3 += id_offset; atom3 += id_offset;
atom4 += id_offset; atom4 += id_offset;
} }
itype += type_offset;
switch (utils::is_type(typestr)) {
case 0: { // numeric
itype = utils::inumeric(FLERR, typestr, false, lmp) + type_offset;
if ((itype < 1) || (itype > ndihedraltypes))
error->all(FLERR, "Invalid dihedral type {} in {}: {}", itype, location,
utils::trim(buf));
if (labelflag) itype = ilabel[itype - 1];
break;
}
case 1: { // type label
if (!atom->labelmapflag) error->all(FLERR, "Invalid {}: {}", location, utils::trim(buf));
itype = lmap->find(typestr, Atom::DIHEDRAL);
if (itype == -1) error->all(FLERR, "Invalid {}: {}", location, utils::trim(buf));
break;
}
default: // invalid
error->one(FLERR, "Invalid {}: {}", location, utils::trim(buf));
break;
}
if ((atom1 <= 0) || (atom1 > map_tag_max) || if ((atom1 <= 0) || (atom1 > map_tag_max) ||
(atom2 <= 0) || (atom2 > map_tag_max) || (atom2 <= 0) || (atom2 > map_tag_max) ||
@ -1411,7 +1526,7 @@ void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset,
(atom2 == atom3) || (atom2 == atom4) || (atom3 == atom4)) (atom2 == atom3) || (atom2 == atom4) || (atom3 == atom4))
error->one(FLERR, "Invalid atom ID in {}: {}", location, utils::trim(buf)); error->one(FLERR, "Invalid atom ID in {}: {}", location, utils::trim(buf));
if (itype <= 0 || itype > ndihedraltypes) if (itype <= 0 || itype > ndihedraltypes)
error->one(FLERR, "Invalid dihedral type in {}: {}", location, utils::trim(buf)); error->one(FLERR, "Invalid dihedral type {} in {}: {}", itype, location, utils::trim(buf));
if ((m = map(atom2)) >= 0) { if ((m = map(atom2)) >= 0) {
if (count) count[m]++; if (count) count[m]++;
else { else {
@ -1471,39 +1586,63 @@ void Atom::data_dihedrals(int n, char *buf, int *count, tagint id_offset,
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset, void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset,
int type_offset) int type_offset, int labelflag, int *ilabel)
{ {
int m,itype; int m,itype;
tagint atom1,atom2,atom3,atom4; tagint atom1,atom2,atom3,atom4;
char *next; char *next;
std::string typestr;
int newton_bond = force->newton_bond; int newton_bond = force->newton_bond;
auto location = "Impropers section of data file"; auto location = "Impropers section of data file";
for (int i = 0; i < n; i++) { for (int i = 0; i < n; i++) {
next = strchr(buf,'\n'); next = strchr(buf,'\n');
if (!next) error->all(FLERR, "Missing data in Impropers section of data file"); if (!next) error->all(FLERR, "Missing data in {}", location);
*next = '\0'; *next = '\0';
ValueTokenizer values(utils::trim_comment(buf)); auto values = Tokenizer(buf).as_vector();
// skip over empty or comment lines int nwords = values.size();
if (values.has_next()) { for (std::size_t i = 0; i < values.size(); ++i) {
try { if (utils::strmatch(values[i], "^#")) {
values.next_int(); nwords = i;
itype = values.next_int(); break;
atom1 = values.next_tagint();
atom2 = values.next_tagint();
atom3 = values.next_tagint();
atom4 = values.next_tagint();
if (values.has_next()) throw TokenizerException("Too many tokens","");
} catch (TokenizerException &e) {
error->one(FLERR,"{} in {}: {}", e.what(), location, utils::trim(buf));
} }
}
// skip over empty or comment lines
// Impropers line is: number(ignored), bond type, atomID 1, atomID 2, atomID 3, atomID 4
if (nwords > 0) {
if (nwords != 6) error->all(FLERR, "Incorrect format in {}: {}", location, utils::trim(buf));
typestr = utils::utf8_subst(values[1]);
atom1 = utils::tnumeric(FLERR, values[2], false, lmp);
atom2 = utils::tnumeric(FLERR, values[3], false, lmp);
atom3 = utils::tnumeric(FLERR, values[4], false, lmp);
atom4 = utils::tnumeric(FLERR, values[5], false, lmp);
if (id_offset) { if (id_offset) {
atom1 += id_offset; atom1 += id_offset;
atom2 += id_offset; atom2 += id_offset;
atom3 += id_offset; atom3 += id_offset;
atom4 += id_offset; atom4 += id_offset;
} }
itype += type_offset;
switch (utils::is_type(typestr)) {
case 0: { // numeric
itype = utils::inumeric(FLERR, typestr, false, lmp) + type_offset;
if ((itype < 1) || (itype > nimpropertypes))
error->all(FLERR, "Invalid improper type {} in {}: {}", itype, location,
utils::trim(buf));
if (labelflag) itype = ilabel[itype - 1];
break;
}
case 1: { // type label
if (!atom->labelmapflag) error->all(FLERR, "Invalid {}: {}", location, utils::trim(buf));
itype = lmap->find(typestr, Atom::IMPROPER);
if (itype == -1) error->all(FLERR, "Invalid {}: {}", location, utils::trim(buf));
break;
}
default: // invalid
error->one(FLERR, "Invalid {}: {}", location, utils::trim(buf));
break;
}
if ((atom1 <= 0) || (atom1 > map_tag_max) || if ((atom1 <= 0) || (atom1 > map_tag_max) ||
(atom2 <= 0) || (atom2 > map_tag_max) || (atom2 <= 0) || (atom2 > map_tag_max) ||
@ -1513,7 +1652,7 @@ void Atom::data_impropers(int n, char *buf, int *count, tagint id_offset,
(atom2 == atom3) || (atom2 == atom4) || (atom3 == atom4)) (atom2 == atom3) || (atom2 == atom4) || (atom3 == atom4))
error->one(FLERR, "Invalid atom ID in {}: {}", location, utils::trim(buf)); error->one(FLERR, "Invalid atom ID in {}: {}", location, utils::trim(buf));
if (itype <= 0 || itype > nimpropertypes) if (itype <= 0 || itype > nimpropertypes)
error->one(FLERR, "Invalid improper type in {}: {}", location, utils::trim(buf)); error->one(FLERR, "Invalid improper type {} in {}: {}", itype, location, utils::trim(buf));
if ((m = map(atom2)) >= 0) { if ((m = map(atom2)) >= 0) {
if (count) count[m]++; if (count) count[m]++;
else { else {
@ -1717,30 +1856,63 @@ void Atom::allocate_type_arrays()
called from reading of data file called from reading of data file
type_offset may be used when reading multiple data files type_offset may be used when reading multiple data files
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
// clang-format on
void Atom::set_mass(const char *file, int line, const char *str, int type_offset) void Atom::set_mass(const char *file, int line, const char *str, int type_offset, int labelflag,
int *ilabel)
{ {
if (mass == nullptr) error->all(file, line, "Cannot set mass for atom style {}", atom_style); if (mass == nullptr) error->all(file, line, "Cannot set mass for atom style {}", atom_style);
int itype; int itype;
double mass_one; double mass_one;
ValueTokenizer values(utils::trim_comment(str)); auto location = "Masses section of data file";
if (values.has_next()) { auto values = Tokenizer(str).as_vector();
try { int nwords = values.size();
itype = values.next_int() + type_offset; for (std::size_t i = 0; i < values.size(); ++i) {
mass_one = values.next_double(); if (utils::strmatch(values[i], "^#")) {
if (values.has_next()) throw TokenizerException("Too many tokens", ""); nwords = i;
break;
}
}
if (nwords != 2) error->all(file, line, "Invalid format in {}: {}", location, str);
auto typestr = utils::utf8_subst(values[0]);
if (itype < 1 || itype > ntypes) throw TokenizerException("Invalid atom type", ""); switch (utils::is_type(typestr)) {
if (mass_one <= 0.0) throw TokenizerException("Invalid mass value", "");
} catch (TokenizerException &e) { case 0: { // numeric
error->all(file,line,"{} in Masses section of data file: {}", e.what(), utils::trim(str)); itype = utils::inumeric(file, line, typestr, false, lmp);
if ((itype < 1) || (itype > ntypes))
error->all(file, line, "Invalid atom type {} in {}: {}", itype, location, utils::trim(str));
if (labelflag) itype = ilabel[itype - 1];
break;
} }
case 1: { // type label
if (!atom->labelmapflag)
error->all(file, line, "Invalid atom type in {}: {}", location, utils::trim(str));
itype = lmap->find(typestr, Atom::ATOM);
if (itype == -1)
error->all(file, line, "Unknown atom type {} in {}: {}", typestr, location,
utils::trim(str));
break;
}
default: // invalid
error->one(file, line, "Invalid {}: {}", location, utils::trim(str));
break;
}
itype += type_offset;
mass_one = utils::numeric(file, line, values[1], false, lmp);
if (itype < 1 || itype > ntypes)
error->all(file, line, "Invalid atom type {} in {}: {}", itype, location, utils::trim(str));
if (mass_one <= 0.0)
error->all(file, line, "Invalid mass value {} in {}: {}", mass_one, location, utils::trim(str));
mass[itype] = mass_one; mass[itype] = mass_one;
mass_setflag[itype] = 1; mass_setflag[itype] = 1;
} }
} // clang-format off
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
set a mass and flag it as set set a mass and flag it as set
@ -1765,15 +1937,20 @@ void Atom::set_mass(const char *file, int line, int itype, double value)
void Atom::set_mass(const char *file, int line, int /*narg*/, char **arg) void Atom::set_mass(const char *file, int line, int /*narg*/, char **arg)
{ {
if (mass == nullptr) error->all(file,line, "Cannot set atom mass for atom style {}", atom_style); if (mass == nullptr)
error->all(file,line, "Cannot set per-type atom mass for atom style {}", atom_style);
char *typestr = utils::expand_type(file, line, arg[0], Atom::ATOM, lmp);
if (typestr) arg[0] = typestr;
int lo, hi; int lo, hi;
utils::bounds(file, line, arg[0], 1, ntypes, lo, hi, error); utils::bounds(file, line, arg[0], 1, ntypes, lo, hi, error);
if ((lo < 1) || (hi > ntypes)) if ((lo < 1) || (hi > ntypes))
error->all(file,line,"Invalid type {} for atom mass {}", arg[1]); error->all(file, line, "Invalid atom type {} for atom mass", arg[0]);
const double value = utils::numeric(FLERR, arg[1], false, lmp); const double value = utils::numeric(FLERR, arg[1], false, lmp);
if (value <= 0.0) error->all(file,line,"Invalid atom mass value {}", value); if (value <= 0.0)
error->all(file, line, "Invalid atom mass value {} for type {}", value, arg[0]);
for (int itype = lo; itype <= hi; itype++) { for (int itype = lo; itype <= hi; itype++) {
mass[itype] = value; mass[itype] = value;
@ -2011,6 +2188,16 @@ void Atom::add_molecule_atom(Molecule *onemol, int iatom, int ilocal, tagint off
} }
} }
/* ----------------------------------------------------------------------
allocate space for type label map
------------------------------------------------------------------------- */
void Atom::add_label_map()
{
labelmapflag = 1;
lmap = new LabelMap(lmp,ntypes,nbondtypes,nangletypes,ndihedraltypes,nimpropertypes);
}
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
reorder owned atoms so those in firstgroup appear first reorder owned atoms so those in firstgroup appear first
called by comm->exchange() if atom_modify first group is set called by comm->exchange() if atom_modify first group is set

22
src/atom.h
View File

@ -32,6 +32,8 @@ class Atom : protected Pointers {
enum { DOUBLE, INT, BIGINT }; enum { DOUBLE, INT, BIGINT };
enum { GROW = 0, RESTART = 1, BORDER = 2 }; enum { GROW = 0, RESTART = 1, BORDER = 2 };
enum { ATOMIC = 0, MOLECULAR = 1, TEMPLATE = 2 }; enum { ATOMIC = 0, MOLECULAR = 1, TEMPLATE = 2 };
enum { ATOM = 0, BOND = 1, ANGLE = 2, DIHEDRAL = 3, IMPROPER = 4 };
enum { NUMERIC = 0, LABELS = 1};
enum { MAP_NONE = 0, MAP_ARRAY = 1, MAP_HASH = 2, MAP_YES = 3 }; enum { MAP_NONE = 0, MAP_ARRAY = 1, MAP_HASH = 2, MAP_YES = 3 };
// atom counts // atom counts
@ -181,6 +183,7 @@ class Atom : protected Pointers {
// most are existence flags for per-atom vectors and arrays // most are existence flags for per-atom vectors and arrays
// 1 if variable is used, 0 if not // 1 if variable is used, 0 if not
int labelmapflag, types_style;
int sphere_flag, ellipsoid_flag, line_flag, tri_flag, body_flag; int sphere_flag, ellipsoid_flag, line_flag, tri_flag, body_flag;
int peri_flag, electron_flag; int peri_flag, electron_flag;
int wavepacket_flag, sph_flag; int wavepacket_flag, sph_flag;
@ -251,6 +254,10 @@ class Atom : protected Pointers {
int nmolecule; int nmolecule;
class Molecule **molecules; class Molecule **molecules;
// type label maps
class LabelMap *lmap;
// extra peratom info in restart file destined for fix & diag // extra peratom info in restart file destined for fix & diag
double **extra; double **extra;
@ -324,18 +331,19 @@ class Atom : protected Pointers {
void deallocate_topology(); void deallocate_topology();
void data_atoms(int, char *, tagint, tagint, int, int, double *); void data_atoms(int, char *, tagint, tagint, int, int, double *,
int, int *);
void data_vels(int, char *, tagint); void data_vels(int, char *, tagint);
void data_bonds(int, char *, int *, tagint, int); void data_bonds(int, char *, int *, tagint, int, int, int *);
void data_angles(int, char *, int *, tagint, int); void data_angles(int, char *, int *, tagint, int, int, int *);
void data_dihedrals(int, char *, int *, tagint, int); void data_dihedrals(int, char *, int *, tagint, int, int, int *);
void data_impropers(int, char *, int *, tagint, int); void data_impropers(int, char *, int *, tagint, int, int, int *);
void data_bonus(int, char *, AtomVec *, tagint); void data_bonus(int, char *, AtomVec *, tagint);
void data_bodies(int, char *, AtomVec *, tagint); void data_bodies(int, char *, AtomVec *, tagint);
void data_fix_compute_variable(int, int); void data_fix_compute_variable(int, int);
virtual void allocate_type_arrays(); virtual void allocate_type_arrays();
void set_mass(const char *, int, const char *, int); void set_mass(const char *, int, const char *, int, int, int *);
void set_mass(const char *, int, int, double); void set_mass(const char *, int, int, double);
void set_mass(const char *, int, int, char **); void set_mass(const char *, int, int, char **);
void set_mass(double *); void set_mass(double *);
@ -349,6 +357,8 @@ class Atom : protected Pointers {
std::vector<Molecule *>get_molecule_by_id(const std::string &); std::vector<Molecule *>get_molecule_by_id(const std::string &);
void add_molecule_atom(class Molecule *, int, int, tagint); void add_molecule_atom(class Molecule *, int, int, tagint);
void add_label_map();
void first_reorder(); void first_reorder();
virtual void sort(); virtual void sort();

59
src/atom_vec.cpp
View File

@ -19,6 +19,7 @@
#include "error.h" #include "error.h"
#include "fix.h" #include "fix.h"
#include "force.h" #include "force.h"
#include "label_map.h"
#include "math_const.h" #include "math_const.h"
#include "memory.h" #include "memory.h"
#include "modify.h" #include "modify.h"
@ -1649,12 +1650,24 @@ void AtomVec::create_atom(int itype, double *coord)
atom->nlocal++; atom->nlocal++;
} }
/* ----------------------------------------------------------------------
version of data_atom without extract option
temporary fix for Kokkos compilation
------------------------------------------------------------------------- */
void AtomVec::data_atom(double *coord, imageint imagetmp, const std::vector<std::string> &values)
{
std::string strtmp;
data_atom(coord, imagetmp, values, strtmp);
}
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
unpack one line from Atoms section of data file unpack one line from Atoms section of data file
initialize other peratom quantities initialize other peratom quantities
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */
void AtomVec::data_atom(double *coord, imageint imagetmp, const std::vector<std::string> &values) void AtomVec::data_atom(double *coord, imageint imagetmp, const std::vector<std::string> &values,
std::string &extract)
{ {
int m, n, datatype, cols; int m, n, datatype, cols;
void *pdata; void *pdata;
@ -1692,6 +1705,10 @@ void AtomVec::data_atom(double *coord, imageint imagetmp, const std::vector<std:
} else if (datatype == Atom::INT) { } else if (datatype == Atom::INT) {
if (cols == 0) { if (cols == 0) {
int *vec = *((int **) pdata); int *vec = *((int **) pdata);
if (vec == atom->type) { // custom treatment of atom types
extract = values[ivalue++];
continue;
}
vec[nlocal] = utils::inumeric(FLERR, values[ivalue++], true, lmp); vec[nlocal] = utils::inumeric(FLERR, values[ivalue++], true, lmp);
} else { } else {
int **array = *((int ***) pdata); int **array = *((int ***) pdata);
@ -1712,9 +1729,9 @@ void AtomVec::data_atom(double *coord, imageint imagetmp, const std::vector<std:
// error checks applicable to all styles // error checks applicable to all styles
if (tag[nlocal] <= 0) error->one(FLERR, "Invalid atom ID in Atoms section of data file"); if (tag[nlocal] <= 0)
if (type[nlocal] <= 0 || type[nlocal] > atom->ntypes) error->one(FLERR, "Invalid atom ID {} in line {} of Atoms section of data file",
error->one(FLERR, "Invalid atom type in Atoms section of data file"); tag[nlocal], nlocal+1);
// if needed, modify unpacked values or initialize other peratom values // if needed, modify unpacked values or initialize other peratom values
@ -1806,7 +1823,10 @@ void AtomVec::write_data(FILE *fp, int n, double **buf)
} }
} else if (datatype == Atom::INT) { } else if (datatype == Atom::INT) {
if (cols == 0) { if (cols == 0) {
fmt::print(fp, " {}", ubuf(buf[i][j++]).i); if (atom->types_style == Atom::LABELS &&
atom->peratom[mdata_atom.index[nn]].name == "type") {
fmt::print(fp," {}",atom->lmap->typelabel[ubuf(buf[i][j++]).i-1]);
} else fmt::print(fp, " {}", ubuf(buf[i][j++]).i);
} else { } else {
for (m = 0; m < cols; m++) fmt::print(fp, " {}", ubuf(buf[i][j++]).i); for (m = 0; m < cols; m++) fmt::print(fp, " {}", ubuf(buf[i][j++]).i);
} }
@ -2013,8 +2033,12 @@ int AtomVec::pack_bond(tagint **buf)
void AtomVec::write_bond(FILE *fp, int n, tagint **buf, int index) void AtomVec::write_bond(FILE *fp, int n, tagint **buf, int index)
{ {
std::string typestr;
for (int i = 0; i < n; i++) { for (int i = 0; i < n; i++) {
fmt::print(fp, "{} {} {} {}\n", index, buf[i][0], buf[i][1], buf[i][2]); typestr = std::to_string(buf[i][0]);
if (atom->types_style == Atom::LABELS)
typestr = atom->lmap->btypelabel[buf[i][0]-1];
fmt::print(fp, "{} {} {} {}\n", index, typestr, buf[i][1], buf[i][2]);
index++; index++;
} }
} }
@ -2075,8 +2099,13 @@ int AtomVec::pack_angle(tagint **buf)
void AtomVec::write_angle(FILE *fp, int n, tagint **buf, int index) void AtomVec::write_angle(FILE *fp, int n, tagint **buf, int index)
{ {
std::string typestr;
for (int i = 0; i < n; i++) { for (int i = 0; i < n; i++) {
fmt::print(fp, "{} {} {} {} {}\n", index, buf[i][0], buf[i][1], buf[i][2], buf[i][3]); typestr = std::to_string(buf[i][0]);
if (atom->types_style == Atom::LABELS)
typestr = atom->lmap->atypelabel[buf[i][0]-1];
fmt::print(fp, "{} {} {} {} {}\n", index,
typestr, buf[i][1], buf[i][2], buf[i][3]);
index++; index++;
} }
} }
@ -2135,9 +2164,13 @@ int AtomVec::pack_dihedral(tagint **buf)
void AtomVec::write_dihedral(FILE *fp, int n, tagint **buf, int index) void AtomVec::write_dihedral(FILE *fp, int n, tagint **buf, int index)
{ {
std::string typestr;
for (int i = 0; i < n; i++) { for (int i = 0; i < n; i++) {
fmt::print(fp, "{} {} {} {} {} {}\n", index, buf[i][0], buf[i][1], buf[i][2], buf[i][3], typestr = std::to_string(buf[i][0]);
buf[i][4]); if (atom->types_style == Atom::LABELS)
typestr = atom->lmap->dtypelabel[buf[i][0]-1];
fmt::print(fp, "{} {} {} {} {} {}\n", index, typestr,
buf[i][1], buf[i][2], buf[i][3], buf[i][4]);
index++; index++;
} }
} }
@ -2196,9 +2229,13 @@ int AtomVec::pack_improper(tagint **buf)
void AtomVec::write_improper(FILE *fp, int n, tagint **buf, int index) void AtomVec::write_improper(FILE *fp, int n, tagint **buf, int index)
{ {
std::string typestr;
for (int i = 0; i < n; i++) { for (int i = 0; i < n; i++) {
fmt::print(fp, "{} {} {} {} {} {}\n", index, buf[i][0], buf[i][1], buf[i][2], buf[i][3], typestr = std::to_string(buf[i][0]);
buf[i][4]); if (atom->types_style == Atom::LABELS)
typestr = atom->lmap->itypelabel[buf[i][0]-1];
fmt::print(fp, "{} {} {} {} {} {}\n", index, typestr,
buf[i][1], buf[i][2], buf[i][3], buf[i][4]);
index++; index++;
} }
} }

1
src/atom_vec.h
View File

@ -124,6 +124,7 @@ class AtomVec : protected Pointers {
virtual void create_atom_post(int) {} virtual void create_atom_post(int) {}
virtual void data_atom(double *, imageint, const std::vector<std::string> &); virtual void data_atom(double *, imageint, const std::vector<std::string> &);
virtual void data_atom(double *, imageint, const std::vector<std::string> &, std::string &);
virtual void data_atom_post(int) {} virtual void data_atom_post(int) {}
virtual void data_atom_bonus(int, const std::vector<std::string> &) {} virtual void data_atom_bonus(int, const std::vector<std::string> &) {}
virtual void data_body(int, int, int, int *, double *) {} virtual void data_body(int, int, int, int *, double *) {}

20
src/create_box.cpp
View File

@ -108,46 +108,50 @@ void CreateBox::command(int narg, char **arg)
while (iarg < narg) { while (iarg < narg) {
if (strcmp(arg[iarg], "bond/types") == 0) { if (strcmp(arg[iarg], "bond/types") == 0) {
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "create_box bond/type", error); if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "create_box bond/type", error);
if (!atom->avec->bonds_allow) error->all(FLERR, "No bonds allowed with this atom style"); if (!atom->avec->bonds_allow)
error->all(FLERR, "No bonds allowed with atom style {}", atom->get_style());
atom->nbondtypes = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); atom->nbondtypes = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg], "angle/types") == 0) { } else if (strcmp(arg[iarg], "angle/types") == 0) {
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "create_box angle/types", error); if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "create_box angle/types", error);
if (!atom->avec->angles_allow) error->all(FLERR, "No angles allowed with this atom style"); if (!atom->avec->angles_allow)
error->all(FLERR, "No angles allowed with atom style {}", atom->get_style());
atom->nangletypes = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); atom->nangletypes = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg], "dihedral/types") == 0) { } else if (strcmp(arg[iarg], "dihedral/types") == 0) {
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "create_box dihedral/types", error); if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "create_box dihedral/types", error);
if (!atom->avec->dihedrals_allow) if (!atom->avec->dihedrals_allow)
error->all(FLERR, "No dihedrals allowed with this atom style"); error->all(FLERR, "No dihedrals allowed with atom style {}", atom->get_style());
atom->ndihedraltypes = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); atom->ndihedraltypes = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg], "improper/types") == 0) { } else if (strcmp(arg[iarg], "improper/types") == 0) {
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "create_box improper/types", error); if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "create_box improper/types", error);
if (!atom->avec->impropers_allow) if (!atom->avec->impropers_allow)
error->all(FLERR, "No impropers allowed with this atom style"); error->all(FLERR, "No impropers allowed with atom style {}", atom->get_style());
atom->nimpropertypes = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); atom->nimpropertypes = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg], "extra/bond/per/atom") == 0) { } else if (strcmp(arg[iarg], "extra/bond/per/atom") == 0) {
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "create_box extra/bond/per/atom", error); if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "create_box extra/bond/per/atom", error);
if (!atom->avec->bonds_allow) error->all(FLERR, "No bonds allowed with this atom style"); if (!atom->avec->bonds_allow)
error->all(FLERR, "No bonds allowed with atom style {}", atom->get_style());
atom->bond_per_atom = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); atom->bond_per_atom = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg], "extra/angle/per/atom") == 0) { } else if (strcmp(arg[iarg], "extra/angle/per/atom") == 0) {
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "create_box extra/angle/per/atom", error); if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "create_box extra/angle/per/atom", error);
if (!atom->avec->angles_allow) error->all(FLERR, "No angles allowed with this atom style"); if (!atom->avec->angles_allow)
error->all(FLERR, "No angles allowed with atom style {}", atom->get_style());
atom->angle_per_atom = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); atom->angle_per_atom = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg], "extra/dihedral/per/atom") == 0) { } else if (strcmp(arg[iarg], "extra/dihedral/per/atom") == 0) {
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "create_box extra/dihedral/per/atom", error); if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "create_box extra/dihedral/per/atom", error);
if (!atom->avec->dihedrals_allow) if (!atom->avec->dihedrals_allow)
error->all(FLERR, "No dihedrals allowed with this atom style"); error->all(FLERR, "No dihedrals allowed with atom style {}", atom->get_style());
atom->dihedral_per_atom = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); atom->dihedral_per_atom = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg], "extra/improper/per/atom") == 0) { } else if (strcmp(arg[iarg], "extra/improper/per/atom") == 0) {
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "create_box extra/improper/per/atom", error); if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "create_box extra/improper/per/atom", error);
if (!atom->avec->impropers_allow) if (!atom->avec->impropers_allow)
error->all(FLERR, "No impropers allowed with this atom style"); error->all(FLERR, "No impropers allowed with atom style {}", atom->get_style());
atom->improper_per_atom = utils::inumeric(FLERR, arg[iarg + 1], false, lmp); atom->improper_per_atom = utils::inumeric(FLERR, arg[iarg + 1], false, lmp);
iarg += 2; iarg += 2;
} else if (strcmp(arg[iarg], "extra/special/per/atom") == 0) { } else if (strcmp(arg[iarg], "extra/special/per/atom") == 0) {

54
src/input.cpp
View File

@ -33,6 +33,7 @@
#include "improper.h" #include "improper.h"
#include "integrate.h" #include "integrate.h"
#include "kspace.h" #include "kspace.h"
#include "label_map.h"
#include "memory.h" #include "memory.h"
#include "min.h" #include "min.h"
#include "modify.h" #include "modify.h"
@ -789,6 +790,7 @@ int Input::execute_command()
else if (!strcmp(command,"improper_style")) improper_style(); else if (!strcmp(command,"improper_style")) improper_style();
else if (!strcmp(command,"kspace_modify")) kspace_modify(); else if (!strcmp(command,"kspace_modify")) kspace_modify();
else if (!strcmp(command,"kspace_style")) kspace_style(); else if (!strcmp(command,"kspace_style")) kspace_style();
else if (!strcmp(command,"labelmap")) labelmap();
else if (!strcmp(command,"lattice")) lattice(); else if (!strcmp(command,"lattice")) lattice();
else if (!strcmp(command,"mass")) mass(); else if (!strcmp(command,"mass")) mass();
else if (!strcmp(command,"min_modify")) min_modify(); else if (!strcmp(command,"min_modify")) min_modify();
@ -1326,7 +1328,10 @@ void Input::angle_coeff()
error->all(FLERR,"Angle_coeff command before angle_style is defined"); error->all(FLERR,"Angle_coeff command before angle_style is defined");
if (atom->avec->angles_allow == 0) if (atom->avec->angles_allow == 0)
error->all(FLERR,"Angle_coeff command when no angles allowed"); error->all(FLERR,"Angle_coeff command when no angles allowed");
char *newarg = utils::expand_type(FLERR, arg[0], Atom::ANGLE, lmp);
if (newarg) arg[0] = newarg;
force->angle->coeff(narg,arg); force->angle->coeff(narg,arg);
delete[] newarg;
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
@ -1367,7 +1372,10 @@ void Input::bond_coeff()
error->all(FLERR,"Bond_coeff command before bond_style is defined"); error->all(FLERR,"Bond_coeff command before bond_style is defined");
if (atom->avec->bonds_allow == 0) if (atom->avec->bonds_allow == 0)
error->all(FLERR,"Bond_coeff command when no bonds allowed"); error->all(FLERR,"Bond_coeff command when no bonds allowed");
char *newarg = utils::expand_type(FLERR, arg[0], Atom::BOND, lmp);
if (newarg) arg[0] = newarg;
force->bond->coeff(narg,arg); force->bond->coeff(narg,arg);
delete[] newarg;
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
@ -1470,7 +1478,10 @@ void Input::dihedral_coeff()
error->all(FLERR,"Dihedral_coeff command before dihedral_style is defined"); error->all(FLERR,"Dihedral_coeff command before dihedral_style is defined");
if (atom->avec->dihedrals_allow == 0) if (atom->avec->dihedrals_allow == 0)
error->all(FLERR,"Dihedral_coeff command when no dihedrals allowed"); error->all(FLERR,"Dihedral_coeff command when no dihedrals allowed");
char *newarg = utils::expand_type(FLERR, arg[0], Atom::DIHEDRAL, lmp);
if (newarg) arg[0] = newarg;
force->dihedral->coeff(narg,arg); force->dihedral->coeff(narg,arg);
delete[] newarg;
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
@ -1547,7 +1558,10 @@ void Input::improper_coeff()
error->all(FLERR,"Improper_coeff command before improper_style is defined"); error->all(FLERR,"Improper_coeff command before improper_style is defined");
if (atom->avec->impropers_allow == 0) if (atom->avec->impropers_allow == 0)
error->all(FLERR,"Improper_coeff command when no impropers allowed"); error->all(FLERR,"Improper_coeff command when no impropers allowed");
char *newarg = utils::expand_type(FLERR, arg[0], Atom::IMPROPER, lmp);
if (newarg) arg[0] = newarg;
force->improper->coeff(narg,arg); force->improper->coeff(narg,arg);
delete[] newarg;
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
@ -1577,6 +1591,14 @@ void Input::kspace_style()
force->create_kspace(arg[0],1); force->create_kspace(arg[0],1);
if (force->kspace) force->kspace->settings(narg-1,&arg[1]); if (force->kspace) force->kspace->settings(narg-1,&arg[1]);
} }
/* ---------------------------------------------------------------------- */
void Input::labelmap()
{
if (domain->box_exist == 0) error->all(FLERR,"Labelmap command before simulation box is defined");
if (!atom->labelmapflag) atom->add_label_map();
atom->lmap->modify_lmap(narg,arg);
}
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
@ -1676,14 +1698,12 @@ void Input::package()
} else if (strcmp(arg[0],"kokkos") == 0) { } else if (strcmp(arg[0],"kokkos") == 0) {
if (lmp->kokkos == nullptr || lmp->kokkos->kokkos_exists == 0) if (lmp->kokkos == nullptr || lmp->kokkos->kokkos_exists == 0)
error->all(FLERR, error->all(FLERR, "Package kokkos command without KOKKOS package enabled");
"Package kokkos command without KOKKOS package enabled");
lmp->kokkos->accelerator(narg-1,&arg[1]); lmp->kokkos->accelerator(narg-1,&arg[1]);
} else if (strcmp(arg[0],"omp") == 0) { } else if (strcmp(arg[0],"omp") == 0) {
if (!modify->check_package("OMP")) if (!modify->check_package("OMP"))
error->all(FLERR, error->all(FLERR, "Package omp command without OPENMP package installed");
"Package omp command without OPENMP package installed");
std::string fixcmd = "package_omp all OMP"; std::string fixcmd = "package_omp all OMP";
for (int i = 1; i < narg; i++) fixcmd += std::string(" ") + arg[i]; for (int i = 1; i < narg; i++) fixcmd += std::string(" ") + arg[i];
@ -1691,14 +1711,13 @@ void Input::package()
} else if (strcmp(arg[0],"intel") == 0) { } else if (strcmp(arg[0],"intel") == 0) {
if (!modify->check_package("INTEL")) if (!modify->check_package("INTEL"))
error->all(FLERR, error->all(FLERR, "Package intel command without INTEL package installed");
"Package intel command without INTEL package installed");
std::string fixcmd = "package_intel all INTEL"; std::string fixcmd = "package_intel all INTEL";
for (int i = 1; i < narg; i++) fixcmd += std::string(" ") + arg[i]; for (int i = 1; i < narg; i++) fixcmd += std::string(" ") + arg[i];
modify->add_fix(fixcmd); modify->add_fix(fixcmd);
} else error->all(FLERR,"Illegal package command"); } else error->all(FLERR,"Unknown package keyword: {}", arg[0]);
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */
@ -1712,7 +1731,28 @@ void Input::pair_coeff()
if ((narg < 2) || (force->pair->one_coeff && ((strcmp(arg[0],"*") != 0) if ((narg < 2) || (force->pair->one_coeff && ((strcmp(arg[0],"*") != 0)
|| (strcmp(arg[1],"*") != 0)))) || (strcmp(arg[1],"*") != 0))))
error->all(FLERR,"Incorrect args for pair coefficients"); error->all(FLERR,"Incorrect args for pair coefficients");
char *newarg0 = utils::expand_type(FLERR, arg[0], Atom::ATOM, lmp);
if (newarg0) arg[0] = newarg0;
char *newarg1 = utils::expand_type(FLERR, arg[1], Atom::ATOM, lmp);
if (newarg1) arg[1] = newarg1;
// if arg[1] < arg[0], and neither contain a wildcard, reorder
int itype,jtype;
if (strchr(arg[0],'*') == nullptr && strchr(arg[1],'*') == nullptr) {
itype = utils::numeric(FLERR,arg[0],false,lmp);
jtype = utils::numeric(FLERR,arg[1],false,lmp);
if (jtype < itype) {
char *str = arg[0];
arg[0] = arg[1];
arg[1] = str;
}
}
force->pair->coeff(narg,arg); force->pair->coeff(narg,arg);
delete[] newarg0;
delete[] newarg1;
} }
/* ---------------------------------------------------------------------- */ /* ---------------------------------------------------------------------- */

4
src/input.h
View File

@ -37,8 +37,7 @@ class Input : protected Pointers {
void file(); // process all input void file(); // process all input
void file(const char *); // process an input script void file(const char *); // process an input script
char *one(const std::string &); // process a single command char *one(const std::string &); // process a single command
void substitute(char *&, char *&, int &, int &, int); void substitute(char *&, char *&, int &, int &, int); // substitute for variables in a string
// substitute for variables in a string
void write_echo(const std::string &); // send text to active echo file pointers void write_echo(const std::string &); // send text to active echo file pointers
protected: protected:
@ -113,6 +112,7 @@ class Input : protected Pointers {
void improper_style(); void improper_style();
void kspace_modify(); void kspace_modify();
void kspace_style(); void kspace_style();
void labelmap();
void lattice(); void lattice();
void mass(); void mass();
void min_modify(); void min_modify();

489
src/label_map.cpp Normal file
View File

@ -0,0 +1,489 @@
/* ----------------------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
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.
------------------------------------------------------------------------- */
#include "label_map.h"
#include "atom.h"
#include "comm.h"
#include "error.h"
#include "force.h"
#include "memory.h"
#include <cstring>
using namespace LAMMPS_NS;
/* ---------------------------------------------------------------------- */
LabelMap::LabelMap(LAMMPS *_lmp, int _natomtypes, int _nbondtypes, int _nangletypes,
int _ndihedraltypes, int _nimpropertypes) :
Pointers(_lmp),
natomtypes(_natomtypes), nbondtypes(_nbondtypes), nangletypes(_nangletypes),
ndihedraltypes(_ndihedraltypes), nimpropertypes(_nimpropertypes)
{
lmap2lmap.atom = lmap2lmap.bond = lmap2lmap.angle = lmap2lmap.dihedral = lmap2lmap.improper =
nullptr;
reset_type_labels();
}
/* ---------------------------------------------------------------------- */
LabelMap::~LabelMap()
{
delete[] lmap2lmap.atom;
delete[] lmap2lmap.bond;
delete[] lmap2lmap.angle;
delete[] lmap2lmap.dihedral;
delete[] lmap2lmap.improper;
}
/* ----------------------------------------------------------------------
reset/allocate character-based type arrays (labels) of length ntypes
------------------------------------------------------------------------- */
void LabelMap::reset_type_labels()
{
typelabel_map.clear();
typelabel.resize(natomtypes);
delete[] lmap2lmap.atom;
lmap2lmap.atom = new int[natomtypes];
for (auto &i : typelabel) i.clear();
memset(lmap2lmap.atom, 0, natomtypes * sizeof(int));
btypelabel_map.clear();
btypelabel.resize(nbondtypes);
delete[] lmap2lmap.bond;
for (auto &i : btypelabel) i.clear();
lmap2lmap.bond = new int[nbondtypes];
memset(lmap2lmap.bond, 0, nbondtypes * sizeof(int));
atypelabel_map.clear();
atypelabel.resize(nangletypes);
delete[] lmap2lmap.angle;
for (auto &i : atypelabel) i.clear();
lmap2lmap.angle = new int[nangletypes];
memset(lmap2lmap.angle, 0, nangletypes * sizeof(int));
dtypelabel_map.clear();
dtypelabel.resize(ndihedraltypes);
delete[] lmap2lmap.dihedral;
for (auto &i : dtypelabel) i.clear();
lmap2lmap.dihedral = new int[ndihedraltypes];
memset(lmap2lmap.dihedral, 0, ndihedraltypes * sizeof(int));
itypelabel_map.clear();
itypelabel.resize(nimpropertypes);
delete[] lmap2lmap.improper;
for (auto &i : itypelabel) i.clear();
lmap2lmap.improper = new int[nimpropertypes];
memset(lmap2lmap.improper, 0, nimpropertypes * sizeof(int));
}
/* ----------------------------------------------------------------------
labelmap command in input script
------------------------------------------------------------------------- */
void LabelMap::modify_lmap(int narg, char **arg)
{
if ((narg < 1) || ((narg > 2) && ((narg % 2) == 0)))
error->all(FLERR, "Incorrect number of arguments for labelmap command");
int ntypes;
std::vector<std::string> *labels;
std::unordered_map<std::string, int> *labels_map;
const std::string tlabel(arg[0]);
if (tlabel == "atom") {
ntypes = natomtypes;
labels = &typelabel;
labels_map = &typelabel_map;
} else if (tlabel == "bond") {
ntypes = nbondtypes;
labels = &btypelabel;
labels_map = &btypelabel_map;
} else if (tlabel == "angle") {
ntypes = nangletypes;
labels = &atypelabel;
labels_map = &atypelabel_map;
} else if (tlabel == "dihedral") {
ntypes = ndihedraltypes;
labels = &dtypelabel;
labels_map = &dtypelabel_map;
} else if (tlabel == "improper") {
ntypes = nimpropertypes;
labels = &itypelabel;
labels_map = &itypelabel_map;
} else if (tlabel == "clear") {
if (narg != 1) error->all(FLERR, "Incorrect number of arguments for labelmap clear command");
reset_type_labels();
return;
} else if (tlabel == "write") {
if (narg != 2) error->all(FLERR, "Incorrect number of arguments for labelmap write command");
write_map(arg[1]);
return;
} else
error->all(FLERR, "Unknown labelmap keyword {}", tlabel);
int iarg = 1;
if (narg == 1) utils::missing_cmd_args(FLERR, "labelmap " + tlabel, error);
while (iarg < narg) {
if (iarg + 2 > narg) utils::missing_cmd_args(FLERR, "labelmap " + tlabel, error);
if (ntypes < 1) error->all(FLERR, "No {} types allowed with current box settings", tlabel);
int itype = utils::inumeric(FLERR, arg[iarg++], false, lmp);
if ((itype < 1) || (itype > ntypes))
error->all(FLERR, "Labelmap {} type {} must be within 1-{}", tlabel, itype, ntypes);
std::string slabel = utils::utf8_subst(utils::trim(arg[iarg++]));
if (utils::is_type(slabel) != 1)
error->all(FLERR, "Type label string {} for {} type {} is invalid", slabel, tlabel, itype);
int found = search(slabel, (*labels_map));
if ((found != -1) && (found != itype))
error->all(FLERR, "The {} type label {} is already in use for type {}", tlabel, slabel,
(*labels_map)[slabel]);
std::string &str = (*labels)[itype - 1];
if (!str.empty()) (*labels_map).erase(str);
str = slabel;
(*labels_map)[slabel] = itype;
}
}
/* ----------------------------------------------------------------------
copy another map (lmap2) into this one
if label already exists, leave in place
else, put new label in next available slot
------------------------------------------------------------------------- */
void LabelMap::merge_lmap(LabelMap *lmap2, int mode)
{
switch (mode) {
case Atom::ATOM:
for (auto &it : lmap2->typelabel) find_or_create(it, typelabel, typelabel_map);
break;
case Atom::BOND:
for (auto &it : lmap2->btypelabel) find_or_create(it, btypelabel, btypelabel_map);
break;
case Atom::ANGLE:
for (auto &it : lmap2->atypelabel) find_or_create(it, atypelabel, atypelabel_map);
break;
case Atom::DIHEDRAL:
for (auto &it : lmap2->dtypelabel) find_or_create(it, dtypelabel, dtypelabel_map);
break;
case Atom::IMPROPER:
for (auto &it : lmap2->itypelabel) find_or_create(it, itypelabel, itypelabel_map);
break;
}
}
/* ----------------------------------------------------------------------
get mapping between this label map and another (lmap2)
values of lmap2lmap point to equivalent types in lmap2
------------------------------------------------------------------------- */
void LabelMap::create_lmap2lmap(LabelMap *lmap2, int mode)
{
switch (mode) {
case Atom::ATOM:
for (int i = 0; i < natomtypes; ++i)
lmap2lmap.atom[i] = search(typelabel[i], lmap2->typelabel_map);
break;
case Atom::BOND:
for (int i = 0; i < nbondtypes; ++i)
lmap2lmap.bond[i] = search(btypelabel[i], lmap2->btypelabel_map);
break;
case Atom::ANGLE:
for (int i = 0; i < nangletypes; ++i)
lmap2lmap.angle[i] = search(atypelabel[i], lmap2->atypelabel_map);
break;
case Atom::DIHEDRAL:
for (int i = 0; i < ndihedraltypes; ++i)
lmap2lmap.dihedral[i] = search(dtypelabel[i], lmap2->dtypelabel_map);
break;
case Atom::IMPROPER:
for (int i = 0; i < nimpropertypes; ++i)
lmap2lmap.improper[i] = search(itypelabel[i], lmap2->itypelabel_map);
break;
}
}
/* ----------------------------------------------------------------------
find type label with name or create type if it doesn't exist
return numeric type
------------------------------------------------------------------------- */
int LabelMap::find_or_create(const std::string &mylabel, std::vector<std::string> &labels,
std::unordered_map<std::string, int> &labels_map)
{
auto search = labels_map.find(mylabel);
if (search != labels_map.end()) return search->second;
// if no match found, create new label at next available index
// label map assumed to be intialized with numeric index
// user labels are assumed to be alphanumeric (not a number)
auto labels_map_size = labels_map.size();
if (labels_map_size < labels.size()) {
labels[labels_map_size] = mylabel;
int index = static_cast<int>(labels_map_size + 1);
labels_map[mylabel] = index;
return index;
}
// if label cannot be found or created, need more space reserved
error->all(FLERR, "Topology type exceeds system topology type");
// never reaches here, just to prevent compiler warning
return -1;
}
/* ----------------------------------------------------------------------
return numeric type given a type label
return -1 if type not yet defined
------------------------------------------------------------------------- */
int LabelMap::find(const std::string &mylabel, int mode) const
{
switch (mode) {
case Atom::ATOM:
return search(mylabel, typelabel_map);
break;
case Atom::BOND:
return search(mylabel, btypelabel_map);
break;
case Atom::ANGLE:
return search(mylabel, atypelabel_map);
break;
case Atom::DIHEDRAL:
return search(mylabel, dtypelabel_map);
break;
case Atom::IMPROPER:
return search(mylabel, itypelabel_map);
break;
default:
return -1;
}
}
/* ----------------------------------------------------------------------
get type given type labels map
return -1 if type not yet defined
------------------------------------------------------------------------- */
int LabelMap::search(const std::string &mylabel,
const std::unordered_map<std::string, int> &labels_map) const
{
auto search = labels_map.find(mylabel);
if (search == labels_map.end()) return -1;
return search->second;
}
/* ----------------------------------------------------------------------
check that all types have been assigned a unique type label
------------------------------------------------------------------------- */
bool LabelMap::is_complete(int mode) const
{
switch (mode) {
case Atom::ATOM:
return static_cast<int>(typelabel_map.size()) == natomtypes;
break;
case Atom::BOND:
return static_cast<int>(btypelabel_map.size()) == nbondtypes;
break;
case Atom::ANGLE:
return static_cast<int>(atypelabel_map.size()) == nangletypes;
break;
case Atom::DIHEDRAL:
return static_cast<int>(dtypelabel_map.size()) == ndihedraltypes;
break;
case Atom::IMPROPER:
return static_cast<int>(itypelabel_map.size()) == nimpropertypes;
break;
}
return false;
}
/* ----------------------------------------------------------------------
proc 0 writes to data file
------------------------------------------------------------------------- */
void LabelMap::write_data(FILE *fp)
{
if (is_complete(Atom::ATOM)) {
fmt::print(fp, "\nAtom Type Labels\n\n");
for (int i = 0; i < natomtypes; i++) fmt::print(fp, "{} {}\n", i + 1, typelabel[i]);
}
if (force->bond && is_complete(Atom::BOND)) {
fmt::print(fp, "\nBond Type Labels\n\n");
for (int i = 0; i < nbondtypes; i++) fmt::print(fp, "{} {}\n", i + 1, btypelabel[i]);
}
if (force->angle && is_complete(Atom::ANGLE)) {
fmt::print(fp, "\nAngle Type Labels\n\n");
for (int i = 0; i < nangletypes; i++) fmt::print(fp, "{} {}\n", i + 1, atypelabel[i]);
}
if (force->dihedral && is_complete(Atom::DIHEDRAL)) {
fmt::print(fp, "\nDihedral Type Labels\n\n");
for (int i = 0; i < ndihedraltypes; i++) fmt::print(fp, "{} {}\n", i + 1, dtypelabel[i]);
}
if (force->improper && is_complete(Atom::IMPROPER)) {
fmt::print(fp, "\nImproper Type Labels\n\n");
for (int i = 0; i < nimpropertypes; i++) fmt::print(fp, "{} {}\n", i + 1, itypelabel[i]);
}
}
/* ----------------------------------------------------------------------
proc 0 reads from restart file, bcasts
------------------------------------------------------------------------- */
void LabelMap::read_restart(FILE *fp)
{
char *charlabel;
for (int i = 0; i < natomtypes; i++) {
charlabel = read_string(fp);
typelabel[i] = charlabel;
typelabel_map[charlabel] = i + 1;
delete[] charlabel;
}
for (int i = 0; i < nbondtypes; i++) {
charlabel = read_string(fp);
btypelabel[i] = charlabel;
btypelabel_map[charlabel] = i + 1;
delete[] charlabel;
}
for (int i = 0; i < nangletypes; i++) {
charlabel = read_string(fp);
atypelabel[i] = charlabel;
atypelabel_map[charlabel] = i + 1;
delete[] charlabel;
}
for (int i = 0; i < ndihedraltypes; i++) {
charlabel = read_string(fp);
dtypelabel[i] = charlabel;
dtypelabel_map[charlabel] = i + 1;
delete[] charlabel;
}
for (int i = 0; i < nimpropertypes; i++) {
charlabel = read_string(fp);
itypelabel[i] = charlabel;
itypelabel_map[charlabel] = i + 1;
delete[] charlabel;
}
}
/* ----------------------------------------------------------------------
proc 0 writes to restart file
------------------------------------------------------------------------- */
void LabelMap::write_restart(FILE *fp)
{
for (int i = 0; i < natomtypes; i++) write_string(typelabel[i], fp);
for (int i = 0; i < nbondtypes; i++) write_string(btypelabel[i], fp);
for (int i = 0; i < nangletypes; i++) write_string(atypelabel[i], fp);
for (int i = 0; i < ndihedraltypes; i++) write_string(dtypelabel[i], fp);
for (int i = 0; i < nimpropertypes; i++) write_string(itypelabel[i], fp);
}
/* ----------------------------------------------------------------------
read a char string (including nullptr) and bcast it
str is allocated here, ptr is returned, caller must deallocate
------------------------------------------------------------------------- */
char *LabelMap::read_string(FILE *fp)
{
int n = read_int(fp);
if (n < 0) error->all(FLERR, "Illegal size string or corrupt restart");
char *value = new char[n];
if (comm->me == 0) utils::sfread(FLERR, value, sizeof(char), n, fp, nullptr, error);
MPI_Bcast(value, n, MPI_CHAR, 0, world);
return value;
}
/* ----------------------------------------------------------------------
write a flag and a C-style char string (including the terminating null
byte) into the restart file
------------------------------------------------------------------------- */
void LabelMap::write_string(const std::string &str, FILE *fp)
{
const char *cstr = str.c_str();
int n = strlen(cstr) + 1;
fwrite(&n, sizeof(int), 1, fp);
fwrite(cstr, sizeof(char), n, fp);
}
/* ----------------------------------------------------------------------
read an int from restart file and bcast it
------------------------------------------------------------------------- */
int LabelMap::read_int(FILE *fp)
{
int value;
if ((comm->me == 0) && (fread(&value, sizeof(int), 1, fp) < 1)) value = -1;
MPI_Bcast(&value, 1, MPI_INT, 0, world);
return value;
}
/* ----------------------------------------------------------------------
write out all current label map values as labelmap commands
------------------------------------------------------------------------- */
void LabelMap::write_map(const std::string &filename)
{
if (comm->me == 0) {
FILE *fp = fopen(filename.c_str(), "w");
if (!fp) error->one(FLERR, "Cannot open label map file {}: {}", filename, utils::getsyserror());
if (typelabel_map.size() > 0) {
fputs("labelmap atom", fp);
for (int i = 0; i < natomtypes; ++i)
if (!typelabel[i].empty()) fmt::print(fp, " {} \"\"\" {} \"\"\"", i + 1, typelabel[i]);
fputc('\n', fp);
}
if (btypelabel_map.size() > 0) {
fputs("labelmap bond", fp);
for (int i = 0; i < nbondtypes; ++i)
if (!btypelabel[i].empty()) fmt::print(fp, " {} \"\"\" {} \"\"\"", i + 1, btypelabel[i]);
fputc('\n', fp);
}
if (atypelabel_map.size() > 0) {
fputs("labelmap angle", fp);
for (int i = 0; i < nangletypes; ++i)
if (!atypelabel[i].empty()) fmt::print(fp, " {} \"\"\" {} \"\"\"", i + 1, atypelabel[i]);
fputc('\n', fp);
}
if (dtypelabel_map.size() > 0) {
fputs("labelmap dihedral", fp);
for (int i = 0; i < ndihedraltypes; ++i)
if (!dtypelabel[i].empty()) fmt::print(fp, " {} \"\"\" {} \"\"\"", i + 1, dtypelabel[i]);
fputc('\n', fp);
}
if (itypelabel_map.size() > 0) {
fputs("labelmap improper", fp);
for (int i = 0; i < nimpropertypes; ++i)
if (!itypelabel[i].empty()) fmt::print(fp, " {} \"\"\" {} \"\"\"", i + 1, itypelabel[i]);
fputc('\n', fp);
}
fclose(fp);
}
}

78
src/label_map.h Normal file
View File

@ -0,0 +1,78 @@
/* -*- c++ -*- ----------------------------------------------------------
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
https://www.lammps.org/, Sandia National Laboratories
Steve Plimpton, sjplimp@sandia.gov
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.
------------------------------------------------------------------------- */
#ifndef LMP_LABEL_MAP_H
#define LMP_LABEL_MAP_H
#include "pointers.h" // IWYU pragma: export
#include <unordered_map>
namespace LAMMPS_NS {
class LabelMap : protected Pointers {
friend class AtomVec;
friend class ReadData;
public:
LabelMap(LAMMPS *lmp, int, int, int, int, int);
~LabelMap();
void modify_lmap(int, char **); // labelmap command in the input script
void merge_lmap(LabelMap *, int); // copy another lmap into this one
void create_lmap2lmap(LabelMap *, int); // index mapping between two lmaps
int find(const std::string &, int) const; // find numeric type of type label
bool is_complete(int) const; // check if all types are assigned
// input/output for atom class label map
void write_data(FILE *);
void read_restart(FILE *fp);
void write_restart(FILE *);
protected:
int natomtypes, nbondtypes, nangletypes, ndihedraltypes, nimpropertypes;
std::vector<std::string> typelabel, btypelabel, atypelabel;
std::vector<std::string> dtypelabel, itypelabel;
std::unordered_map<std::string, int> typelabel_map;
std::unordered_map<std::string, int> btypelabel_map;
std::unordered_map<std::string, int> atypelabel_map;
std::unordered_map<std::string, int> dtypelabel_map;
std::unordered_map<std::string, int> itypelabel_map;
// per-type data struct mapping this label map to another
struct Lmap2Lmap {
int *atom;
int *bond;
int *angle;
int *dihedral;
int *improper;
};
Lmap2Lmap lmap2lmap;
void reset_type_labels();
int find_or_create(const std::string &, std::vector<std::string> &,
std::unordered_map<std::string, int> &); // look up type or create new type
int search(const std::string &,
const std::unordered_map<std::string, int> &) const; // look up type index
char *read_string(FILE *);
void write_string(const std::string &, FILE *);
int read_int(FILE *);
void write_map(const std::string &);
};
} // namespace LAMMPS_NS
#endif

3
src/lmprestart.h
View File

@ -37,8 +37,7 @@ enum{VERSION,SMALLINT,TAGINT,BIGINT,
COMM_MODE,COMM_CUTOFF,COMM_VEL,NO_PAIR, COMM_MODE,COMM_CUTOFF,COMM_VEL,NO_PAIR,
EXTRA_BOND_PER_ATOM,EXTRA_ANGLE_PER_ATOM,EXTRA_DIHEDRAL_PER_ATOM, EXTRA_BOND_PER_ATOM,EXTRA_ANGLE_PER_ATOM,EXTRA_DIHEDRAL_PER_ATOM,
EXTRA_IMPROPER_PER_ATOM,EXTRA_SPECIAL_PER_ATOM,ATOM_MAXSPECIAL, EXTRA_IMPROPER_PER_ATOM,EXTRA_SPECIAL_PER_ATOM,ATOM_MAXSPECIAL,
NELLIPSOIDS,NLINES,NTRIS,NBODIES, NELLIPSOIDS,NLINES,NTRIS,NBODIES,ATIME,ATIMESTEP,LABELMAP};
ATIME,ATIMESTEP};
#define LB_FACTOR 1.1 #define LB_FACTOR 1.1

662
src/molecule.cpp
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File diff suppressed because it is too large Load Diff

21
src/output.cpp
View File

@ -237,11 +237,9 @@ void Output::setup(int memflag)
last_dump[idump] = ntimestep; last_dump[idump] = ntimestep;
} }
// calculate timestep and/or time for next dump // calculate timestep or time for next dump
// set next_dump and next_time_dump, 0 arg for setup() // set next_dump and next_time_dump
// only do this if dump written or dump has not been written yet
if (writeflag || last_dump[idump] < 0)
calculate_next_dump(SETUP,idump,ntimestep); calculate_next_dump(SETUP,idump,ntimestep);
// if dump not written now, use addstep_compute_all() // if dump not written now, use addstep_compute_all()
@ -268,11 +266,11 @@ void Output::setup(int memflag)
if (restart_flag && update->restrict_output == 0) { if (restart_flag && update->restrict_output == 0) {
if (restart_flag_single) { if (restart_flag_single) {
if (restart_every_single) if (restart_every_single) {
next_restart_single = next_restart_single =
(ntimestep/restart_every_single)*restart_every_single + (ntimestep/restart_every_single)*restart_every_single +
restart_every_single; restart_every_single;
else { } else {
auto nextrestart = static_cast<bigint> auto nextrestart = static_cast<bigint>
(input->variable->compute_equal(ivar_restart_single)); (input->variable->compute_equal(ivar_restart_single));
if (nextrestart <= ntimestep) if (nextrestart <= ntimestep)
@ -365,7 +363,7 @@ void Output::setup(int memflag)
modify->clearstep_compute(); modify->clearstep_compute();
// perform dump // perform dump
// reset next_dump and next_time_dump, 1 arg for write() // set next_dump and next_time_dump
dump[idump]->write(); dump[idump]->write();
last_dump[idump] = ntimestep; last_dump[idump] = ntimestep;
@ -388,7 +386,6 @@ void Output::setup(int memflag)
if (next_restart == ntimestep) { if (next_restart == ntimestep) {
if (next_restart_single == ntimestep) { if (next_restart_single == ntimestep) {
std::string file = restart1; std::string file = restart1;
std::size_t found = file.find('*'); std::size_t found = file.find('*');
if (found != std::string::npos) if (found != std::string::npos)
@ -407,6 +404,7 @@ void Output::setup(int memflag)
modify->addstep_compute(next_restart_single); modify->addstep_compute(next_restart_single);
} }
} }
if (next_restart_double == ntimestep) { if (next_restart_double == ntimestep) {
if (last_restart != ntimestep) { if (last_restart != ntimestep) {
if (restart_toggle == 0) { if (restart_toggle == 0) {
@ -417,6 +415,7 @@ void Output::setup(int memflag)
restart_toggle = 0; restart_toggle = 0;
} }
} }
if (restart_every_double) next_restart_double += restart_every_double; if (restart_every_double) next_restart_double += restart_every_double;
else { else {
modify->clearstep_compute(); modify->clearstep_compute();
@ -489,8 +488,9 @@ void Output::calculate_next_dump(int which, int idump, bigint ntimestep)
if (every_dump[idump]) { if (every_dump[idump]) {
// which = SETUP: nextdump = next multiple of every_dump // which = SETUP: next_dump = next multiple of every_dump
// which = WRITE: increment nextdump by every_dump // which = WRITE: increment next_dump by every_dump
// current step is already multiple of every_dump
if (which == SETUP) if (which == SETUP)
next_dump[idump] = (ntimestep/every_dump[idump])*every_dump[idump] + every_dump[idump]; next_dump[idump] = (ntimestep/every_dump[idump])*every_dump[idump] + every_dump[idump];
@ -728,7 +728,6 @@ void Output::reset_dt()
next = MIN(next,next_thermo); next = MIN(next,next_thermo);
} }
/* ---------------------------------------------------------------------- /* ----------------------------------------------------------------------
add a Dump to list of Dumps add a Dump to list of Dumps
------------------------------------------------------------------------- */ ------------------------------------------------------------------------- */

1
src/pair_hybrid.h
View File

@ -25,6 +25,7 @@ PairStyle(hybrid,PairHybrid);
namespace LAMMPS_NS { namespace LAMMPS_NS {
class PairHybrid : public Pair { class PairHybrid : public Pair {
friend class AtomVecDielectric;
friend class ComputeSpin; friend class ComputeSpin;
friend class FixGPU; friend class FixGPU;
friend class FixIntel; friend class FixIntel;

910
src/read_data.cpp
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File diff suppressed because it is too large Load Diff

13
src/read_data.h
View File

@ -44,8 +44,7 @@ class ReadData : public Command {
int nlocal_previous; int nlocal_previous;
bigint natoms; bigint natoms;
bigint nbonds, nangles, ndihedrals, nimpropers; bigint nbonds, nangles, ndihedrals, nimpropers;
int ntypes; int ntypes, nbondtypes, nangletypes, ndihedraltypes, nimpropertypes;
int nbondtypes, nangletypes, ndihedraltypes, nimpropertypes;
bigint nellipsoids; bigint nellipsoids;
class AtomVecEllipsoid *avec_ellipsoid; class AtomVecEllipsoid *avec_ellipsoid;
@ -56,6 +55,10 @@ class ReadData : public Command {
bigint nbodies; bigint nbodies;
class AtomVecBody *avec_body; class AtomVecBody *avec_body;
// type labels
class LabelMap *lmap;
// box info // box info
double boxlo[3], boxhi[3]; double boxlo[3], boxhi[3];
@ -64,7 +67,8 @@ class ReadData : public Command {
// optional args // optional args
int addflag, offsetflag, shiftflag, coeffflag; int addflag, offsetflag, shiftflag, coeffflag, settypeflag;
int tlabelflag, blabelflag, alabelflag, dlabelflag, ilabelflag;
tagint addvalue; tagint addvalue;
int toffset, boffset, aoffset, doffset, ioffset; int toffset, boffset, aoffset, doffset, ioffset;
double shift[3]; double shift[3];
@ -85,7 +89,7 @@ class ReadData : public Command {
void header(int); void header(int);
void parse_keyword(int); void parse_keyword(int);
void skip_lines(bigint); void skip_lines(bigint);
void parse_coeffs(char *, const char *, int, int, int); void parse_coeffs(char *, const char *, int, int, int, int, int *);
int style_match(const char *, const char *); int style_match(const char *, const char *);
void atoms(); void atoms();
@ -107,6 +111,7 @@ class ReadData : public Command {
void anglecoeffs(int); void anglecoeffs(int);
void dihedralcoeffs(int); void dihedralcoeffs(int);
void impropercoeffs(int); void impropercoeffs(int);
void typelabels(int);
void fix(Fix *, char *); void fix(Fix *, char *);
}; };

10
src/read_restart.cpp
View File

@ -27,6 +27,7 @@
#include "group.h" #include "group.h"
#include "improper.h" #include "improper.h"
#include "irregular.h" #include "irregular.h"
#include "label_map.h"
#include "memory.h" #include "memory.h"
#include "modify.h" #include "modify.h"
#include "mpiio.h" #include "mpiio.h"
@ -559,6 +560,10 @@ std::string ReadRestart::file_search(const std::string &inpfile)
bigint maxnum = -1; bigint maxnum = -1;
loc = pattern.find('*'); loc = pattern.find('*');
if (loc != std::string::npos) { if (loc != std::string::npos) {
// the regex matcher in utils::strmatch() only checks the first 256 characters.
if (loc > 256)
error->one(FLERR, "Filename part before '*' is too long to find restart with largest step");
// convert pattern to equivalent regexp // convert pattern to equivalent regexp
pattern.replace(loc,1,"\\d+"); pattern.replace(loc,1,"\\d+");
@ -889,6 +894,11 @@ void ReadRestart::type_arrays()
atom->set_mass(mass); atom->set_mass(mass);
delete[] mass; delete[] mass;
} else if (flag == LABELMAP) {
read_int();
atom->add_label_map();
atom->lmap->read_restart(fp);
} else error->all(FLERR, } else error->all(FLERR,
"Invalid flag in type arrays section of restart file"); "Invalid flag in type arrays section of restart file");

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