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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@15352 f3b2605a-c512-4ea7-a41b-209d697bcdaa

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2016-07-22 22:46:14 +00:00
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18
doc/html/_sources/compute_angle_local.txt
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@ -8,12 +8,12 @@ Syntax
.. parsed-literal::
compute ID group-ID angle/local input1 input2 ...
compute ID group-ID angle/local value1 value2 ...
* ID, group-ID are documented in :doc:`compute <compute>` command
* angle/local = style name of this compute command
* one or more keywords may be appended
* keyword = *theta* or *eng*
* one or more values may be appended
* value = *theta* or *eng*
.. parsed-literal::
*theta* = tabulate angles
@ -37,6 +37,10 @@ interactions. The number of datums generated, aggregated across all
processors, equals the number of angles in the system, modified by the
group parameter as explained below.
The value *theta* is the angle for the 3 atoms in the interaction.
The value *eng* is the interaction energy for the angle.
The local data stored by this command is generated by looping over all
the atoms owned on a processor and their angles. An angle will only
be included if all 3 atoms in the angle are in the specified compute
@ -55,6 +59,14 @@ For example, angle output from the :doc:`compute property/local <compute_propert
with data from this command and output by the :doc:`dump local <dump>`
command in a consistent way.
Here is an example of how to do this:
.. parsed-literal::
compute 1 all property/local atype aatom1 aatom2 aatom3
compute 2 all angle/local theta eng
dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_2[1] c_2[2]
**Output info:**
This compute calculates a local vector or local array depending on the

15
doc/html/_sources/compute_bond_local.txt
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@ -8,12 +8,12 @@ Syntax
.. parsed-literal::
compute ID group-ID bond/local input1 input2 ...
compute ID group-ID bond/local value1 value2 ...
* ID, group-ID are documented in :doc:`compute <compute>` command
* bond/local = style name of this compute command
* one or more keywords may be appended
* keyword = *dist* or *eng*
* one or more values may be appended
* value = *dist* or *eng* or *force*
.. parsed-literal::
*dist* = bond distance
@ -38,6 +38,13 @@ interactions. The number of datums generated, aggregated across all
processors, equals the number of bonds in the system, modified
by the group parameter as explained below.
The value *dist* is the length of the bond.
The value *eng* is the interaction energy for the bond.
The value *force* is the force acting between the pair of atoms in the
bond.
The local data stored by this command is generated by looping over all
the atoms owned on a processor and their bonds. A bond will only be
included if both atoms in the bond are in the specified compute group.
@ -60,7 +67,7 @@ Here is an example of how to do this:
.. parsed-literal::
compute 1 all property/local batom1 batom2 btype
compute 1 all property/local btype batom1 batom2
compute 2 all bond/local dist eng
dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_2[1] c_2[2]

17
doc/html/_sources/compute_dihedral_local.txt
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@ -8,12 +8,12 @@ Syntax
.. parsed-literal::
compute ID group-ID dihedral/local input1 input2 ...
compute ID group-ID dihedral/local value1 value2 ...
* ID, group-ID are documented in :doc:`compute <compute>` command
* dihedral/local = style name of this compute command
* one or more keywords may be appended
* keyword = *phi*
* one or more values may be appended
* value = *phi*
.. parsed-literal::
*phi* = tabulate dihedral angles
@ -35,6 +35,9 @@ interactions. The number of datums generated, aggregated across all
processors, equals the number of angles in the system, modified by the
group parameter as explained below.
The value *phi* is the dihedral angle, as defined in the diagram on
the :doc:`dihedral_style <dihedral_style>` doc page.
The local data stored by this command is generated by looping over all
the atoms owned on a processor and their dihedrals. A dihedral will
only be included if all 4 atoms in the dihedral are in the specified
@ -49,6 +52,14 @@ For example, dihedral output from the :doc:`compute property/local <compute_prop
with data from this command and output by the :doc:`dump local <dump>`
command in a consistent way.
Here is an example of how to do this:
.. parsed-literal::
compute 1 all property/local dtype datom1 datom2 datom3 datom4
compute 2 all dihedral/local phi
dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_1[5] c_2[1]
**Output info:**
This compute calculates a local vector or local array depending on the

18
doc/html/_sources/compute_improper_local.txt
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@ -8,12 +8,12 @@ Syntax
.. parsed-literal::
compute ID group-ID improper/local input1 input2 ...
compute ID group-ID improper/local value1 value2 ...
* ID, group-ID are documented in :doc:`compute <compute>` command
* improper/local = style name of this compute command
* one or more keywords may be appended
* keyword = *chi*
* one or more values may be appended
* value = *chi*
.. parsed-literal::
*chi* = tabulate improper angles
@ -35,6 +35,10 @@ interactions. The number of datums generated, aggregated across all
processors, equals the number of impropers in the system, modified by
the group parameter as explained below.
The value *chi* is the improper angle, as defined in the doc pages for
the individual improper styles listed on
:doc:`improper_style <improper_style>` doc page.
The local data stored by this command is generated by looping over all
the atoms owned on a processor and their impropers. An improper will
only be included if all 4 atoms in the improper are in the specified
@ -49,6 +53,14 @@ For example, improper output from the :doc:`compute property/local <compute_prop
with data from this command and output by the :doc:`dump local <dump>`
command in a consistent way.
Here is an example of how to do this:
.. parsed-literal::
compute 1 all property/local itype iatom1 iatom2 iatom3 iatom4
compute 2 all improper/local chi
dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_1[3] c_1[4] c_1[5] c_2[1]
**Output info:**
This compute calculates a local vector or local array depending on the

54
doc/html/_sources/compute_pair_local.txt
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@ -8,12 +8,12 @@ Syntax
.. parsed-literal::
compute ID group-ID pair/local input1 input2 ...
compute ID group-ID pair/local value1 value2 ... keyword args ...
* ID, group-ID are documented in :doc:`compute <compute>` command
* pair/local = style name of this compute command
* zero or more keywords may be appended
* keyword = *dist* or *eng* or *force* or *fx* or *fy* or *fz* or *pN*
* one or more values may be appended
* value = *dist* or *eng* or *force* or *fx* or *fy* or *fz* or *pN*
.. parsed-literal::
*dist* = pairwise distance
@ -22,6 +22,12 @@ Syntax
*fx*\ ,\ *fy*\ ,\ *fz* = components of pairwise force
*pN* = pair style specific quantities for allowed N values
* zero or more keyword/arg pairs may be appended
* keyword = *cutoff*
.. parsed-literal::
*cutoff* arg = *type* or *radius*
Examples
@ -49,13 +55,13 @@ force cutoff distance for that interaction, as defined by the
:doc:`pair_style <pair_style>` and :doc:`pair_coeff <pair_coeff>`
commands.
The output *dist* is the distance bewteen the pair of atoms.
The value *dist* is the distance bewteen the pair of atoms.
The output *eng* is the interaction energy for the pair of atoms.
The value *eng* is the interaction energy for the pair of atoms.
The output *force* is the force acting between the pair of atoms,
which is positive for a repulsive force and negative for an attractive
force. The outputs *fx*\ , *fy*\ , and *fz* are the xyz components of
The value *force* is the force acting between the pair of atoms, which
is positive for a repulsive force and negative for an attractive
force. The values *fx*\ , *fy*\ , and *fz* are the xyz components of
*force* on atom I.
A pair style may define additional pairwise quantities which can be
@ -66,10 +72,18 @@ which calculate the tangential force between two particles and return
its components and magnitude acting on atom I for N = 1,2,3,4. See
individual pair styles for detils.
The output *dist* will be in distance :doc:`units <units>`. The output
*eng* will be in energy :doc:`units <units>`. The outputs *force*\ ,
*fx*\ , *fy*\ , and *fz* will be in force :doc:`units <units>`. The output
*pN* will be in whatever units the pair style defines.
The value *dist* will be in distance :doc:`units <units>`. The value
*eng* will be in energy :doc:`units <units>`. The values *force*\ , *fx*\ ,
*fy*\ , and *fz* will be in force :doc:`units <units>`. The values *pN*
will be in whatever units the pair style defines.
The optional *cutoff* keyword determines how the force cutoff distance
for an interaction is determined. For the default setting of *type*\ ,
the pairwise cutoff defined by the :doc:`pair_style <pair_style>`
command for the types of the two atoms is used. For the *radius*
setting, the sum of the radii of the two particles is used as a
cutoff. For example, this is appropriate for granular particles which
only interact when they are overlapping, as computed by `granular pair styles <pair_gran.txt>`_.
Note that as atoms migrate from processor to processor, there will be
no consistent ordering of the entries within the local vector or array
@ -80,6 +94,14 @@ For example, pair output from the :doc:`compute property/local <compute_property
with data from this command and output by the :doc:`dump local <dump>`
command in a consistent way.
Here is an example of how to do this:
.. parsed-literal::
compute 1 all property/local patom1 patom2
compute 2 all pair/local dist eng force
dump 1 all local 1000 tmp.dump index c_1[1] c_1[2] c_2[1] c_2[2] c_2[3]
.. note::
For pairs, if two atoms I,J are involved in 1-2, 1-3, 1-4
@ -110,7 +132,8 @@ options.
The output for *dist* will be in distance :doc:`units <units>`. The
output for *eng* will be in energy :doc:`units <units>`. The output for
*force* will be in force :doc:`units <units>`.
*force*\ , *fx*\ , *fy*\ , and *fz* will be in force :doc:`units <units>`.
The outpur for *pN* will be in whatever units the pair style defines.
Restrictions
""""""""""""
@ -121,7 +144,10 @@ Related commands
:doc:`dump local <dump>`, :doc:`compute property/local <compute_property_local>`
**Default:** none
Default
"""""""
The keyword default is cutoff = type.
.. _lws: http://lammps.sandia.gov

44
doc/html/_sources/compute_property_local.txt
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@ -8,19 +8,19 @@ Syntax
.. parsed-literal::
compute ID group-ID property/local input1 input2 ...
compute ID group-ID property/local attribute1 attribute2 ... keyword args ...
* ID, group-ID are documented in :doc:`compute <compute>` command
* property/local = style name of this compute command
* input = one or more attributes
* one or more attributes may be appended
.. parsed-literal::
possible attributes = natom1 natom2 ntype1 ntype2
patom1 patom2 ptype1 ptype2
batom1 batom2 btype
aatom1 aatom2 aatom3 atype
datom1 datom2 datom3 dtype
iatom1 iatom2 iatom3 itype
possible attributes = natom1 natom2 ntype1 ntype2
patom1 patom2 ptype1 ptype2
batom1 batom2 btype
aatom1 aatom2 aatom3 atype
datom1 datom2 datom3 dtype
iatom1 iatom2 iatom3 itype
.. parsed-literal::
@ -37,6 +37,12 @@ Syntax
iatom1, iatom2, iatom3, iatom4 = IDs of 4 atoms in each improper
itype = improper type of each improper
* zero or more keyword/arg pairs may be appended
* keyword = *cutoff*
.. parsed-literal::
*cutoff* arg = *type* or *radius*
Examples
@ -56,9 +62,9 @@ to bond information, then the number of datums generated, aggregated
across all processors, equals the number of bonds in the system.
Ditto for pairs, angles, etc.
If multiple input attributes are specified then they must all generate
the same amount of information, so that the resulting local array has
the same number of rows for each column. This means that only bond
If multiple attributes are specified then they must all generate the
same amount of information, so that the resulting local array has the
same number of rows for each column. This means that only bond
attributes can be specified together, or angle attributes, etc. Bond
and angle attributes can not be mixed in the same compute
property/local command.
@ -74,6 +80,15 @@ force cutoff distance for that pair to be included, as defined by the
:doc:`pair_style <pair_style>` and :doc:`pair_coeff <pair_coeff>`
commands.
The optional *cutoff* keyword determines how the force cutoff distance
for an interaction is determined for the *patom1* and *patom2*
attributes. For the default setting of *type*\ , the pairwise cutoff
defined by the :doc:`pair_style <pair_style>` command for the types of
the two atoms is used. For the *radius* setting, the sum of the radii
of the two particles is used as a cutoff. For example, this is
appropriate for granular particles which only interact when they are
overlapping, as computed by `granular pair styles <pair_gran.txt>`_.
If the inputs are bond, angle, etc attributes, the local data is
generated by looping over all the atoms owned on a processor and
extracting bond, angle, etc info. For bonds, info about an individual
@ -122,6 +137,8 @@ The attributes that start with "a", "d", "i", refer to similar values
for :doc:`angles <angle_style>`, :doc:`dihedrals <dihedral_style>`, and
:doc:`impropers <improper_style>`.
The optional *cutoff* keyword
**Output info:**
This compute calculates a local vector or local array depending on the
@ -145,7 +162,10 @@ Related commands
:doc:`dump local <dump>`, :doc:`compute reduce <compute_reduce>`
**Default:** none
Default
"""""""
The keyword default is cutoff = type.
.. _lws: http://lammps.sandia.gov

6
doc/html/_sources/compute_sna_atom.txt
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@ -14,9 +14,9 @@ Syntax
.. parsed-literal::
compute ID group-ID sna/atom ntypes rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
compute ID group-ID snad/atom ntypes rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
compute ID group-ID snav/atom ntypes rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
compute ID group-ID sna/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
compute ID group-ID snad/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
compute ID group-ID snav/atom rcutfac rfac0 twojmax R_1 R_2 ... w_1 w_2 ... keyword values ...
* ID, group-ID are documented in :doc:`compute <compute>` command
* sna/atom = style name of this compute command