Merge pull request #2536 from jtclemm/multi_epcc
Add faster method for multi neighboring
This commit is contained in:
Axel Kohlmeyer
@ -108,6 +108,8 @@ Lowercase directories
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+-------------+------------------------------------------------------------------+
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+-------------+------------------------------------------------------------------+
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| msst | MSST shock dynamics |
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| msst | MSST shock dynamics |
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+-------------+------------------------------------------------------------------+
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+-------------+------------------------------------------------------------------+
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| multi | multi neighboring for systems with large interaction disparities |
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+-------------+------------------------------------------------------------------+
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| nb3b | use of non-bonded 3-body harmonic pair style |
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| nb3b | use of non-bonded 3-body harmonic pair style |
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+-------------+------------------------------------------------------------------+
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+-------------+------------------------------------------------------------------+
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| neb | nudged elastic band (NEB) calculation for barrier finding |
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| neb | nudged elastic band (NEB) calculation for barrier finding |
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@ -11,13 +11,17 @@ Syntax
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comm_modify keyword value ...
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comm_modify keyword value ...
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* zero or more keyword/value pairs may be appended
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* zero or more keyword/value pairs may be appended
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* keyword = *mode* or *cutoff* or *cutoff/multi* or *group* or *vel*
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* keyword = *mode* or *cutoff* or *cutoff/multi* or *multi/reduce* or *group* or *vel*
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.. parsed-literal::
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.. parsed-literal::
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*mode* value = *single* or *multi* = communicate atoms within a single or multiple distances
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*mode* value = *single*, *multi*, or *multi/old* = communicate atoms within a single or multiple distances
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*cutoff* value = Rcut (distance units) = communicate atoms from this far away
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*cutoff* value = Rcut (distance units) = communicate atoms from this far away
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*cutoff/multi* type value
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*cutoff/multi* collection value
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collection = atom collection or collection range (supports asterisk notation)
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value = Rcut (distance units) = communicate atoms for selected types from this far away
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*reduce/multi* arg = none = reduce number of communicated ghost atoms for multi style
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*cutoff/multi/old* type value
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type = atom type or type range (supports asterisk notation)
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type = atom type or type range (supports asterisk notation)
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value = Rcut (distance units) = communicate atoms for selected types from this far away
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value = Rcut (distance units) = communicate atoms for selected types from this far away
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*group* value = group-ID = only communicate atoms in the group
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*group* value = group-ID = only communicate atoms in the group
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@ -28,7 +32,7 @@ Examples
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.. code-block:: LAMMPS
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.. code-block:: LAMMPS
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comm_modify mode multi
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comm_modify mode multi reduce/multi
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comm_modify mode multi group solvent
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comm_modify mode multi group solvent
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comm_modift mode multi cutoff/multi 1 10.0 cutoff/multi 2*4 15.0
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comm_modift mode multi cutoff/multi 1 10.0 cutoff/multi 2*4 15.0
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comm_modify vel yes
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comm_modify vel yes
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@ -62,12 +66,18 @@ sub-domain. The distance is by default the maximum of the neighbor
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cutoff across all atom type pairs.
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cutoff across all atom type pairs.
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For many systems this is an efficient algorithm, but for systems with
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For many systems this is an efficient algorithm, but for systems with
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widely varying cutoffs for different type pairs, the *multi* mode can
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widely varying cutoffs for different type pairs, the *multi* or *multi/old* mode can
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be faster. In this case, each atom type is assigned its own distance
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be faster. In *multi*, each atom is assigned to a collection which should
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correspond to a set of atoms with similar interaction cutoffs.
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In this case, each atom collection is assigned its own distance
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cutoff for communication purposes, and fewer atoms will be
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cutoff for communication purposes, and fewer atoms will be
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communicated. See the :doc:`neighbor multi <neighbor>` command for a
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communicated. in *multi/old*, a similar technique is used but atoms
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neighbor list construction option that may also be beneficial for
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are grouped by atom type. See the :doc:`neighbor multi <neighbor>` and
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simulations of this kind.
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:doc:`neighbor multi/old <neighbor>` commands for
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neighbor list construction options that may also be beneficial for
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simulations of this kind. The *multi* communiction mode is only compatable
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with the *multi* neighbor style. The *multi/old* communication mode is compatble
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with both the *multi* and *multi/old* neighbor styles.
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The *cutoff* keyword allows you to extend the ghost cutoff distance
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The *cutoff* keyword allows you to extend the ghost cutoff distance
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for communication mode *single*\ , which is the distance from the borders
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for communication mode *single*\ , which is the distance from the borders
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@ -87,12 +97,26 @@ warning is printed, if this bond based estimate is larger than the
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communication cutoff used.
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communication cutoff used.
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The *cutoff/multi* option is equivalent to *cutoff*\ , but applies to
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The *cutoff/multi* option is equivalent to *cutoff*\ , but applies to
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communication mode *multi* instead. Since in this case the communication
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communication mode *multi* instead. Since the communication
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cutoffs are determined per atom type, a type specifier is needed and
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cutoffs are determined per atom collections, a collection specifier is needed and
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cutoff for one or multiple types can be extended. Also ranges of types
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cutoff for one or multiple collections can be extended. Also ranges of collections
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using the usual asterisk notation can be given. For granular pair styles,
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using the usual asterisk notation can be given.
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the default cutoff is set to the sum of the current maximum atomic radii
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Collections are indexed from 1 to N where N is the total number of collections.
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for each type.
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Note that the arguments for *cutoff/multi* are parsed right before each
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simulation to account for potential changes in the number of collections.
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Custom cutoffs are preserved between runs but if collections are redefined,
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one may want to respecify communication cutoffs.
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For granular pair styles,the default cutoff is set to the sum of the
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current maximum atomic radii for each collection.
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The *cutoff/multi/old* option is similar to *cutoff/multi* except it
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operates on atom types as opposed to collections.
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The *reduce/multi* option applies to *multi* and sets the communication
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cutoff for a particle equal to the maximum interaction distance between particles
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in the same collection. This reduces the number of
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ghost atoms that need to be communicated. This method is only compatible with the
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*multi* neighbor style and requires a half neighbor list and Newton on.
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See the :doc:`neighbor multi <neighbor>` command for more information.
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These are simulation scenarios in which it may be useful or even
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These are simulation scenarios in which it may be useful or even
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necessary to set a ghost cutoff > neighbor cutoff:
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necessary to set a ghost cutoff > neighbor cutoff:
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@ -14,7 +14,7 @@ Syntax
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.. parsed-literal::
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.. parsed-literal::
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keyword = *delay* or *every* or *check* or *once* or *cluster* or *include* or *exclude* or *page* or *one* or *binsize*
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keyword = *delay* or *every* or *check* or *once* or *cluster* or *include* or *exclude* or *page* or *one* or *binsize* or *collection/type* or *collection/interval*
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*delay* value = N
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*delay* value = N
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N = delay building until this many steps since last build
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N = delay building until this many steps since last build
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*every* value = M
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*every* value = M
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@ -47,6 +47,12 @@ Syntax
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N = max number of neighbors of one atom
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N = max number of neighbors of one atom
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*binsize* value = size
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*binsize* value = size
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size = bin size for neighbor list construction (distance units)
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size = bin size for neighbor list construction (distance units)
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*collection/type* values = N arg1 ... argN
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N = number of custom collections
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arg = N separate lists of types (see below)
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*collection/interval* values = N arg1 ... argN
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N = number of custom collections
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arg = N separate cutoffs for intervals (see below)
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Examples
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Examples
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""""""""
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""""""""
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@ -58,6 +64,8 @@ Examples
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neigh_modify exclude group frozen frozen check no
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neigh_modify exclude group frozen frozen check no
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neigh_modify exclude group residue1 chain3
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neigh_modify exclude group residue1 chain3
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neigh_modify exclude molecule/intra rigid
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neigh_modify exclude molecule/intra rigid
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neigh_modify collection/type 2 1*2,5 3*4
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neigh_modify collection/interval 2 1.0 10.0
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Description
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Description
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"""""""""""
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"""""""""""
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@ -188,8 +196,9 @@ atom can have.
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The *binsize* option allows you to specify what size of bins will be
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The *binsize* option allows you to specify what size of bins will be
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used in neighbor list construction to sort and find neighboring atoms.
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used in neighbor list construction to sort and find neighboring atoms.
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By default, for :doc:`neighbor style bin <neighbor>`, LAMMPS uses bins
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By default, for :doc:`neighbor style bin <neighbor>`, LAMMPS uses bins
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that are 1/2 the size of the maximum pair cutoff. For :doc:`neighbor style multi <neighbor>`, the bins are 1/2 the size of the minimum pair
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that are 1/2 the size of the maximum pair cutoff. For :doc:`neighbor style multi <neighbor>`,
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cutoff. Typically these are good values for minimizing the time for
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the bins are 1/2 the size of the collection interaction cutoff.
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Typically these are good values for minimizing the time for
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neighbor list construction. This setting overrides the default.
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neighbor list construction. This setting overrides the default.
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If you make it too big, there is little overhead due to
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If you make it too big, there is little overhead due to
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looping over bins, but more atoms are checked. If you make it too
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looping over bins, but more atoms are checked. If you make it too
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@ -197,6 +206,30 @@ small, the optimal number of atoms is checked, but bin overhead goes
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up. If you set the binsize to 0.0, LAMMPS will use the default
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up. If you set the binsize to 0.0, LAMMPS will use the default
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binsize of 1/2 the cutoff.
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binsize of 1/2 the cutoff.
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The *collection/type* option allows you to define collections of atom
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types, used by the *multi* neighbor mode. By grouping atom types with
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similar physical size or interaction cutoff lengths, one may be able
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to improve performance by reducing
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overhead. You must first specify the number of collections N to be
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defined followed by N lists of types. Each list consists of a series of type
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ranges separated by commas. The range can be specified as a
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single numeric value, or a wildcard asterisk can be used to specify a range
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of values. This takes the form "\*" or "\*n" or "n\*" or "m\*n". For
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example, if M = the number of atom types, then an asterisk with no numeric
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values means all types from 1 to M. A leading asterisk means all types
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from 1 to n (inclusive). A trailing asterisk means all types from n to M
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(inclusive). A middle asterisk means all types from m to n (inclusive).
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Note that all atom types must be included in exactly one of the N collections.
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The *collection/interval* option provides a similar capability.
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This command allows a user to define collections by specifying a
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series of cutoff intervals. LAMMPS will automatically sort atoms into these intervals
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based on their type-dependent cutoffs or their finite size.
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You must first specify the number of collections N to be
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defined followed by N values representing the upper cutoff of each interval.
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This command is particularly useful for granular pairstyles where the interaction distance
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of particles depends on their radius and may not depend on their atom type.
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Restrictions
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Restrictions
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""""""""""""
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""""""""""""
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@ -11,7 +11,7 @@ Syntax
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neighbor skin style
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neighbor skin style
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* skin = extra distance beyond force cutoff (distance units)
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* skin = extra distance beyond force cutoff (distance units)
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* style = *bin* or *nsq* or *multi*
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* style = *bin* or *nsq* or *multi* or *multi/old*
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Examples
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Examples
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""""""""
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""""""""
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@ -55,14 +55,31 @@ For the *bin* style, the bin size is set to 1/2 of
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the largest cutoff distance between any pair of atom types and a
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the largest cutoff distance between any pair of atom types and a
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single set of bins is defined to search over for all atom types. This
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single set of bins is defined to search over for all atom types. This
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can be inefficient if one pair of types has a very long cutoff, but
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can be inefficient if one pair of types has a very long cutoff, but
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other type pairs have a much shorter cutoff. For style *multi* the
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other type pairs have a much shorter cutoff. The *multi* style uses
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bin size is set to 1/2 of the shortest cutoff distance and multiple
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different sized bins for collections of different sized particles, where
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sets of bins are defined to search over for different atom types.
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"size" may mean the physical size of the particle or its cutoff
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distance for interacting with other particles. Different
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sets of bins are then used to construct the neighbor lists as as further
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described by Shire, Hanley, and Stratford :ref:`(Shire) <bytype-Shire>`.
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This imposes some extra setup overhead, but the searches themselves
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This imposes some extra setup overhead, but the searches themselves
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may be much faster for the short-cutoff cases.
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may be much faster. By default, each atom type defines a separate
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See the :doc:`comm_modify mode multi <comm_modify>` command for a
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collection of particles. For systems where two or more atom types
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communication option that may also be beneficial for simulations of
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have the same size (either physical size or cutoff distance), the
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this kind.
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definition of collections can be customized, which can result in less
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overhead and faster performance. See the :doc:`neigh_modify <neigh_modify>`
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command for how to define custom collections. Whether the collection
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definition is customized or not, also see the
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:doc:`comm_modify mode multi <comm_modify>` command for communication
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options that further improve performance in a manner consistent with
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neighbor style multi.
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An alternate style, *multi/old*, sets the bin size to 1/2 of the shortest
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cutoff distance and multiple sets of bins are defined to search over for
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different atom types. This algorithm used to be the default *multi*
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algorithm in LAMMPS but was found to be significantly slower than the new
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approach. For now we are keeping the old option in case there are use cases
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where multi/old outperforms the new multi style.
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The :doc:`neigh_modify <neigh_modify>` command has additional options
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The :doc:`neigh_modify <neigh_modify>` command has additional options
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that control how often neighbor lists are built and which pairs are
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that control how often neighbor lists are built and which pairs are
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@ -90,3 +107,9 @@ Default
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| 0.001 bin for units = si, skin = 0.001 meters = 1.0 mm
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| 0.001 bin for units = si, skin = 0.001 meters = 1.0 mm
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| 0.1 bin for units = cgs, skin = 0.1 cm = 1.0 mm
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| 0.1 bin for units = cgs, skin = 0.1 cm = 1.0 mm
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----------
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.. _bytype-Shire:
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**(Shire)** Shire, Hanley and Stratford, Comp Part Mech, (2020).
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@ -86,7 +86,7 @@ pair_style gran/hertz/history &
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${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
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${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
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pair_coeff * *
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pair_coeff * *
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neighbor ${skin} bin
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neighbor ${skin} multi
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thermo ${logfreq}
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thermo ${logfreq}
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comm_style brick
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comm_style brick
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@ -49,7 +49,7 @@ pair_style gran/hertz/history &
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${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
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${kn} ${kt} ${gamma_n} ${gamma_t} ${coeffFric} 1
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pair_coeff * *
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pair_coeff * *
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neighbor ${skin} bin
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neighbor ${skin} multi
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thermo ${logfreq}
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thermo ${logfreq}
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comm_style brick
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comm_style brick
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20015
examples/multi/data.powerlaw
Normal file
20015
examples/multi/data.powerlaw
Normal file
File diff suppressed because it is too large
Load Diff
67
examples/multi/in.colloid
Normal file
67
examples/multi/in.colloid
Normal file
@ -0,0 +1,67 @@
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# Big colloid particles and small LJ particles
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units lj
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atom_style sphere
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dimension 2
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lattice sq 0.1
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region box block 0 60 0 60 -0.5 0.5
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create_box 5 box
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create_atoms 1 box
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#Roughly equally partition atoms between types 1-4
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set group all type/fraction 2 0.500 23984
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set group all type/fraction 3 0.333 43684
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set group all type/fraction 4 0.250 87811
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# remove two spheres of small particles and add large particles in the voids
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region sphere1 sphere 60.0 60.0 0.0 30.0 units box
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region sphere2 sphere 130.0 130.0 0.0 30.0 units box
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delete_atoms region sphere1
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delete_atoms region sphere2
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create_atoms 5 single 60.0 60.0 0.0 units box
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create_atoms 5 single 130.0 130.0 0.0 units box
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set type 1 mass 400
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set type 2 mass 1
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velocity all create 1.44 87287 loop geom
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# multi neighbor and comm for efficiency
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neighbor 1 multi #multi/old
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neigh_modify delay 0 collection/type 2 1*4 5
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comm_modify mode multi reduce/multi #multi/old
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# colloid potential
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pair_style colloid 20.0
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pair_coeff * * 144.0 1.0 0.0 0.0 3.0
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pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0
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pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0
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pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0
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pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0
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pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0
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fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 &
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mtk no pchain 0 tchain 1
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fix 2 all enforce2d
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#dump 1 all atom 1000 dump.colloid
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#dump 2 all image 1000 image.*.jpg type type &
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# zoom 1.5 center d 0.5 0.5 0.5
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#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
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#dump 3 all movie 1000 movie.mpg type type &
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# zoom 1.5 center d 0.5 0.5 0.5
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#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
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thermo_style custom step temp epair etotal press vol
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thermo 100
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timestep 0.005
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||||||
|
|
||||||
|
run 2000
|
||||||
50
examples/multi/in.granular
Normal file
50
examples/multi/in.granular
Normal file
@ -0,0 +1,50 @@
|
|||||||
|
# Big colloid particles and small LJ particles
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style sphere
|
||||||
|
dimension 2
|
||||||
|
|
||||||
|
lattice sq 0.5
|
||||||
|
region box block 0 60 0 60 -0.5 0.5
|
||||||
|
create_box 2 box
|
||||||
|
create_atoms 1 box
|
||||||
|
change_box all triclinic
|
||||||
|
|
||||||
|
# remove two spheres of small particles and add large particles in the voids
|
||||||
|
region sphere1 sphere 20.0 20.0 0.0 10.0 units box
|
||||||
|
region sphere2 sphere 60.0 60.0 0.0 10.0 units box
|
||||||
|
delete_atoms region sphere1
|
||||||
|
delete_atoms region sphere2
|
||||||
|
create_atoms 2 single 20.0 20.0 0.0 units box
|
||||||
|
create_atoms 2 single 60.0 60.0 0.0 units box
|
||||||
|
|
||||||
|
set type 2 mass 400
|
||||||
|
set type 1 mass 1
|
||||||
|
set type 2 diameter 20
|
||||||
|
set type 1 diameter 1
|
||||||
|
|
||||||
|
velocity all create 1.44 87287 loop geom
|
||||||
|
|
||||||
|
# multi neighbor and comm for efficiency
|
||||||
|
|
||||||
|
neighbor 1 multi #multi/old
|
||||||
|
neigh_modify delay 0 collection/interval 2 1 20
|
||||||
|
comm_modify mode multi vel yes reduce/multi #multi/old
|
||||||
|
|
||||||
|
# granular potential
|
||||||
|
|
||||||
|
pair_style granular
|
||||||
|
pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity
|
||||||
|
|
||||||
|
fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0
|
||||||
|
fix 2 all enforce2d
|
||||||
|
fix 3 all deform 1 xy erate 1e-3
|
||||||
|
|
||||||
|
#dump 1 all custom 1000 dump.granular id x y z radius
|
||||||
|
|
||||||
|
thermo_style custom step temp epair etotal press vol
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
timestep 0.005
|
||||||
|
|
||||||
|
run 2000
|
||||||
33
examples/multi/in.powerlaw
Normal file
33
examples/multi/in.powerlaw
Normal file
@ -0,0 +1,33 @@
|
|||||||
|
# Shear power-law distributed granular particles
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style sphere
|
||||||
|
dimension 2
|
||||||
|
read_data data.powerlaw
|
||||||
|
change_box all triclinic
|
||||||
|
|
||||||
|
# multi neighbor and comm for efficiency
|
||||||
|
|
||||||
|
neighbor 1 multi
|
||||||
|
neigh_modify delay 0 collection/interval 6 1.5 3 10 30 100 200
|
||||||
|
comm_modify mode multi vel yes reduce/multi
|
||||||
|
|
||||||
|
# granular potential
|
||||||
|
|
||||||
|
pair_style granular
|
||||||
|
pair_coeff * * hooke 20.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity
|
||||||
|
|
||||||
|
# fixes
|
||||||
|
|
||||||
|
fix 1 all nve/sphere
|
||||||
|
fix 2 all enforce2d
|
||||||
|
fix 3 all deform 1 xy erate 1e-4
|
||||||
|
|
||||||
|
# dump 1 all custom 20000 dump.granular id x y z radius
|
||||||
|
|
||||||
|
thermo_style custom step temp epair etotal press vol pxy
|
||||||
|
thermo 100
|
||||||
|
|
||||||
|
timestep 0.005
|
||||||
|
|
||||||
|
run 1000
|
||||||
183
examples/multi/log.30Nov20.colloid.intel.1
Normal file
183
examples/multi/log.30Nov20.colloid.intel.1
Normal file
@ -0,0 +1,183 @@
|
|||||||
|
LAMMPS (24 Dec 2020)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Big colloid particles and small LJ particles
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style sphere
|
||||||
|
dimension 2
|
||||||
|
|
||||||
|
lattice sq 0.1
|
||||||
|
Lattice spacing in x,y,z = 3.1622777 3.1622777 3.1622777
|
||||||
|
region box block 0 60 0 60 -0.5 0.5
|
||||||
|
create_box 5 box
|
||||||
|
Created orthogonal box = (0.0000000 0.0000000 -1.5811388) to (189.73666 189.73666 1.5811388)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 3600 atoms
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
|
||||||
|
#Roughly equally partition atoms between types 1-4
|
||||||
|
set group all type/fraction 2 0.500 23984
|
||||||
|
Setting atom values ...
|
||||||
|
1768 settings made for type/fraction
|
||||||
|
set group all type/fraction 3 0.333 43684
|
||||||
|
Setting atom values ...
|
||||||
|
1255 settings made for type/fraction
|
||||||
|
set group all type/fraction 4 0.250 87811
|
||||||
|
Setting atom values ...
|
||||||
|
927 settings made for type/fraction
|
||||||
|
|
||||||
|
# remove two spheres of small particles and add large particles in the voids
|
||||||
|
region sphere1 sphere 60.0 60.0 0.0 30.0 units box
|
||||||
|
region sphere2 sphere 130.0 130.0 0.0 30.0 units box
|
||||||
|
delete_atoms region sphere1
|
||||||
|
Deleted 289 atoms, new total = 3311
|
||||||
|
delete_atoms region sphere2
|
||||||
|
Deleted 287 atoms, new total = 3024
|
||||||
|
create_atoms 5 single 60.0 60.0 0.0 units box
|
||||||
|
Created 1 atoms
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
create_atoms 5 single 130.0 130.0 0.0 units box
|
||||||
|
Created 1 atoms
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
|
set type 1 mass 400
|
||||||
|
Setting atom values ...
|
||||||
|
753 settings made for mass
|
||||||
|
set type 2 mass 1
|
||||||
|
Setting atom values ...
|
||||||
|
722 settings made for mass
|
||||||
|
|
||||||
|
velocity all create 1.44 87287 loop geom
|
||||||
|
|
||||||
|
# multi neighbor and comm for efficiency
|
||||||
|
|
||||||
|
neighbor 1 multi #multi/old
|
||||||
|
neigh_modify delay 0 collection/type 2 1*4 5
|
||||||
|
comm_modify mode multi reduce/multi #multi/old
|
||||||
|
|
||||||
|
# colloid potential
|
||||||
|
|
||||||
|
pair_style colloid 20.0
|
||||||
|
pair_coeff * * 144.0 1.0 0.0 0.0 3.0
|
||||||
|
pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0
|
||||||
|
pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0
|
||||||
|
pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0
|
||||||
|
pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0
|
||||||
|
pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1
|
||||||
|
fix 2 all enforce2d
|
||||||
|
|
||||||
|
#dump 1 all atom 1000 dump.colloid
|
||||||
|
|
||||||
|
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
|
||||||
|
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
|
||||||
|
|
||||||
|
#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5
|
||||||
|
#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
|
||||||
|
|
||||||
|
thermo_style custom step temp epair etotal press vol
|
||||||
|
thermo 1000
|
||||||
|
|
||||||
|
timestep 0.005
|
||||||
|
|
||||||
|
run 50000
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 31
|
||||||
|
ghost atom cutoff = 31
|
||||||
|
binsize = 2, bins = 95 95 2
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair colloid, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/multi/newton
|
||||||
|
stencil: half/multi/2d
|
||||||
|
bin: multi
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 4.385 | 4.385 | 4.385 Mbytes
|
||||||
|
Step Temp E_pair TotEng Press Volume
|
||||||
|
0 1.44 0 1.4395241 0.121 36000
|
||||||
|
1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399
|
||||||
|
2000 1.8589993 -0.11434676 1.7440382 0.097157151 58590.69
|
||||||
|
3000 1.8984314 -0.093445816 1.8043582 0.07444246 77824.12
|
||||||
|
4000 1.9603204 -0.07451891 1.8851536 0.066010381 90951.299
|
||||||
|
5000 2.0298924 -0.073898174 1.9553234 0.075791214 90146.92
|
||||||
|
6000 2.0797015 -0.086800285 1.992214 0.082095164 78182.702
|
||||||
|
7000 2.0867886 -0.10960963 1.9764893 0.10103655 63990.386
|
||||||
|
8000 2.0803886 -0.12736298 1.9523381 0.12561727 52648.372
|
||||||
|
9000 2.0605661 -0.14572043 1.9141648 0.15154081 44589.764
|
||||||
|
10000 2.0636909 -0.18556771 1.8774412 0.1604707 38996.941
|
||||||
|
11000 2.0498344 -0.20303461 1.8461224 0.18295046 34927.993
|
||||||
|
12000 2.0466611 -0.2217963 1.8241884 0.23031182 31760.363
|
||||||
|
13000 2.0441824 -0.24716826 1.7963386 0.22167931 29178.226
|
||||||
|
14000 2.047513 -0.26988172 1.7769547 0.24070752 26991.372
|
||||||
|
15000 2.0154283 -0.26144354 1.7533187 0.27587713 25247.715
|
||||||
|
16000 2.0160849 -0.28106984 1.7343488 0.32297139 23703.607
|
||||||
|
17000 2.0184729 -0.31071368 1.7070922 0.29815613 22300.6
|
||||||
|
18000 2.0237288 -0.33944941 1.6836106 0.3262795 21098.856
|
||||||
|
19000 2.0329827 -0.35438937 1.6779215 0.33691952 19989.867
|
||||||
|
20000 2.021113 -0.37316841 1.6472766 0.39687648 18978.666
|
||||||
|
21000 2.0352439 -0.40857976 1.6259915 0.38632613 18146.277
|
||||||
|
22000 2.0158566 -0.41271329 1.6024771 0.41480502 17409.593
|
||||||
|
23000 2.0170409 -0.42611776 1.5902566 0.40446612 16748.968
|
||||||
|
24000 2.0108878 -0.43899286 1.5712304 0.42075035 16086.941
|
||||||
|
25000 2.0218394 -0.47012156 1.5510497 0.46655183 15460.154
|
||||||
|
26000 2.0100713 -0.47985916 1.5295479 0.45575323 15013.774
|
||||||
|
27000 2.0251738 -0.5016665 1.5228381 0.50151992 14591.521
|
||||||
|
28000 2.0062966 -0.50284394 1.5027897 0.5462034 14135.093
|
||||||
|
29000 2.0146666 -0.53126035 1.4827405 0.60379062 13725.945
|
||||||
|
30000 2.0036455 -0.53246643 1.4705169 0.56784088 13417.305
|
||||||
|
31000 2.0127662 -0.54487777 1.4672233 0.6427741 13139.392
|
||||||
|
32000 2.0221816 -0.5625554 1.4589579 0.60695012 12779.609
|
||||||
|
33000 2.024983 -0.59515221 1.4291616 0.60005385 12584.572
|
||||||
|
34000 2.0184045 -0.59033569 1.4274018 0.62519753 12355.49
|
||||||
|
35000 2.0155635 -0.61190466 1.4029927 0.71044196 12106.819
|
||||||
|
36000 2.0252503 -0.61581601 1.408765 0.68805882 11728.608
|
||||||
|
37000 2.0112487 -0.64540754 1.3651765 0.66981639 11475.772
|
||||||
|
38000 2.0147475 -0.64161981 1.3724619 0.71130901 11285.511
|
||||||
|
39000 2.0213092 -0.67174661 1.3488946 0.6969697 11044.647
|
||||||
|
40000 2.0178739 -0.67924699 1.3379601 0.77309897 10824.198
|
||||||
|
41000 1.9952353 -0.67490899 1.3196669 0.76592358 10646.649
|
||||||
|
42000 2.002415 -0.70533555 1.2964178 0.81084741 10519.804
|
||||||
|
43000 2.0211625 -0.71370366 1.3067909 0.77355048 10434.893
|
||||||
|
44000 2.0252106 -0.72635544 1.2981859 0.83770143 10132.262
|
||||||
|
45000 2.0126446 -0.75197714 1.2600024 0.88927993 9946.7842
|
||||||
|
46000 2.0431159 -0.78445975 1.257981 0.84492327 9869.8151
|
||||||
|
47000 2.0199724 -0.76967899 1.2496259 0.90977181 9653.4334
|
||||||
|
48000 2.0109636 -0.78968551 1.2206135 0.89458323 9496.7246
|
||||||
|
49000 2.0131059 -0.79687252 1.2155681 0.91239613 9418.3093
|
||||||
|
50000 2.0073361 -0.79981468 1.206858 0.98524334 9289.4715
|
||||||
|
Loop time of 19.7532 on 1 procs for 50000 steps with 3026 atoms
|
||||||
|
|
||||||
|
Performance: 1093493.133 tau/day, 2531.234 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 | 10.789 | 10.789 | 10.789 | 0.0 | 54.62
|
||||||
|
Neigh | 2.6848 | 2.6848 | 2.6848 | 0.0 | 13.59
|
||||||
|
Comm | 0.53244 | 0.53244 | 0.53244 | 0.0 | 2.70
|
||||||
|
Output | 0.0010482 | 0.0010482 | 0.0010482 | 0.0 | 0.01
|
||||||
|
Modify | 4.9599 | 4.9599 | 4.9599 | 0.0 | 25.11
|
||||||
|
Other | | 0.7856 | | | 3.98
|
||||||
|
|
||||||
|
Nlocal: 3026.00 ave 3026 max 3026 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 584.000 ave 584 max 584 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 25892.0 ave 25892 max 25892 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 25892
|
||||||
|
Ave neighs/atom = 8.5565102
|
||||||
|
Neighbor list builds = 4330
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Please see the log.cite file for references relevant to this simulation
|
||||||
|
|
||||||
|
Total wall time: 0:00:19
|
||||||
183
examples/multi/log.30Nov20.colloid.intel.4
Normal file
183
examples/multi/log.30Nov20.colloid.intel.4
Normal file
@ -0,0 +1,183 @@
|
|||||||
|
LAMMPS (24 Dec 2020)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Big colloid particles and small LJ particles
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style sphere
|
||||||
|
dimension 2
|
||||||
|
|
||||||
|
lattice sq 0.1
|
||||||
|
Lattice spacing in x,y,z = 3.1622777 3.1622777 3.1622777
|
||||||
|
region box block 0 60 0 60 -0.5 0.5
|
||||||
|
create_box 5 box
|
||||||
|
Created orthogonal box = (0.0000000 0.0000000 -1.5811388) to (189.73666 189.73666 1.5811388)
|
||||||
|
2 by 2 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 3600 atoms
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
|
||||||
|
#Roughly equally partition atoms between types 1-4
|
||||||
|
set group all type/fraction 2 0.500 23984
|
||||||
|
Setting atom values ...
|
||||||
|
1768 settings made for type/fraction
|
||||||
|
set group all type/fraction 3 0.333 43684
|
||||||
|
Setting atom values ...
|
||||||
|
1255 settings made for type/fraction
|
||||||
|
set group all type/fraction 4 0.250 87811
|
||||||
|
Setting atom values ...
|
||||||
|
927 settings made for type/fraction
|
||||||
|
|
||||||
|
# remove two spheres of small particles and add large particles in the voids
|
||||||
|
region sphere1 sphere 60.0 60.0 0.0 30.0 units box
|
||||||
|
region sphere2 sphere 130.0 130.0 0.0 30.0 units box
|
||||||
|
delete_atoms region sphere1
|
||||||
|
Deleted 289 atoms, new total = 3311
|
||||||
|
delete_atoms region sphere2
|
||||||
|
Deleted 287 atoms, new total = 3024
|
||||||
|
create_atoms 5 single 60.0 60.0 0.0 units box
|
||||||
|
Created 1 atoms
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
create_atoms 5 single 130.0 130.0 0.0 units box
|
||||||
|
Created 1 atoms
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
|
set type 1 mass 400
|
||||||
|
Setting atom values ...
|
||||||
|
753 settings made for mass
|
||||||
|
set type 2 mass 1
|
||||||
|
Setting atom values ...
|
||||||
|
722 settings made for mass
|
||||||
|
|
||||||
|
velocity all create 1.44 87287 loop geom
|
||||||
|
|
||||||
|
# multi neighbor and comm for efficiency
|
||||||
|
|
||||||
|
neighbor 1 multi #multi/old
|
||||||
|
neigh_modify delay 0 collection/type 2 1*4 5
|
||||||
|
comm_modify mode multi reduce/multi #multi/old
|
||||||
|
|
||||||
|
# colloid potential
|
||||||
|
|
||||||
|
pair_style colloid 20.0
|
||||||
|
pair_coeff * * 144.0 1.0 0.0 0.0 3.0
|
||||||
|
pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0
|
||||||
|
pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0
|
||||||
|
pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0
|
||||||
|
pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0
|
||||||
|
pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1
|
||||||
|
fix 2 all enforce2d
|
||||||
|
|
||||||
|
#dump 1 all atom 1000 dump.colloid
|
||||||
|
|
||||||
|
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
|
||||||
|
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
|
||||||
|
|
||||||
|
#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5
|
||||||
|
#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
|
||||||
|
|
||||||
|
thermo_style custom step temp epair etotal press vol
|
||||||
|
thermo 1000
|
||||||
|
|
||||||
|
timestep 0.005
|
||||||
|
|
||||||
|
run 50000
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 31
|
||||||
|
ghost atom cutoff = 31
|
||||||
|
binsize = 2, bins = 95 95 2
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair colloid, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/multi/newton
|
||||||
|
stencil: half/multi/2d
|
||||||
|
bin: multi
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 4.327 | 4.329 | 4.330 Mbytes
|
||||||
|
Step Temp E_pair TotEng Press Volume
|
||||||
|
0 1.44 0 1.4395241 0.121 36000
|
||||||
|
1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399
|
||||||
|
2000 1.8590154 -0.11436231 1.7440387 0.097150798 58590.688
|
||||||
|
3000 1.8956738 -0.090814176 1.8042332 0.075557943 77825.289
|
||||||
|
4000 1.9570462 -0.072505537 1.8838939 0.072824365 90931.708
|
||||||
|
5000 2.0376745 -0.083247829 1.9537533 0.068496975 90055.295
|
||||||
|
6000 2.0744887 -0.085395371 1.9884077 0.0821927 78070.648
|
||||||
|
7000 2.1002183 -0.11654617 1.9829781 0.10523249 63934.448
|
||||||
|
8000 2.0818325 -0.13271654 1.948428 0.11909162 52636.484
|
||||||
|
9000 2.0693987 -0.16404154 1.9046733 0.14702552 44539.609
|
||||||
|
10000 2.0667772 -0.19779488 1.8682993 0.17245383 38822.542
|
||||||
|
11000 2.0640582 -0.22114917 1.842227 0.18083079 34788.927
|
||||||
|
12000 2.0308462 -0.20353105 1.8266441 0.20640739 31706.009
|
||||||
|
13000 2.0395895 -0.24217765 1.7967378 0.21832952 29152.654
|
||||||
|
14000 2.030848 -0.2586169 1.77156 0.26577748 27068.89
|
||||||
|
15000 2.0222966 -0.27554585 1.7460825 0.2777169 25272.786
|
||||||
|
16000 2.0398867 -0.31547563 1.723737 0.27763622 23666.792
|
||||||
|
17000 2.03026 -0.32453791 1.7050512 0.28099246 22272.809
|
||||||
|
18000 2.0345512 -0.35026242 1.6836164 0.36600779 21023.172
|
||||||
|
19000 2.0242864 -0.35813231 1.6654851 0.33415432 19941.244
|
||||||
|
20000 2.0132465 -0.36563904 1.6469422 0.403365 18979.884
|
||||||
|
21000 2.0280384 -0.4075867 1.6197815 0.37205362 18152.487
|
||||||
|
22000 2.0206494 -0.40600336 1.6139782 0.42704594 17370.812
|
||||||
|
23000 2.0395761 -0.45083258 1.5880695 0.40276343 16700.427
|
||||||
|
24000 2.017203 -0.44930293 1.5672335 0.43867313 16161.79
|
||||||
|
25000 2.0191846 -0.4672218 1.5512955 0.47031215 15622.756
|
||||||
|
26000 2.0131624 -0.46436088 1.5481363 0.51717944 15141.645
|
||||||
|
27000 2.0322461 -0.50659994 1.5249745 0.49218933 14627.657
|
||||||
|
28000 2.0169304 -0.50555565 1.5107082 0.55547935 14186.079
|
||||||
|
29000 2.024656 -0.52258414 1.5014028 0.59125812 13759.99
|
||||||
|
30000 2.0153725 -0.53585947 1.478847 0.57235811 13384.355
|
||||||
|
31000 2.0163261 -0.56383766 1.4518221 0.58232057 13098.196
|
||||||
|
32000 2.0109673 -0.56784395 1.4424588 0.58282178 12831.934
|
||||||
|
33000 2.0099169 -0.57625621 1.4329964 0.65139601 12479.442
|
||||||
|
34000 2.0238152 -0.60189607 1.4212503 0.62659152 12210.628
|
||||||
|
35000 2.0359989 -0.62654733 1.4087787 0.67574446 11972.725
|
||||||
|
36000 2.0222689 -0.62880837 1.3927923 0.66602146 11690.049
|
||||||
|
37000 1.9982569 -0.62746376 1.3701328 0.71326589 11433.825
|
||||||
|
38000 1.9969836 -0.63975181 1.3565719 0.72799891 11285.497
|
||||||
|
39000 2.0071087 -0.65781805 1.3486274 0.79121297 11107.469
|
||||||
|
40000 2.0243046 -0.6881221 1.3355135 0.77519099 10943.846
|
||||||
|
41000 2.0351657 -0.70309175 1.3314014 0.68815156 10742.515
|
||||||
|
42000 2.0224788 -0.70975664 1.3120538 0.80484619 10505.657
|
||||||
|
43000 2.0123135 -0.70818545 1.3034631 0.84204556 10353.024
|
||||||
|
44000 1.999883 -0.70981202 1.2894101 0.94070546 10212.224
|
||||||
|
45000 2.0127291 -0.73338075 1.2786832 0.82095205 10109.959
|
||||||
|
46000 2.0109037 -0.75130029 1.2589389 0.88538358 9953.4822
|
||||||
|
47000 1.9879175 -0.73152019 1.2557404 0.92089629 9832.892
|
||||||
|
48000 2.0108204 -0.76655178 1.2436041 0.95379465 9633.6453
|
||||||
|
49000 1.9868193 -0.76613798 1.2200247 0.88790224 9504.2918
|
||||||
|
50000 2.0141467 -0.80029827 1.2131829 1.0064263 9346.3268
|
||||||
|
Loop time of 6.98615 on 4 procs for 50000 steps with 3026 atoms
|
||||||
|
|
||||||
|
Performance: 3091831.080 tau/day, 7157.016 timesteps/s
|
||||||
|
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 2.2795 | 2.5856 | 2.9414 | 17.4 | 37.01
|
||||||
|
Neigh | 0.62273 | 0.70156 | 0.76736 | 7.4 | 10.04
|
||||||
|
Comm | 1.0765 | 1.4945 | 1.8884 | 28.6 | 21.39
|
||||||
|
Output | 0.00076496 | 0.0008953 | 0.0012832 | 0.0 | 0.01
|
||||||
|
Modify | 1.718 | 1.7755 | 1.827 | 3.7 | 25.41
|
||||||
|
Other | | 0.4281 | | | 6.13
|
||||||
|
|
||||||
|
Nlocal: 756.500 ave 839 max 673 min
|
||||||
|
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||||
|
Nghost: 292.500 ave 307 max 282 min
|
||||||
|
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||||
|
Neighs: 6435.25 ave 7367 max 5493 min
|
||||||
|
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 25741
|
||||||
|
Ave neighs/atom = 8.5066094
|
||||||
|
Neighbor list builds = 4335
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Please see the log.cite file for references relevant to this simulation
|
||||||
|
|
||||||
|
Total wall time: 0:00:07
|
||||||
183
examples/multi/log.30Nov20.colloid.old.intel.1
Normal file
183
examples/multi/log.30Nov20.colloid.old.intel.1
Normal file
@ -0,0 +1,183 @@
|
|||||||
|
LAMMPS (24 Dec 2020)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Big colloid particles and small LJ particles
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style sphere
|
||||||
|
dimension 2
|
||||||
|
|
||||||
|
lattice sq 0.1
|
||||||
|
Lattice spacing in x,y,z = 3.1622777 3.1622777 3.1622777
|
||||||
|
region box block 0 60 0 60 -0.5 0.5
|
||||||
|
create_box 5 box
|
||||||
|
Created orthogonal box = (0.0000000 0.0000000 -1.5811388) to (189.73666 189.73666 1.5811388)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 3600 atoms
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
|
||||||
|
#Roughly equally partition atoms between types 1-4
|
||||||
|
set group all type/fraction 2 0.500 23984
|
||||||
|
Setting atom values ...
|
||||||
|
1768 settings made for type/fraction
|
||||||
|
set group all type/fraction 3 0.333 43684
|
||||||
|
Setting atom values ...
|
||||||
|
1255 settings made for type/fraction
|
||||||
|
set group all type/fraction 4 0.250 87811
|
||||||
|
Setting atom values ...
|
||||||
|
927 settings made for type/fraction
|
||||||
|
|
||||||
|
# remove two spheres of small particles and add large particles in the voids
|
||||||
|
region sphere1 sphere 60.0 60.0 0.0 30.0 units box
|
||||||
|
region sphere2 sphere 130.0 130.0 0.0 30.0 units box
|
||||||
|
delete_atoms region sphere1
|
||||||
|
Deleted 289 atoms, new total = 3311
|
||||||
|
delete_atoms region sphere2
|
||||||
|
Deleted 287 atoms, new total = 3024
|
||||||
|
create_atoms 5 single 60.0 60.0 0.0 units box
|
||||||
|
Created 1 atoms
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
create_atoms 5 single 130.0 130.0 0.0 units box
|
||||||
|
Created 1 atoms
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
|
set type 1 mass 400
|
||||||
|
Setting atom values ...
|
||||||
|
753 settings made for mass
|
||||||
|
set type 2 mass 1
|
||||||
|
Setting atom values ...
|
||||||
|
722 settings made for mass
|
||||||
|
|
||||||
|
velocity all create 1.44 87287 loop geom
|
||||||
|
|
||||||
|
# multi neighbor and comm for efficiency
|
||||||
|
|
||||||
|
neighbor 1 multi/old #multi
|
||||||
|
neigh_modify delay 0 #multi/custom 2 1*4 5
|
||||||
|
comm_modify mode multi/old #multi multi/reduce
|
||||||
|
|
||||||
|
# colloid potential
|
||||||
|
|
||||||
|
pair_style colloid 20.0
|
||||||
|
pair_coeff * * 144.0 1.0 0.0 0.0 3.0
|
||||||
|
pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0
|
||||||
|
pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0
|
||||||
|
pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0
|
||||||
|
pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0
|
||||||
|
pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1
|
||||||
|
fix 2 all enforce2d
|
||||||
|
|
||||||
|
#dump 1 all atom 1000 dump.colloid
|
||||||
|
|
||||||
|
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
|
||||||
|
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
|
||||||
|
|
||||||
|
#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5
|
||||||
|
#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
|
||||||
|
|
||||||
|
thermo_style custom step temp epair etotal press vol
|
||||||
|
thermo 1000
|
||||||
|
|
||||||
|
timestep 0.005
|
||||||
|
|
||||||
|
run 50000
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 31
|
||||||
|
ghost atom cutoff = 31
|
||||||
|
binsize = 2, bins = 95 95 2
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair colloid, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/multi/old/newton
|
||||||
|
stencil: half/multi/old/2d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 4.496 | 4.496 | 4.496 Mbytes
|
||||||
|
Step Temp E_pair TotEng Press Volume
|
||||||
|
0 1.44 0 1.4395241 0.121 36000
|
||||||
|
1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399
|
||||||
|
2000 1.8589993 -0.11434676 1.7440382 0.097157151 58590.69
|
||||||
|
3000 1.8984314 -0.093445816 1.8043582 0.07444246 77824.12
|
||||||
|
4000 1.9603204 -0.07451891 1.8851536 0.066010381 90951.299
|
||||||
|
5000 2.0298924 -0.073898174 1.9553234 0.075791214 90146.92
|
||||||
|
6000 2.0797015 -0.086800284 1.992214 0.082095164 78182.702
|
||||||
|
7000 2.086794 -0.10961479 1.9764895 0.10103993 63990.387
|
||||||
|
8000 2.082863 -0.12779588 1.9543788 0.12672452 52629.802
|
||||||
|
9000 2.0718275 -0.15189022 1.9192526 0.14728063 44541.722
|
||||||
|
10000 2.0603856 -0.18054161 1.8791631 0.16715133 38940.135
|
||||||
|
11000 2.046791 -0.20458359 1.841531 0.19532742 34907.116
|
||||||
|
12000 2.0406846 -0.2252868 1.8147234 0.2036178 31740.208
|
||||||
|
13000 2.0369763 -0.23721632 1.7990869 0.25542564 29079.901
|
||||||
|
14000 2.0376121 -0.26282517 1.7741135 0.24722118 26947.344
|
||||||
|
15000 2.0312772 -0.2851101 1.7454959 0.2801199 25180.963
|
||||||
|
16000 2.0080448 -0.28992973 1.7174515 0.30099318 23723.043
|
||||||
|
17000 2.0234993 -0.30440169 1.7184289 0.3193226 22342.977
|
||||||
|
18000 2.0216103 -0.32036933 1.7005729 0.3460322 21068.99
|
||||||
|
19000 2.0493952 -0.37711533 1.6716026 0.33804972 20013.325
|
||||||
|
20000 2.0307894 -0.38462795 1.6454903 0.37041981 19092.745
|
||||||
|
21000 2.0328577 -0.39442652 1.6377594 0.36327057 18260.298
|
||||||
|
22000 2.0325613 -0.40481002 1.6270796 0.42756691 17447.199
|
||||||
|
23000 2.0199358 -0.42175719 1.5975111 0.40948041 16768.71
|
||||||
|
24000 2.0149952 -0.43618764 1.5781417 0.45406069 16187.334
|
||||||
|
25000 2.0153221 -0.45884172 1.5558143 0.52717203 15605.577
|
||||||
|
26000 2.0099026 -0.47080566 1.5384327 0.49181459 15088.041
|
||||||
|
27000 2.0128537 -0.49799999 1.5141885 0.53907465 14590.392
|
||||||
|
28000 2.0287266 -0.53112525 1.4969309 0.59750714 14208.419
|
||||||
|
29000 2.0143609 -0.53175704 1.4819381 0.56118773 13840.642
|
||||||
|
30000 2.0235262 -0.53923416 1.4836234 0.52579997 13500.15
|
||||||
|
31000 2.0390444 -0.57976823 1.4586023 0.5760349 13082.091
|
||||||
|
32000 2.018046 -0.57797686 1.4394022 0.59127933 12761.726
|
||||||
|
33000 2.0059068 -0.57185148 1.4333925 0.58992758 12473.866
|
||||||
|
34000 1.9828456 -0.57147221 1.4107181 0.77593228 12208.869
|
||||||
|
35000 1.9900097 -0.58349168 1.4058604 0.681968 11937.285
|
||||||
|
36000 2.0271405 -0.64374859 1.382722 0.63152587 11675.264
|
||||||
|
37000 2.0032809 -0.63520712 1.3674117 0.71639384 11440.274
|
||||||
|
38000 2.0000566 -0.63941617 1.3599795 0.74099652 11235.252
|
||||||
|
39000 1.9872705 -0.64765522 1.3389586 0.7575743 11080.857
|
||||||
|
40000 2.0224403 -0.6795645 1.3422075 0.82918546 10861.905
|
||||||
|
41000 2.0137595 -0.69863075 1.3144633 0.80397759 10712.981
|
||||||
|
42000 1.9950915 -0.68892531 1.3055069 0.77631365 10632.931
|
||||||
|
43000 2.0080851 -0.70534369 1.3020778 0.82408436 10408.82
|
||||||
|
44000 2.0239806 -0.73189482 1.2914169 0.83228695 10227.18
|
||||||
|
45000 2.0019542 -0.72613202 1.2751606 0.9145618 10044.013
|
||||||
|
46000 2.0173095 -0.75370218 1.2629407 0.99791312 9837.9611
|
||||||
|
47000 1.9921201 -0.75875076 1.232711 1.0047839 9711.2083
|
||||||
|
48000 2.0283587 -0.79063641 1.237052 0.83617499 9610.9933
|
||||||
|
49000 2.0051919 -0.79078067 1.2137485 0.95651813 9411.7165
|
||||||
|
50000 2.0140985 -0.81796958 1.1954634 0.93791038 9296.069
|
||||||
|
Loop time of 28.5339 on 1 procs for 50000 steps with 3026 atoms
|
||||||
|
|
||||||
|
Performance: 756994.490 tau/day, 1752.302 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 | 10.918 | 10.918 | 10.918 | 0.0 | 38.26
|
||||||
|
Neigh | 10.375 | 10.375 | 10.375 | 0.0 | 36.36
|
||||||
|
Comm | 1.2856 | 1.2856 | 1.2856 | 0.0 | 4.51
|
||||||
|
Output | 0.0010955 | 0.0010955 | 0.0010955 | 0.0 | 0.00
|
||||||
|
Modify | 5.0132 | 5.0132 | 5.0132 | 0.0 | 17.57
|
||||||
|
Other | | 0.9412 | | | 3.30
|
||||||
|
|
||||||
|
Nlocal: 3026.00 ave 3026 max 3026 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 2292.00 ave 2292 max 2292 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 25767.0 ave 25767 max 25767 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 25767
|
||||||
|
Ave neighs/atom = 8.5152016
|
||||||
|
Neighbor list builds = 4332
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Please see the log.cite file for references relevant to this simulation
|
||||||
|
|
||||||
|
Total wall time: 0:00:28
|
||||||
183
examples/multi/log.30Nov20.colloid.old.intel.4
Normal file
183
examples/multi/log.30Nov20.colloid.old.intel.4
Normal file
@ -0,0 +1,183 @@
|
|||||||
|
LAMMPS (24 Dec 2020)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Big colloid particles and small LJ particles
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style sphere
|
||||||
|
dimension 2
|
||||||
|
|
||||||
|
lattice sq 0.1
|
||||||
|
Lattice spacing in x,y,z = 3.1622777 3.1622777 3.1622777
|
||||||
|
region box block 0 60 0 60 -0.5 0.5
|
||||||
|
create_box 5 box
|
||||||
|
Created orthogonal box = (0.0000000 0.0000000 -1.5811388) to (189.73666 189.73666 1.5811388)
|
||||||
|
2 by 2 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 3600 atoms
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
|
||||||
|
#Roughly equally partition atoms between types 1-4
|
||||||
|
set group all type/fraction 2 0.500 23984
|
||||||
|
Setting atom values ...
|
||||||
|
1768 settings made for type/fraction
|
||||||
|
set group all type/fraction 3 0.333 43684
|
||||||
|
Setting atom values ...
|
||||||
|
1255 settings made for type/fraction
|
||||||
|
set group all type/fraction 4 0.250 87811
|
||||||
|
Setting atom values ...
|
||||||
|
927 settings made for type/fraction
|
||||||
|
|
||||||
|
# remove two spheres of small particles and add large particles in the voids
|
||||||
|
region sphere1 sphere 60.0 60.0 0.0 30.0 units box
|
||||||
|
region sphere2 sphere 130.0 130.0 0.0 30.0 units box
|
||||||
|
delete_atoms region sphere1
|
||||||
|
Deleted 289 atoms, new total = 3311
|
||||||
|
delete_atoms region sphere2
|
||||||
|
Deleted 287 atoms, new total = 3024
|
||||||
|
create_atoms 5 single 60.0 60.0 0.0 units box
|
||||||
|
Created 1 atoms
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
create_atoms 5 single 130.0 130.0 0.0 units box
|
||||||
|
Created 1 atoms
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
|
set type 1 mass 400
|
||||||
|
Setting atom values ...
|
||||||
|
753 settings made for mass
|
||||||
|
set type 2 mass 1
|
||||||
|
Setting atom values ...
|
||||||
|
722 settings made for mass
|
||||||
|
|
||||||
|
velocity all create 1.44 87287 loop geom
|
||||||
|
|
||||||
|
# multi neighbor and comm for efficiency
|
||||||
|
|
||||||
|
neighbor 1 multi/old #multi
|
||||||
|
neigh_modify delay 0 #multi/custom 2 1*4 5
|
||||||
|
comm_modify mode multi/old #multi multi/reduce
|
||||||
|
|
||||||
|
# colloid potential
|
||||||
|
|
||||||
|
pair_style colloid 20.0
|
||||||
|
pair_coeff * * 144.0 1.0 0.0 0.0 3.0
|
||||||
|
pair_coeff 1 5 75.4 1.0 0.0 20.0 14.0
|
||||||
|
pair_coeff 2 5 75.4 1.0 0.0 20.0 14.0
|
||||||
|
pair_coeff 3 5 75.4 1.0 0.0 20.0 14.0
|
||||||
|
pair_coeff 4 5 75.4 1.0 0.0 20.0 14.0
|
||||||
|
pair_coeff 5 5 39.5 1.0 20.0 20.0 30.0
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1
|
||||||
|
fix 2 all enforce2d
|
||||||
|
|
||||||
|
#dump 1 all atom 1000 dump.colloid
|
||||||
|
|
||||||
|
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
|
||||||
|
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
|
||||||
|
|
||||||
|
#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5
|
||||||
|
#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
|
||||||
|
|
||||||
|
thermo_style custom step temp epair etotal press vol
|
||||||
|
thermo 1000
|
||||||
|
|
||||||
|
timestep 0.005
|
||||||
|
|
||||||
|
run 50000
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 31
|
||||||
|
ghost atom cutoff = 31
|
||||||
|
binsize = 2, bins = 95 95 2
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair colloid, perpetual
|
||||||
|
attributes: half, newton on
|
||||||
|
pair build: half/multi/old/newton
|
||||||
|
stencil: half/multi/old/2d
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 4.404 | 4.406 | 4.410 Mbytes
|
||||||
|
Step Temp E_pair TotEng Press Volume
|
||||||
|
0 1.44 0 1.4395241 0.121 36000
|
||||||
|
1000 1.8856066 -0.15771717 1.7272663 0.13840578 42574.399
|
||||||
|
2000 1.8590154 -0.11436231 1.7440387 0.097150798 58590.688
|
||||||
|
3000 1.8956738 -0.090814168 1.8042332 0.075557943 77825.289
|
||||||
|
4000 1.9567884 -0.072243657 1.8838981 0.072836007 90931.521
|
||||||
|
5000 2.0386455 -0.084279096 1.9536927 0.06867562 90054.581
|
||||||
|
6000 2.0816461 -0.093158646 1.9877995 0.082802397 78084.994
|
||||||
|
7000 2.0854943 -0.10553618 1.979269 0.10230351 63886.068
|
||||||
|
8000 2.0923948 -0.14072173 1.9509816 0.11775174 52590.899
|
||||||
|
9000 2.0687841 -0.15957251 1.9085279 0.14963059 44575.69
|
||||||
|
10000 2.0607467 -0.18970216 1.8703636 0.17210861 39016.271
|
||||||
|
11000 2.0538523 -0.20866031 1.8445133 0.18554787 34992.223
|
||||||
|
12000 2.0408745 -0.22276635 1.8174337 0.21228473 31794.869
|
||||||
|
13000 2.0366678 -0.24217764 1.7938171 0.22999314 29186.441
|
||||||
|
14000 2.0470314 -0.26923854 1.7771164 0.2576977 26941.432
|
||||||
|
15000 2.0262458 -0.27296827 1.7526079 0.25960813 25184.491
|
||||||
|
16000 2.0410096 -0.30940081 1.7309343 0.27842776 23619.633
|
||||||
|
17000 2.027379 -0.32411477 1.7025943 0.32102949 22231.582
|
||||||
|
18000 2.0338405 -0.34468182 1.6884866 0.3306203 21028.933
|
||||||
|
19000 2.032206 -0.36558904 1.6659454 0.33926726 19958.945
|
||||||
|
20000 2.0347643 -0.3915229 1.642569 0.33718716 19054.271
|
||||||
|
21000 2.0242901 -0.38913219 1.634489 0.38062225 18190.934
|
||||||
|
22000 2.0207557 -0.41078199 1.6093059 0.40143768 17422.03
|
||||||
|
23000 2.0069068 -0.42062708 1.5856165 0.40146954 16717.999
|
||||||
|
24000 2.0300595 -0.4536262 1.5757624 0.49229743 16097.323
|
||||||
|
25000 2.0347548 -0.47655047 1.5575319 0.46787969 15564.848
|
||||||
|
26000 2.0180789 -0.46537586 1.5520362 0.48541997 15072.597
|
||||||
|
27000 2.0150506 -0.4886202 1.5257645 0.53829749 14621.24
|
||||||
|
28000 2.0175464 -0.50951413 1.5073655 0.50140171 14253.441
|
||||||
|
29000 2.0186127 -0.53911975 1.4788258 0.52955802 13930.266
|
||||||
|
30000 2.0006844 -0.52621334 1.4738099 0.60130639 13650.051
|
||||||
|
31000 2.0179614 -0.54573939 1.4715551 0.58747508 13285.903
|
||||||
|
32000 2.0333208 -0.57431851 1.4583303 0.62631039 12894.077
|
||||||
|
33000 2.0017273 -0.57778326 1.4232825 0.61159622 12595.987
|
||||||
|
34000 2.0063025 -0.58192939 1.4237101 0.66174764 12316.964
|
||||||
|
35000 2.0174782 -0.60591394 1.4108976 0.63571024 12063.433
|
||||||
|
36000 2.025112 -0.64319133 1.3812514 0.62829458 11930.246
|
||||||
|
37000 2.0431268 -0.64342323 1.3990283 0.68038546 11651.664
|
||||||
|
38000 2.0064271 -0.63716263 1.3686014 0.72167175 11345.421
|
||||||
|
39000 2.0284014 -0.67236471 1.3553663 0.68693225 11062.293
|
||||||
|
40000 2.0181711 -0.6962559 1.3212483 0.76033095 10864.176
|
||||||
|
41000 1.9908152 -0.66607906 1.3240783 0.90250403 10812.599
|
||||||
|
42000 2.0007084 -0.68853623 1.311511 0.88096905 10627.922
|
||||||
|
43000 1.998883 -0.69053805 1.3076844 0.81765345 10469.928
|
||||||
|
44000 2.0197069 -0.72507021 1.2939693 0.87004916 10194.954
|
||||||
|
45000 2.0112835 -0.72638581 1.284233 0.99236207 9968.2662
|
||||||
|
46000 2.0195002 -0.75152677 1.2673061 0.92706763 9751.1162
|
||||||
|
47000 1.983694 -0.75006702 1.2329714 0.8945741 9652.1453
|
||||||
|
48000 1.9977505 -0.77207122 1.225019 0.92107083 9647.1543
|
||||||
|
49000 2.0000901 -0.76254934 1.2368798 1.0320945 9536.2823
|
||||||
|
50000 2.0150929 -0.80463979 1.2097872 0.99556424 9324.0277
|
||||||
|
Loop time of 10.7578 on 4 procs for 50000 steps with 3026 atoms
|
||||||
|
|
||||||
|
Performance: 2007847.166 tau/day, 4647.794 timesteps/s
|
||||||
|
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 2.3814 | 2.6878 | 2.9507 | 15.2 | 24.98
|
||||||
|
Neigh | 2.3959 | 2.6615 | 2.9677 | 16.2 | 24.74
|
||||||
|
Comm | 2.4113 | 2.9894 | 3.5621 | 29.6 | 27.79
|
||||||
|
Output | 0.00077024 | 0.00091029 | 0.0012971 | 0.0 | 0.01
|
||||||
|
Modify | 1.7966 | 1.8497 | 1.907 | 3.8 | 17.19
|
||||||
|
Other | | 0.5686 | | | 5.29
|
||||||
|
|
||||||
|
Nlocal: 756.500 ave 838 max 693 min
|
||||||
|
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||||
|
Nghost: 1282.50 ave 1333 max 1216 min
|
||||||
|
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||||
|
Neighs: 6426.25 ave 7350 max 5786 min
|
||||||
|
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 25705
|
||||||
|
Ave neighs/atom = 8.4947125
|
||||||
|
Neighbor list builds = 4326
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Please see the log.cite file for references relevant to this simulation
|
||||||
|
|
||||||
|
Total wall time: 0:00:10
|
||||||
175
examples/multi/log.30Nov20.granular.intel.1
Normal file
175
examples/multi/log.30Nov20.granular.intel.1
Normal file
@ -0,0 +1,175 @@
|
|||||||
|
LAMMPS (24 Dec 2020)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Big colloid particles and small LJ particles
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style sphere
|
||||||
|
dimension 2
|
||||||
|
|
||||||
|
lattice sq 0.5
|
||||||
|
Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136
|
||||||
|
region box block 0 60 0 60 -0.5 0.5
|
||||||
|
create_box 2 box
|
||||||
|
Created orthogonal box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 3600 atoms
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
change_box all triclinic
|
||||||
|
Changing box ...
|
||||||
|
triclinic box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) with tilt (0.0000000 0.0000000 0.0000000)
|
||||||
|
|
||||||
|
# remove two spheres of small particles and add large particles in the voids
|
||||||
|
region sphere1 sphere 20.0 20.0 0.0 10.0 units box
|
||||||
|
region sphere2 sphere 60.0 60.0 0.0 10.0 units box
|
||||||
|
delete_atoms region sphere1
|
||||||
|
Deleted 154 atoms, new total = 3446
|
||||||
|
delete_atoms region sphere2
|
||||||
|
Deleted 158 atoms, new total = 3288
|
||||||
|
create_atoms 2 single 20.0 20.0 0.0 units box
|
||||||
|
Created 1 atoms
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
create_atoms 2 single 60.0 60.0 0.0 units box
|
||||||
|
Created 1 atoms
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
|
set type 2 mass 400
|
||||||
|
Setting atom values ...
|
||||||
|
2 settings made for mass
|
||||||
|
set type 1 mass 1
|
||||||
|
Setting atom values ...
|
||||||
|
3288 settings made for mass
|
||||||
|
set type 2 diameter 20
|
||||||
|
Setting atom values ...
|
||||||
|
2 settings made for diameter
|
||||||
|
set type 1 diameter 1
|
||||||
|
Setting atom values ...
|
||||||
|
3288 settings made for diameter
|
||||||
|
|
||||||
|
velocity all create 1.44 87287 loop geom
|
||||||
|
|
||||||
|
# multi neighbor and comm for efficiency
|
||||||
|
|
||||||
|
neighbor 1 multi #multi/old
|
||||||
|
neigh_modify delay 0 collection/interval 2 1 20
|
||||||
|
comm_modify mode multi vel yes reduce/multi #multi/old
|
||||||
|
|
||||||
|
# colloid potential
|
||||||
|
|
||||||
|
pair_style granular
|
||||||
|
pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity
|
||||||
|
|
||||||
|
fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0
|
||||||
|
fix 2 all enforce2d
|
||||||
|
fix 3 all deform 1 xy erate 1e-3
|
||||||
|
|
||||||
|
#dump 1 all custom 1000 dump.granular id x y z radius
|
||||||
|
|
||||||
|
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
|
||||||
|
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
|
||||||
|
|
||||||
|
#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5
|
||||||
|
#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
|
||||||
|
|
||||||
|
thermo_style custom step temp epair etotal press vol
|
||||||
|
thermo 1000
|
||||||
|
|
||||||
|
timestep 0.005
|
||||||
|
|
||||||
|
run 50000
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 21
|
||||||
|
ghost atom cutoff = 21
|
||||||
|
binsize = 1, bins = 85 85 2
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair granular, perpetual
|
||||||
|
attributes: half, newton on, size, history
|
||||||
|
pair build: half/size/multi/newton/tri
|
||||||
|
stencil: half/multi/2d/tri
|
||||||
|
bin: multi
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 10.29 | 10.29 | 10.29 Mbytes
|
||||||
|
Step Temp E_pair TotEng Press Volume
|
||||||
|
0 1.44 0 1.4395623 0.66837658 7200
|
||||||
|
1000 0.32604952 0 0.32595042 0.17341597 7862.5013
|
||||||
|
2000 0.12631038 0 0.12627198 0.069126477 8216.6956
|
||||||
|
3000 0.069351715 0 0.069330635 0.040799593 8344.1931
|
||||||
|
4000 0.045023755 0 0.04501007 0.029184795 8239.1832
|
||||||
|
5000 0.032735149 0 0.0327252 0.025640841 7943.5691
|
||||||
|
6000 0.026205227 0 0.026197262 0.021206924 7617.6672
|
||||||
|
7000 0.02165475 0 0.021648168 0.018789365 7255.2897
|
||||||
|
8000 0.018299317 0 0.018293755 0.019272158 6887.3386
|
||||||
|
9000 0.016283763 0 0.016278813 0.020434892 6524.0274
|
||||||
|
10000 0.015148918 0 0.015144313 0.021650465 6168.4941
|
||||||
|
11000 0.014180465 0 0.014176155 0.022320009 5823.98
|
||||||
|
12000 0.013505744 0 0.013501639 0.023978674 5492.4853
|
||||||
|
13000 0.013009585 0 0.01300563 0.024391329 5175.7455
|
||||||
|
14000 0.012494373 0 0.012490576 0.027331543 4874.3212
|
||||||
|
15000 0.012057669 0 0.012054004 0.030561239 4589.518
|
||||||
|
16000 0.011510988 0 0.01150749 0.034613772 4321.1694
|
||||||
|
17000 0.011198594 0 0.01119519 0.042263536 4070.0115
|
||||||
|
18000 0.010978603 0 0.010975266 0.053637275 3836.0304
|
||||||
|
19000 0.010768789 0 0.010765516 0.069472547 3619.75
|
||||||
|
20000 0.0102256 0 0.010222492 0.085332898 3420.2738
|
||||||
|
21000 0.0089630315 0 0.0089603072 0.11199196 3236.9821
|
||||||
|
22000 0.006565581 0 0.0065635854 0.14807426 3071.3012
|
||||||
|
23000 0.0050916998 0 0.0050901522 0.1903446 2923.4162
|
||||||
|
24000 0.0040345997 0 0.0040333734 0.237983 2792.2658
|
||||||
|
25000 0.0032995328 0 0.0032985299 0.29120001 2677.7475
|
||||||
|
26000 0.0024157863 0 0.002415052 0.33851944 2578.4972
|
||||||
|
27000 0.0020664445 0 0.0020658164 0.37561848 2491.0264
|
||||||
|
28000 0.0017843883 0 0.0017838459 0.41119961 2412.3871
|
||||||
|
29000 0.0011813262 0 0.0011809672 0.44749341 2341.7208
|
||||||
|
30000 0.00063084711 0 0.00063065536 0.4879202 2279.0452
|
||||||
|
31000 0.00056027405 0 0.00056010376 0.52932126 2224.9456
|
||||||
|
32000 0.00053304715 0 0.00053288513 0.56822504 2179.1224
|
||||||
|
33000 0.00052245707 0 0.00052229826 0.60025509 2140.5345
|
||||||
|
34000 0.00073726189 0 0.0007370378 0.62001489 2106.3045
|
||||||
|
35000 0.00075804791 0 0.0007578175 0.6359631 2072.525
|
||||||
|
36000 0.00052579203 0 0.00052563222 0.65678516 2038.1907
|
||||||
|
37000 0.00036977909 0 0.0003696667 0.68784389 2005.5831
|
||||||
|
38000 0.00036252798 0 0.00036241779 0.72116044 1977.7441
|
||||||
|
39000 0.00036254566 0 0.00036243547 0.74720837 1954.9127
|
||||||
|
40000 0.00036237175 0 0.00036226161 0.76605408 1934.6006
|
||||||
|
41000 0.00032453104 0 0.00032443239 0.78424188 1914.1939
|
||||||
|
42000 0.00025394755 0 0.00025387036 0.80529272 1893.064
|
||||||
|
43000 0.00021067821 0 0.00021061418 0.82962095 1872.365
|
||||||
|
44000 0.00017927684 0 0.00017922235 0.85522899 1853.531
|
||||||
|
45000 0.0001464225 0 0.000146378 0.87925998 1837.2423
|
||||||
|
46000 0.00012922979 0 0.00012919051 0.8986549 1822.9227
|
||||||
|
47000 0.0001643557 0 0.00016430575 0.91743602 1809.0605
|
||||||
|
48000 0.00020154753 0 0.00020148627 0.93686779 1794.9227
|
||||||
|
49000 0.00017742528 0 0.00017737135 0.94988773 1780.3811
|
||||||
|
50000 0.00015150521 0 0.00015145916 0.97929588 1764.7507
|
||||||
|
Loop time of 54.9135 on 1 procs for 50000 steps with 3290 atoms
|
||||||
|
|
||||||
|
Performance: 393345.914 tau/day, 910.523 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 | 44.691 | 44.691 | 44.691 | 0.0 | 81.38
|
||||||
|
Neigh | 0.21653 | 0.21653 | 0.21653 | 0.0 | 0.39
|
||||||
|
Comm | 0.75388 | 0.75388 | 0.75388 | 0.0 | 1.37
|
||||||
|
Output | 0.0011999 | 0.0011999 | 0.0011999 | 0.0 | 0.00
|
||||||
|
Modify | 8.4718 | 8.4718 | 8.4718 | 0.0 | 15.43
|
||||||
|
Other | | 0.7794 | | | 1.42
|
||||||
|
|
||||||
|
Nlocal: 3290.00 ave 3290 max 3290 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 525.000 ave 525 max 525 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 26732.0 ave 26732 max 26732 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 26732
|
||||||
|
Ave neighs/atom = 8.1252280
|
||||||
|
Neighbor list builds = 342
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Please see the log.cite file for references relevant to this simulation
|
||||||
|
|
||||||
|
Total wall time: 0:00:54
|
||||||
175
examples/multi/log.30Nov20.granular.intel.4
Normal file
175
examples/multi/log.30Nov20.granular.intel.4
Normal file
@ -0,0 +1,175 @@
|
|||||||
|
LAMMPS (24 Dec 2020)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Big colloid particles and small LJ particles
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style sphere
|
||||||
|
dimension 2
|
||||||
|
|
||||||
|
lattice sq 0.5
|
||||||
|
Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136
|
||||||
|
region box block 0 60 0 60 -0.5 0.5
|
||||||
|
create_box 2 box
|
||||||
|
Created orthogonal box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678)
|
||||||
|
2 by 2 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 3600 atoms
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
change_box all triclinic
|
||||||
|
Changing box ...
|
||||||
|
triclinic box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) with tilt (0.0000000 0.0000000 0.0000000)
|
||||||
|
|
||||||
|
# remove two spheres of small particles and add large particles in the voids
|
||||||
|
region sphere1 sphere 20.0 20.0 0.0 10.0 units box
|
||||||
|
region sphere2 sphere 60.0 60.0 0.0 10.0 units box
|
||||||
|
delete_atoms region sphere1
|
||||||
|
Deleted 154 atoms, new total = 3446
|
||||||
|
delete_atoms region sphere2
|
||||||
|
Deleted 158 atoms, new total = 3288
|
||||||
|
create_atoms 2 single 20.0 20.0 0.0 units box
|
||||||
|
Created 1 atoms
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
create_atoms 2 single 60.0 60.0 0.0 units box
|
||||||
|
Created 1 atoms
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
|
set type 2 mass 400
|
||||||
|
Setting atom values ...
|
||||||
|
2 settings made for mass
|
||||||
|
set type 1 mass 1
|
||||||
|
Setting atom values ...
|
||||||
|
3288 settings made for mass
|
||||||
|
set type 2 diameter 20
|
||||||
|
Setting atom values ...
|
||||||
|
2 settings made for diameter
|
||||||
|
set type 1 diameter 1
|
||||||
|
Setting atom values ...
|
||||||
|
3288 settings made for diameter
|
||||||
|
|
||||||
|
velocity all create 1.44 87287 loop geom
|
||||||
|
|
||||||
|
# multi neighbor and comm for efficiency
|
||||||
|
|
||||||
|
neighbor 1 multi #multi/old
|
||||||
|
neigh_modify delay 0 collection/interval 2 1 20
|
||||||
|
comm_modify mode multi vel yes reduce/multi #multi/old
|
||||||
|
|
||||||
|
# colloid potential
|
||||||
|
|
||||||
|
pair_style granular
|
||||||
|
pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity
|
||||||
|
|
||||||
|
fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0
|
||||||
|
fix 2 all enforce2d
|
||||||
|
fix 3 all deform 1 xy erate 1e-3
|
||||||
|
|
||||||
|
#dump 1 all custom 1000 dump.granular id x y z radius
|
||||||
|
|
||||||
|
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
|
||||||
|
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
|
||||||
|
|
||||||
|
#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5
|
||||||
|
#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
|
||||||
|
|
||||||
|
thermo_style custom step temp epair etotal press vol
|
||||||
|
thermo 1000
|
||||||
|
|
||||||
|
timestep 0.005
|
||||||
|
|
||||||
|
run 50000
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 21
|
||||||
|
ghost atom cutoff = 21
|
||||||
|
binsize = 1, bins = 85 85 2
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair granular, perpetual
|
||||||
|
attributes: half, newton on, size, history
|
||||||
|
pair build: half/size/multi/newton/tri
|
||||||
|
stencil: half/multi/2d/tri
|
||||||
|
bin: multi
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 10.09 | 10.10 | 10.10 Mbytes
|
||||||
|
Step Temp E_pair TotEng Press Volume
|
||||||
|
0 1.44 0 1.4395623 0.66837658 7200
|
||||||
|
1000 0.32605303 0 0.32595393 0.17341558 7862.5037
|
||||||
|
2000 0.12631567 0 0.12627728 0.069188881 8216.7174
|
||||||
|
3000 0.069373812 0 0.069352726 0.040740832 8344.2982
|
||||||
|
4000 0.045084633 0 0.045070929 0.029328609 8239.3656
|
||||||
|
5000 0.032681746 0 0.032671813 0.025416741 7943.7831
|
||||||
|
6000 0.026301239 0 0.026293245 0.021418793 7617.8426
|
||||||
|
7000 0.021666723 0 0.021660138 0.018961011 7255.9338
|
||||||
|
8000 0.018141337 0 0.018135823 0.019306113 6887.4963
|
||||||
|
9000 0.015922309 0 0.015917469 0.020033398 6524.016
|
||||||
|
10000 0.014744547 0 0.014740066 0.020959503 6168.1945
|
||||||
|
11000 0.013872852 0 0.013868636 0.021708943 5823.3153
|
||||||
|
12000 0.013321594 0 0.013317545 0.02332141 5491.4979
|
||||||
|
13000 0.01269964 0 0.012695779 0.024796428 5174.6263
|
||||||
|
14000 0.01227055 0 0.012266821 0.027785072 4873.4516
|
||||||
|
15000 0.012120508 0 0.012116824 0.029656636 4588.8603
|
||||||
|
16000 0.011612027 0 0.011608498 0.034695109 4320.4674
|
||||||
|
17000 0.011216697 0 0.011213288 0.042746966 4069.4275
|
||||||
|
18000 0.010950166 0 0.010946838 0.053528994 3835.5439
|
||||||
|
19000 0.010887635 0 0.010884325 0.069684492 3619.562
|
||||||
|
20000 0.010563449 0 0.010560238 0.08654561 3420.2636
|
||||||
|
21000 0.0092336323 0 0.0092308257 0.11286068 3237.1408
|
||||||
|
22000 0.006929086 0 0.0069269799 0.15018917 3072.0438
|
||||||
|
23000 0.0052239156 0 0.0052223277 0.19067193 2924.441
|
||||||
|
24000 0.0044210081 0 0.0044196644 0.23908686 2793.2426
|
||||||
|
25000 0.0034916086 0 0.0034905473 0.29112824 2678.7912
|
||||||
|
26000 0.002549072 0 0.0025482972 0.33567824 2579.3738
|
||||||
|
27000 0.0020890726 0 0.0020884377 0.37328514 2491.0502
|
||||||
|
28000 0.001772982 0 0.0017724431 0.41079958 2411.9111
|
||||||
|
29000 0.001127719 0 0.0011273762 0.44752241 2341.1888
|
||||||
|
30000 0.00053266563 0 0.00053250373 0.48791815 2278.5611
|
||||||
|
31000 0.00050278646 0 0.00050263364 0.52896525 2224.5328
|
||||||
|
32000 0.00051880956 0 0.00051865187 0.56884574 2178.6674
|
||||||
|
33000 0.00054908167 0 0.00054891477 0.6016387 2140.3696
|
||||||
|
34000 0.00075213884 0 0.00075191023 0.62070188 2106.6504
|
||||||
|
35000 0.00081295162 0 0.00081270452 0.63492031 2073.0077
|
||||||
|
36000 0.00056699821 0 0.00056682587 0.65608409 2038.3251
|
||||||
|
37000 0.0003540723 0 0.00035396468 0.68803919 2005.497
|
||||||
|
38000 0.00031139738 0 0.00031130273 0.72103717 1977.7345
|
||||||
|
39000 0.00034087822 0 0.00034077461 0.74697975 1954.8979
|
||||||
|
40000 0.00035452426 0 0.0003544165 0.76682035 1934.5695
|
||||||
|
41000 0.00030882258 0 0.00030872871 0.78390763 1914.3326
|
||||||
|
42000 0.00025492799 0 0.00025485051 0.80439795 1893.1474
|
||||||
|
43000 0.00021545017 0 0.00021538468 0.82803644 1872.073
|
||||||
|
44000 0.00017293257 0 0.00017288 0.85436769 1852.6548
|
||||||
|
45000 0.00014097725 0 0.0001409344 0.8796181 1836.0087
|
||||||
|
46000 0.0001139199 0 0.00011388527 0.90006173 1821.7977
|
||||||
|
47000 0.00012678598 0 0.00012674745 0.90876359 1808.4913
|
||||||
|
48000 0.00013796773 0 0.00013792579 0.93661523 1793.8082
|
||||||
|
49000 0.00014723144 0 0.00014718669 0.95869417 1779.1875
|
||||||
|
50000 0.00013610653 0 0.00013606516 0.97777198 1765.3247
|
||||||
|
Loop time of 17.7405 on 4 procs for 50000 steps with 3290 atoms
|
||||||
|
|
||||||
|
Performance: 1217551.996 tau/day, 2818.407 timesteps/s
|
||||||
|
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 6.6629 | 9.6168 | 12.444 | 76.6 | 54.21
|
||||||
|
Neigh | 0.049771 | 0.055182 | 0.06133 | 2.0 | 0.31
|
||||||
|
Comm | 1.7883 | 4.6306 | 7.6179 | 111.5 | 26.10
|
||||||
|
Output | 0.00085342 | 0.0010606 | 0.0015425 | 0.9 | 0.01
|
||||||
|
Modify | 2.7244 | 2.895 | 3.0436 | 8.2 | 16.32
|
||||||
|
Other | | 0.5419 | | | 3.05
|
||||||
|
|
||||||
|
Nlocal: 822.500 ave 897 max 779 min
|
||||||
|
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||||
|
Nghost: 190.500 ave 211 max 179 min
|
||||||
|
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||||
|
Neighs: 6665.75 ave 7329 max 6104 min
|
||||||
|
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||||
|
|
||||||
|
Total # of neighbors = 26663
|
||||||
|
Ave neighs/atom = 8.1042553
|
||||||
|
Neighbor list builds = 342
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Please see the log.cite file for references relevant to this simulation
|
||||||
|
|
||||||
|
Total wall time: 0:00:17
|
||||||
175
examples/multi/log.30Nov20.granular.old.intel.1
Normal file
175
examples/multi/log.30Nov20.granular.old.intel.1
Normal file
@ -0,0 +1,175 @@
|
|||||||
|
LAMMPS (24 Dec 2020)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Big colloid particles and small LJ particles
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style sphere
|
||||||
|
dimension 2
|
||||||
|
|
||||||
|
lattice sq 0.5
|
||||||
|
Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136
|
||||||
|
region box block 0 60 0 60 -0.5 0.5
|
||||||
|
create_box 2 box
|
||||||
|
Created orthogonal box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 3600 atoms
|
||||||
|
create_atoms CPU = 0.001 seconds
|
||||||
|
change_box all triclinic
|
||||||
|
Changing box ...
|
||||||
|
triclinic box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) with tilt (0.0000000 0.0000000 0.0000000)
|
||||||
|
|
||||||
|
# remove two spheres of small particles and add large particles in the voids
|
||||||
|
region sphere1 sphere 20.0 20.0 0.0 10.0 units box
|
||||||
|
region sphere2 sphere 60.0 60.0 0.0 10.0 units box
|
||||||
|
delete_atoms region sphere1
|
||||||
|
Deleted 154 atoms, new total = 3446
|
||||||
|
delete_atoms region sphere2
|
||||||
|
Deleted 158 atoms, new total = 3288
|
||||||
|
create_atoms 2 single 20.0 20.0 0.0 units box
|
||||||
|
Created 1 atoms
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
create_atoms 2 single 60.0 60.0 0.0 units box
|
||||||
|
Created 1 atoms
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
|
set type 2 mass 400
|
||||||
|
Setting atom values ...
|
||||||
|
2 settings made for mass
|
||||||
|
set type 1 mass 1
|
||||||
|
Setting atom values ...
|
||||||
|
3288 settings made for mass
|
||||||
|
set type 2 diameter 20
|
||||||
|
Setting atom values ...
|
||||||
|
2 settings made for diameter
|
||||||
|
set type 1 diameter 1
|
||||||
|
Setting atom values ...
|
||||||
|
3288 settings made for diameter
|
||||||
|
|
||||||
|
velocity all create 1.44 87287 loop geom
|
||||||
|
|
||||||
|
# multi neighbor and comm for efficiency
|
||||||
|
|
||||||
|
neighbor 1 multi/old #multi
|
||||||
|
neigh_modify delay 0 #collection/interval 2 1 20
|
||||||
|
comm_modify mode multi/old vel yes #reduce/multi
|
||||||
|
|
||||||
|
# colloid potential
|
||||||
|
|
||||||
|
pair_style granular
|
||||||
|
pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity
|
||||||
|
|
||||||
|
fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0
|
||||||
|
fix 2 all enforce2d
|
||||||
|
fix 3 all deform 1 xy erate 1e-3
|
||||||
|
|
||||||
|
#dump 1 all custom 1000 dump.granular id x y z radius
|
||||||
|
|
||||||
|
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
|
||||||
|
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
|
||||||
|
|
||||||
|
#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5
|
||||||
|
#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
|
||||||
|
|
||||||
|
thermo_style custom step temp epair etotal press vol
|
||||||
|
thermo 1000
|
||||||
|
|
||||||
|
timestep 0.005
|
||||||
|
|
||||||
|
run 50000
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 21
|
||||||
|
ghost atom cutoff = 21
|
||||||
|
binsize = 1, bins = 85 85 2
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair granular, perpetual
|
||||||
|
attributes: half, newton on, size, history
|
||||||
|
pair build: half/size/multi/old/newton/tri
|
||||||
|
stencil: half/multi/old/2d/tri
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 10.38 | 10.38 | 10.38 Mbytes
|
||||||
|
Step Temp E_pair TotEng Press Volume
|
||||||
|
0 1.44 0 1.4395623 0.66837658 7200
|
||||||
|
1000 0.32273428 0 0.32263619 0.17174972 7859.8897
|
||||||
|
2000 0.12441598 0 0.12437817 0.067078155 8212.9946
|
||||||
|
3000 0.067389284 0 0.067368801 0.040425551 8336.7112
|
||||||
|
4000 0.044312733 0 0.044299264 0.028220228 8229.0658
|
||||||
|
5000 0.032702163 0 0.032692223 0.024302012 7931.1298
|
||||||
|
6000 0.025856 0 0.025848141 0.021241317 7603.5534
|
||||||
|
7000 0.021437473 0 0.021430957 0.019285494 7243.5757
|
||||||
|
8000 0.018129567 0 0.018124057 0.020738727 6877.4816
|
||||||
|
9000 0.016370159 0 0.016365184 0.020261904 6515.3445
|
||||||
|
10000 0.01500918 0 0.015004618 0.020551803 6160.4475
|
||||||
|
11000 0.014156551 0 0.014152248 0.021324815 5815.4665
|
||||||
|
12000 0.013725406 0 0.013721235 0.021159958 5483.6304
|
||||||
|
13000 0.013215746 0 0.013211729 0.021685712 5165.4758
|
||||||
|
14000 0.012398153 0 0.012394384 0.024155434 4862.8657
|
||||||
|
15000 0.011842796 0 0.011839196 0.028503991 4577.9008
|
||||||
|
16000 0.011433182 0 0.011429706 0.033564839 4309.8792
|
||||||
|
17000 0.011166574 0 0.01116318 0.040592677 4058.9964
|
||||||
|
18000 0.01100067 0 0.010997326 0.04899206 3825.155
|
||||||
|
19000 0.010224474 0 0.010221366 0.063670337 3607.6577
|
||||||
|
20000 0.0091360558 0 0.0091332789 0.088230111 3408.5658
|
||||||
|
21000 0.0077336471 0 0.0077312964 0.11769368 3227.7002
|
||||||
|
22000 0.0060202357 0 0.0060184059 0.15272492 3064.3986
|
||||||
|
23000 0.0046705738 0 0.0046691542 0.19450723 2918.0014
|
||||||
|
24000 0.0040248311 0 0.0040236078 0.24161743 2788.4113
|
||||||
|
25000 0.0032075267 0 0.0032065518 0.28976925 2674.5604
|
||||||
|
26000 0.0021358008 0 0.0021351516 0.33635615 2574.9564
|
||||||
|
27000 0.0016902771 0 0.0016897633 0.37624261 2487.2379
|
||||||
|
28000 0.0014038216 0 0.0014033949 0.41492061 2409.2461
|
||||||
|
29000 0.00090262588 0 0.00090235152 0.45392924 2340.0308
|
||||||
|
30000 0.00049466445 0 0.0004945141 0.49295063 2279.2316
|
||||||
|
31000 0.00056998139 0 0.00056980814 0.53299532 2226.5683
|
||||||
|
32000 0.00057327032 0 0.00057309607 0.56856551 2181.7093
|
||||||
|
33000 0.00044845449 0 0.00044831818 0.59623461 2142.7574
|
||||||
|
34000 0.00059840346 0 0.00059822157 0.61758978 2107.1254
|
||||||
|
35000 0.00075311121 0 0.0007528823 0.63756791 2072.7217
|
||||||
|
36000 0.00053773653 0 0.00053757309 0.66026022 2039.1654
|
||||||
|
37000 0.00030439696 0 0.00030430444 0.69059127 2007.7901
|
||||||
|
38000 0.00034435616 0 0.00034425149 0.72166346 1980.7136
|
||||||
|
39000 0.00039692535 0 0.0003968047 0.7468036 1957.9531
|
||||||
|
40000 0.0003542502 0 0.00035414252 0.76604173 1937.3834
|
||||||
|
41000 0.0003094667 0 0.00030937263 0.78323183 1916.7027
|
||||||
|
42000 0.00027258976 0 0.0002725069 0.80315572 1895.0714
|
||||||
|
43000 0.00020659987 0 0.00020653707 0.82746098 1873.5408
|
||||||
|
44000 0.00016023865 0 0.00016018994 0.85418945 1853.8677
|
||||||
|
45000 0.00016112731 0 0.00016107833 0.87913874 1837.1144
|
||||||
|
46000 0.00016131366 0 0.00016126463 0.89921653 1822.7355
|
||||||
|
47000 0.00015754747 0 0.00015749958 0.91653641 1809.0285
|
||||||
|
48000 0.00017794764 0 0.00017789356 0.93582953 1794.7043
|
||||||
|
49000 0.00018879338 0 0.000188736 0.95775166 1780.0323
|
||||||
|
50000 0.00017781117 0 0.00017775712 0.97893641 1765.9442
|
||||||
|
Loop time of 74.6636 on 1 procs for 50000 steps with 3290 atoms
|
||||||
|
|
||||||
|
Performance: 289297.713 tau/day, 669.671 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 | 56.696 | 56.696 | 56.696 | 0.0 | 75.93
|
||||||
|
Neigh | 2.2232 | 2.2232 | 2.2232 | 0.0 | 2.98
|
||||||
|
Comm | 6.1867 | 6.1867 | 6.1867 | 0.0 | 8.29
|
||||||
|
Output | 0.0012016 | 0.0012016 | 0.0012016 | 0.0 | 0.00
|
||||||
|
Modify | 8.432 | 8.432 | 8.432 | 0.0 | 11.29
|
||||||
|
Other | | 1.125 | | | 1.51
|
||||||
|
|
||||||
|
Nlocal: 3290.00 ave 3290 max 3290 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 6295.00 ave 6295 max 6295 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 53729.0 ave 53729 max 53729 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 53729
|
||||||
|
Ave neighs/atom = 16.331003
|
||||||
|
Neighbor list builds = 348
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Please see the log.cite file for references relevant to this simulation
|
||||||
|
|
||||||
|
Total wall time: 0:01:14
|
||||||
175
examples/multi/log.30Nov20.granular.old.intel.4
Normal file
175
examples/multi/log.30Nov20.granular.old.intel.4
Normal file
@ -0,0 +1,175 @@
|
|||||||
|
LAMMPS (24 Dec 2020)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Big colloid particles and small LJ particles
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style sphere
|
||||||
|
dimension 2
|
||||||
|
|
||||||
|
lattice sq 0.5
|
||||||
|
Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136
|
||||||
|
region box block 0 60 0 60 -0.5 0.5
|
||||||
|
create_box 2 box
|
||||||
|
Created orthogonal box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678)
|
||||||
|
2 by 2 by 1 MPI processor grid
|
||||||
|
create_atoms 1 box
|
||||||
|
Created 3600 atoms
|
||||||
|
create_atoms CPU = 0.063 seconds
|
||||||
|
change_box all triclinic
|
||||||
|
Changing box ...
|
||||||
|
triclinic box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) with tilt (0.0000000 0.0000000 0.0000000)
|
||||||
|
|
||||||
|
# remove two spheres of small particles and add large particles in the voids
|
||||||
|
region sphere1 sphere 20.0 20.0 0.0 10.0 units box
|
||||||
|
region sphere2 sphere 60.0 60.0 0.0 10.0 units box
|
||||||
|
delete_atoms region sphere1
|
||||||
|
Deleted 154 atoms, new total = 3446
|
||||||
|
delete_atoms region sphere2
|
||||||
|
Deleted 158 atoms, new total = 3288
|
||||||
|
create_atoms 2 single 20.0 20.0 0.0 units box
|
||||||
|
Created 1 atoms
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
create_atoms 2 single 60.0 60.0 0.0 units box
|
||||||
|
Created 1 atoms
|
||||||
|
create_atoms CPU = 0.000 seconds
|
||||||
|
|
||||||
|
set type 2 mass 400
|
||||||
|
Setting atom values ...
|
||||||
|
2 settings made for mass
|
||||||
|
set type 1 mass 1
|
||||||
|
Setting atom values ...
|
||||||
|
3288 settings made for mass
|
||||||
|
set type 2 diameter 20
|
||||||
|
Setting atom values ...
|
||||||
|
2 settings made for diameter
|
||||||
|
set type 1 diameter 1
|
||||||
|
Setting atom values ...
|
||||||
|
3288 settings made for diameter
|
||||||
|
|
||||||
|
velocity all create 1.44 87287 loop geom
|
||||||
|
|
||||||
|
# multi neighbor and comm for efficiency
|
||||||
|
|
||||||
|
neighbor 1 multi/old #multi
|
||||||
|
neigh_modify delay 0 #collection/interval 2 1 20
|
||||||
|
comm_modify mode multi/old vel yes #reduce/multi
|
||||||
|
|
||||||
|
# colloid potential
|
||||||
|
|
||||||
|
pair_style granular
|
||||||
|
pair_coeff * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity
|
||||||
|
|
||||||
|
fix 1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0
|
||||||
|
fix 2 all enforce2d
|
||||||
|
fix 3 all deform 1 xy erate 1e-3
|
||||||
|
|
||||||
|
#dump 1 all custom 1000 dump.granular id x y z radius
|
||||||
|
|
||||||
|
#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
|
||||||
|
#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
|
||||||
|
|
||||||
|
#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5
|
||||||
|
#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
|
||||||
|
|
||||||
|
thermo_style custom step temp epair etotal press vol
|
||||||
|
thermo 1000
|
||||||
|
|
||||||
|
timestep 0.005
|
||||||
|
|
||||||
|
run 50000
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 21
|
||||||
|
ghost atom cutoff = 21
|
||||||
|
binsize = 1, bins = 85 85 2
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair granular, perpetual
|
||||||
|
attributes: half, newton on, size, history
|
||||||
|
pair build: half/size/multi/old/newton/tri
|
||||||
|
stencil: half/multi/old/2d/tri
|
||||||
|
bin: standard
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 10.20 | 10.20 | 10.20 Mbytes
|
||||||
|
Step Temp E_pair TotEng Press Volume
|
||||||
|
0 1.44 0 1.4395623 0.66837658 7200
|
||||||
|
1000 0.32273428 0 0.32263619 0.17174972 7859.8897
|
||||||
|
2000 0.12441598 0 0.12437817 0.067078155 8212.9946
|
||||||
|
3000 0.067389284 0 0.067368801 0.040425551 8336.7112
|
||||||
|
4000 0.044312733 0 0.044299264 0.028220228 8229.0658
|
||||||
|
5000 0.032702163 0 0.032692223 0.024302012 7931.1298
|
||||||
|
6000 0.025856 0 0.025848141 0.021241317 7603.5534
|
||||||
|
7000 0.021437473 0 0.021430957 0.019285494 7243.5757
|
||||||
|
8000 0.018129567 0 0.018124057 0.020738727 6877.4816
|
||||||
|
9000 0.01637016 0 0.016365184 0.020261904 6515.3445
|
||||||
|
10000 0.01500918 0 0.015004618 0.020551803 6160.4475
|
||||||
|
11000 0.014156553 0 0.01415225 0.021324818 5815.4665
|
||||||
|
12000 0.013725412 0 0.01372124 0.021159958 5483.6304
|
||||||
|
13000 0.013215733 0 0.013211716 0.021685624 5165.4758
|
||||||
|
14000 0.012398179 0 0.012394411 0.024155572 4862.8657
|
||||||
|
15000 0.01184269 0 0.01183909 0.028504106 4577.901
|
||||||
|
16000 0.01143291 0 0.011429435 0.033564204 4309.88
|
||||||
|
17000 0.011166204 0 0.01116281 0.040588854 4058.9972
|
||||||
|
18000 0.011000875 0 0.010997532 0.048998904 3825.1569
|
||||||
|
19000 0.010225905 0 0.010222797 0.063669588 3607.6622
|
||||||
|
20000 0.0091390255 0 0.0091362477 0.088165402 3408.567
|
||||||
|
21000 0.0077382041 0 0.0077358521 0.11770474 3227.6936
|
||||||
|
22000 0.00601731 0 0.0060154811 0.15261994 3064.3873
|
||||||
|
23000 0.0046667591 0 0.0046653407 0.19453819 2917.9782
|
||||||
|
24000 0.0040425749 0 0.0040413461 0.24145833 2788.3897
|
||||||
|
25000 0.0031933217 0 0.0031923511 0.28989713 2674.5164
|
||||||
|
26000 0.0021138997 0 0.0021132571 0.33598673 2574.9312
|
||||||
|
27000 0.001700508 0 0.0016999912 0.37665013 2487.1626
|
||||||
|
28000 0.0014434246 0 0.0014429859 0.41572163 2409.327
|
||||||
|
29000 0.00089885063 0 0.00089857742 0.453431 2340.2313
|
||||||
|
30000 0.00048556478 0 0.00048541719 0.49176025 2279.2155
|
||||||
|
31000 0.00058130972 0 0.00058113303 0.53236818 2226.2349
|
||||||
|
32000 0.00057749847 0 0.00057732294 0.5691506 2181.2738
|
||||||
|
33000 0.00044719326 0 0.00044705733 0.59696179 2142.571
|
||||||
|
34000 0.00060924828 0 0.0006090631 0.61735036 2107.1282
|
||||||
|
35000 0.00077419805 0 0.00077396273 0.63696098 2072.6008
|
||||||
|
36000 0.00055752003 0 0.00055735057 0.65981842 2038.8242
|
||||||
|
37000 0.00031402452 0 0.00031392907 0.69018949 2007.3235
|
||||||
|
38000 0.00034969879 0 0.0003495925 0.72155053 1980.1706
|
||||||
|
39000 0.00041434197 0 0.00041421603 0.74680715 1957.3838
|
||||||
|
40000 0.00037229243 0 0.00037217927 0.76581686 1936.8034
|
||||||
|
41000 0.00031028842 0 0.00031019411 0.78321059 1916.1108
|
||||||
|
42000 0.00026623668 0 0.00026615575 0.80267329 1894.4649
|
||||||
|
43000 0.00020543723 0 0.00020537479 0.82714001 1872.7672
|
||||||
|
44000 0.0001563321 0 0.00015628458 0.85496396 1853.0284
|
||||||
|
45000 0.00014981713 0 0.00014977159 0.87924842 1836.4755
|
||||||
|
46000 0.00015641585 0 0.00015636831 0.89896936 1822.1989
|
||||||
|
47000 0.00016004701 0 0.00015999837 0.91661933 1808.4606
|
||||||
|
48000 0.00017437702 0 0.00017432402 0.93565475 1794.1258
|
||||||
|
49000 0.00018645903 0 0.00018640235 0.95733183 1779.4032
|
||||||
|
50000 0.00018469122 0 0.00018463508 0.96446925 1765.1534
|
||||||
|
Loop time of 30.1448 on 4 procs for 50000 steps with 3290 atoms
|
||||||
|
|
||||||
|
Performance: 716540.413 tau/day, 1658.658 timesteps/s
|
||||||
|
90.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 8.7565 | 12.704 | 16.036 | 89.8 | 42.14
|
||||||
|
Neigh | 0.4494 | 0.56436 | 0.66263 | 11.8 | 1.87
|
||||||
|
Comm | 9.5962 | 12.989 | 17.006 | 90.8 | 43.09
|
||||||
|
Output | 0.00088467 | 0.0011022 | 0.0015811 | 0.9 | 0.00
|
||||||
|
Modify | 2.9732 | 3.0944 | 3.2463 | 7.0 | 10.27
|
||||||
|
Other | | 0.7918 | | | 2.63
|
||||||
|
|
||||||
|
Nlocal: 822.500 ave 859 max 785 min
|
||||||
|
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||||
|
Nghost: 3049.75 ave 3089 max 2999 min
|
||||||
|
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||||
|
Neighs: 13440.5 ave 14459 max 11964 min
|
||||||
|
Histogram: 1 0 0 0 0 1 0 0 1 1
|
||||||
|
|
||||||
|
Total # of neighbors = 53762
|
||||||
|
Ave neighs/atom = 16.341033
|
||||||
|
Neighbor list builds = 348
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Please see the log.cite file for references relevant to this simulation
|
||||||
|
|
||||||
|
Total wall time: 0:00:30
|
||||||
291
examples/multi/log.30Nov20.powerlaw.intel.1
Normal file
291
examples/multi/log.30Nov20.powerlaw.intel.1
Normal file
@ -0,0 +1,291 @@
|
|||||||
|
LAMMPS (24 Dec 2020)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Shear power-law distributed granular particles
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style sphere
|
||||||
|
dimension 2
|
||||||
|
read_data data.powerlaw
|
||||||
|
Reading data file ...
|
||||||
|
triclinic box = (9.9514336 9.9514336 0.0000000) to (331.81396 331.81396 1.0000000) with tilt (0.0000000 0.0000000 0.0000000)
|
||||||
|
1 by 1 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
10000 atoms
|
||||||
|
reading velocities ...
|
||||||
|
10000 velocities
|
||||||
|
read_data CPU = 0.027 seconds
|
||||||
|
change_box all triclinic
|
||||||
|
Changing box ...
|
||||||
|
triclinic box = (9.9514336 9.9514336 0.0000000) to (331.81396 331.81396 1.0000000) with tilt (0.0000000 0.0000000 0.0000000)
|
||||||
|
|
||||||
|
# multi neighbor and comm for efficiency
|
||||||
|
|
||||||
|
neighbor 1 multi
|
||||||
|
neigh_modify delay 0 collection/interval 6 1.5 3 10 30 100 200
|
||||||
|
comm_modify mode multi vel yes reduce/multi
|
||||||
|
|
||||||
|
# granular potential
|
||||||
|
|
||||||
|
pair_style granular
|
||||||
|
pair_coeff * * hooke 20.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity
|
||||||
|
|
||||||
|
# fixes
|
||||||
|
|
||||||
|
fix 1 all nve/sphere
|
||||||
|
fix 2 all enforce2d
|
||||||
|
fix 3 all deform 1 xy erate 1e-4
|
||||||
|
|
||||||
|
# dump 1 all custom 20000 dump.granular id x y z radius
|
||||||
|
|
||||||
|
thermo_style custom step temp epair etotal press vol pxy
|
||||||
|
thermo 1000
|
||||||
|
|
||||||
|
timestep 0.005
|
||||||
|
|
||||||
|
run 200000
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 164.7888
|
||||||
|
ghost atom cutoff = 164.7888
|
||||||
|
binsize = 82.3944, bins = 4 4 1
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair granular, perpetual
|
||||||
|
attributes: half, newton on, size, history
|
||||||
|
pair build: half/size/multi/newton/tri
|
||||||
|
stencil: half/multi/2d/tri
|
||||||
|
bin: multi
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 14.77 | 14.77 | 14.77 Mbytes
|
||||||
|
Step Temp E_pair TotEng Press Volume Pxy
|
||||||
|
0 4.9204851e-05 0 4.9199931e-05 0.61204991 103595.49 -0.00083309917
|
||||||
|
1000 0.00038076464 0 0.00038072657 0.58694623 103595.49 -0.0066712806
|
||||||
|
2000 0.00027986478 0 0.00027983679 0.5845274 103595.49 -0.008880933
|
||||||
|
3000 0.00022105227 0 0.00022103017 0.58295464 103595.49 -0.011327442
|
||||||
|
4000 0.00020888366 0 0.00020886277 0.5826542 103595.49 -0.014147424
|
||||||
|
5000 0.00019912663 0 0.00019910672 0.58175837 103595.49 -0.015685634
|
||||||
|
6000 0.0001989441 0 0.00019892421 0.58170841 103595.49 -0.017379973
|
||||||
|
7000 0.00019307783 0 0.00019305852 0.58133913 103595.49 -0.019556709
|
||||||
|
8000 0.00018132444 0 0.00018130631 0.58134077 103595.49 -0.021609399
|
||||||
|
9000 0.00017909088 0 0.00017907297 0.58117179 103595.49 -0.023603514
|
||||||
|
10000 0.00018391928 0 0.00018390089 0.58070675 103595.49 -0.026026784
|
||||||
|
11000 0.00018985439 0 0.00018983541 0.58006086 103595.49 -0.028574238
|
||||||
|
12000 0.00018903569 0 0.00018901678 0.5794232 103595.49 -0.031151884
|
||||||
|
13000 0.00019070382 0 0.00019068475 0.57890243 103595.49 -0.033469404
|
||||||
|
14000 0.00019371625 0 0.00019369688 0.5787389 103595.49 -0.035646526
|
||||||
|
15000 0.00019833475 0 0.00019831492 0.57883166 103595.49 -0.037709788
|
||||||
|
16000 0.0002011729 0 0.00020115278 0.57875606 103595.49 -0.039452453
|
||||||
|
17000 0.00020285197 0 0.00020283169 0.5786311 103595.49 -0.040960671
|
||||||
|
18000 0.00020319174 0 0.00020317142 0.57842387 103595.49 -0.042257072
|
||||||
|
19000 0.00020290253 0 0.00020288224 0.57795042 103595.49 -0.043364149
|
||||||
|
20000 0.00020509848 0 0.00020507797 0.5771478 103595.49 -0.044392259
|
||||||
|
21000 0.00021803258 0 0.00021801078 0.57569003 103595.49 -0.044749043
|
||||||
|
22000 0.00020751217 0 0.00020749141 0.57477071 103595.49 -0.045719593
|
||||||
|
23000 0.00022053275 0 0.0002205107 0.57409228 103595.49 -0.047332146
|
||||||
|
24000 0.00022689646 0 0.00022687377 0.57325004 103595.49 -0.04871759
|
||||||
|
25000 0.00025224804 0 0.00025222282 0.57283712 103595.49 -0.050254871
|
||||||
|
26000 0.00025343198 0 0.00025340664 0.57238659 103595.49 -0.051604284
|
||||||
|
27000 0.00026689801 0 0.00026687132 0.57221042 103595.49 -0.052915257
|
||||||
|
28000 0.00027867954 0 0.00027865167 0.57197974 103595.49 -0.053832129
|
||||||
|
29000 0.00028697929 0 0.00028695059 0.57177264 103595.49 -0.054693121
|
||||||
|
30000 0.00028857612 0 0.00028854727 0.57145453 103595.49 -0.055559611
|
||||||
|
31000 0.00029228405 0 0.00029225482 0.5711044 103595.49 -0.056492699
|
||||||
|
32000 0.00029648627 0 0.00029645663 0.57060211 103595.49 -0.05729896
|
||||||
|
33000 0.00030524162 0 0.00030521109 0.57002519 103595.49 -0.058201322
|
||||||
|
34000 0.00031725644 0 0.00031722472 0.56920654 103595.49 -0.059128438
|
||||||
|
35000 0.00032273791 0 0.00032270564 0.56844677 103595.49 -0.060009671
|
||||||
|
36000 0.00033013013 0 0.00033009712 0.56795943 103595.49 -0.061074282
|
||||||
|
37000 0.00033942153 0 0.00033938759 0.56749208 103595.49 -0.062058531
|
||||||
|
38000 0.00035141528 0 0.00035138014 0.56682741 103595.49 -0.062953956
|
||||||
|
39000 0.00036126777 0 0.00036123164 0.56655193 103595.49 -0.063757684
|
||||||
|
40000 0.00037765934 0 0.00037762157 0.5661991 103595.49 -0.064535541
|
||||||
|
41000 0.00040834365 0 0.00040830281 0.56554085 103595.49 -0.064688281
|
||||||
|
42000 0.00042857233 0 0.00042852948 0.56474014 103595.49 -0.065262664
|
||||||
|
43000 0.00042692021 0 0.00042687752 0.56362013 103595.49 -0.065276794
|
||||||
|
44000 0.00040298912 0 0.00040294882 0.5631005 103595.49 -0.065626396
|
||||||
|
45000 0.00040947381 0 0.00040943286 0.56291946 103595.49 -0.066167734
|
||||||
|
46000 0.00040202686 0 0.00040198666 0.56273846 103595.49 -0.066543782
|
||||||
|
47000 0.00038914356 0 0.00038910465 0.56265937 103595.49 -0.067359923
|
||||||
|
48000 0.00038429737 0 0.00038425894 0.56274908 103595.49 -0.068231096
|
||||||
|
49000 0.00036912968 0 0.00036909277 0.56261623 103595.49 -0.068791569
|
||||||
|
50000 0.00035203094 0 0.00035199574 0.56257856 103595.49 -0.069298217
|
||||||
|
51000 0.00034403223 0 0.00034399783 0.56236537 103595.49 -0.070273225
|
||||||
|
52000 0.00034132431 0 0.00034129018 0.56220555 103595.49 -0.071740344
|
||||||
|
53000 0.000335692 0 0.00033565843 0.56194913 103595.49 -0.072834415
|
||||||
|
54000 0.00033048196 0 0.00033044891 0.56231491 103595.49 -0.073996938
|
||||||
|
55000 0.00032751145 0 0.00032747869 0.56225025 103595.49 -0.07506664
|
||||||
|
56000 0.00032696951 0 0.00032693682 0.56285506 103595.49 -0.076445354
|
||||||
|
57000 0.00033158698 0 0.00033155382 0.56354729 103595.49 -0.077682996
|
||||||
|
58000 0.00034300009 0 0.00034296579 0.56416964 103595.49 -0.078836604
|
||||||
|
59000 0.00034340257 0 0.00034336823 0.56490867 103595.49 -0.079658197
|
||||||
|
60000 0.00034736137 0 0.00034732663 0.56519398 103595.49 -0.080570223
|
||||||
|
61000 0.00034984523 0 0.00034981025 0.5651693 103595.49 -0.081115325
|
||||||
|
62000 0.00034995431 0 0.00034991932 0.56534549 103595.49 -0.081486038
|
||||||
|
63000 0.00033854269 0 0.00033850883 0.56582558 103595.49 -0.081892374
|
||||||
|
64000 0.00032621515 0 0.00032618253 0.5658388 103595.49 -0.082786608
|
||||||
|
65000 0.00031773942 0 0.00031770764 0.56576287 103595.49 -0.083706189
|
||||||
|
66000 0.00031772736 0 0.00031769558 0.56548117 103595.49 -0.084236463
|
||||||
|
67000 0.0003148631 0 0.00031483161 0.56483795 103595.49 -0.084506082
|
||||||
|
68000 0.00030359752 0 0.00030356716 0.56446443 103595.49 -0.084985509
|
||||||
|
69000 0.00030395128 0 0.00030392088 0.56437593 103595.49 -0.085548157
|
||||||
|
70000 0.00032811658 0 0.00032808376 0.56372411 103595.49 -0.085304154
|
||||||
|
71000 0.00035494531 0 0.00035490981 0.56326137 103595.49 -0.085047806
|
||||||
|
72000 0.0003253841 0 0.00032535156 0.56244462 103595.49 -0.085693663
|
||||||
|
73000 0.00032328895 0 0.00032325662 0.5629287 103595.49 -0.086119464
|
||||||
|
74000 0.00032650113 0 0.00032646848 0.56306166 103595.49 -0.087182721
|
||||||
|
75000 0.00034303222 0 0.00034299792 0.56219559 103595.49 -0.086604025
|
||||||
|
76000 0.00033786129 0 0.0003378275 0.56188071 103595.49 -0.086852177
|
||||||
|
77000 0.00033559735 0 0.00033556379 0.5619155 103595.49 -0.08689764
|
||||||
|
78000 0.00032579863 0 0.00032576605 0.56177059 103595.49 -0.087109469
|
||||||
|
79000 0.00031610815 0 0.00031607654 0.56160391 103595.49 -0.087250861
|
||||||
|
80000 0.00031246546 0 0.00031243422 0.56181676 103595.49 -0.087117648
|
||||||
|
81000 0.00029392131 0 0.00029389192 0.56205441 103595.49 -0.087601617
|
||||||
|
82000 0.00029624453 0 0.00029621491 0.56285229 103595.49 -0.08824145
|
||||||
|
83000 0.00030538821 0 0.00030535767 0.5627754 103595.49 -0.088318188
|
||||||
|
84000 0.00029587833 0 0.00029584874 0.56267246 103595.49 -0.08930338
|
||||||
|
85000 0.00030551128 0 0.00030548073 0.56251282 103595.49 -0.0897211
|
||||||
|
86000 0.00030000969 0 0.00029997969 0.56249642 103595.49 -0.089920789
|
||||||
|
87000 0.00030211667 0 0.00030208646 0.56256648 103595.49 -0.090315024
|
||||||
|
88000 0.00030524995 0 0.00030521943 0.5623007 103595.49 -0.090706456
|
||||||
|
89000 0.00031961257 0 0.00031958061 0.56210244 103595.49 -0.090852204
|
||||||
|
90000 0.0003195337 0 0.00031950175 0.56207472 103595.49 -0.090879606
|
||||||
|
91000 0.00033860446 0 0.0003385706 0.56197196 103595.49 -0.090891252
|
||||||
|
92000 0.0003327551 0 0.00033272183 0.56172473 103595.49 -0.090725694
|
||||||
|
93000 0.00032983619 0 0.00032980321 0.5619443 103595.49 -0.090626404
|
||||||
|
94000 0.00034024354 0 0.00034020952 0.56150371 103595.49 -0.090769983
|
||||||
|
95000 0.00033201405 0 0.00033198084 0.56145998 103595.49 -0.09102312
|
||||||
|
96000 0.00032851608 0 0.00032848323 0.56201045 103595.49 -0.09152522
|
||||||
|
97000 0.0003353172 0 0.00033528367 0.56256203 103595.49 -0.092443634
|
||||||
|
98000 0.00033453146 0 0.00033449801 0.5632537 103595.49 -0.093069693
|
||||||
|
99000 0.00034432742 0 0.00034429299 0.56355465 103595.49 -0.093332298
|
||||||
|
100000 0.00035299312 0 0.00035295782 0.56420115 103595.49 -0.093871701
|
||||||
|
101000 0.00042149444 0 0.00042145229 0.56424332 103595.49 -0.094001873
|
||||||
|
102000 0.0004580706 0 0.0004580248 0.56378535 103595.49 -0.093786943
|
||||||
|
103000 0.00046113464 0 0.00046108853 0.56428549 103595.49 -0.093463429
|
||||||
|
104000 0.00047583409 0 0.00047578651 0.5645355 103595.49 -0.093225615
|
||||||
|
105000 0.00048367276 0 0.00048362439 0.56469488 103595.49 -0.092935582
|
||||||
|
106000 0.00046931008 0 0.00046926315 0.56464923 103595.49 -0.09282958
|
||||||
|
107000 0.00046460766 0 0.00046456119 0.56502528 103595.49 -0.093077749
|
||||||
|
108000 0.00046398187 0 0.00046393547 0.56532911 103595.49 -0.09321949
|
||||||
|
109000 0.00047530523 0 0.0004752577 0.56561281 103595.49 -0.093217991
|
||||||
|
110000 0.00048531886 0 0.00048527033 0.56549262 103595.49 -0.092956034
|
||||||
|
111000 0.00049659003 0 0.00049654038 0.56507505 103595.49 -0.092554122
|
||||||
|
112000 0.00050113619 0 0.00050108607 0.56528891 103595.49 -0.092227508
|
||||||
|
113000 0.0005138896 0 0.00051383821 0.56550655 103595.49 -0.092096556
|
||||||
|
114000 0.00052560295 0 0.00052555039 0.56567551 103595.49 -0.09181586
|
||||||
|
115000 0.00054349317 0 0.00054343882 0.56530917 103595.49 -0.090961623
|
||||||
|
116000 0.00056022902 0 0.00056017299 0.56482302 103595.49 -0.090810658
|
||||||
|
117000 0.00055876064 0 0.00055870476 0.56488791 103595.49 -0.090329656
|
||||||
|
118000 0.00056191427 0 0.00056185808 0.56461166 103595.49 -0.090161067
|
||||||
|
119000 0.0005488829 0 0.00054882801 0.56437975 103595.49 -0.090328459
|
||||||
|
120000 0.00054084712 0 0.00054079303 0.564481 103595.49 -0.090602791
|
||||||
|
121000 0.00053717105 0 0.00053711733 0.56481743 103595.49 -0.090309102
|
||||||
|
122000 0.00053834163 0 0.00053828779 0.56385259 103595.49 -0.090433254
|
||||||
|
123000 0.00053319394 0 0.00053314062 0.56335613 103595.49 -0.090723928
|
||||||
|
124000 0.00053127439 0 0.00053122127 0.5631684 103595.49 -0.091178253
|
||||||
|
125000 0.00053624623 0 0.00053619261 0.56387166 103595.49 -0.091701174
|
||||||
|
126000 0.0005253773 0 0.00052532476 0.5639006 103595.49 -0.092033098
|
||||||
|
127000 0.00052459276 0 0.0005245403 0.56361298 103595.49 -0.092219098
|
||||||
|
128000 0.00054030806 0 0.00054025403 0.56307203 103595.49 -0.092196938
|
||||||
|
129000 0.00055474894 0 0.00055469346 0.5622815 103595.49 -0.09178309
|
||||||
|
130000 0.00057391115 0 0.00057385376 0.56244981 103595.49 -0.09170211
|
||||||
|
131000 0.00058650769 0 0.00058644904 0.56195859 103595.49 -0.090649841
|
||||||
|
132000 0.00058529163 0 0.0005852331 0.56162943 103595.49 -0.090167101
|
||||||
|
133000 0.00062544817 0 0.00062538563 0.5594761 103595.49 -0.088989624
|
||||||
|
134000 0.00063457749 0 0.00063451403 0.55917757 103595.49 -0.089702278
|
||||||
|
135000 0.00065371789 0 0.00065365252 0.55885043 103595.49 -0.090030252
|
||||||
|
136000 0.00070050714 0 0.00070043709 0.55854751 103595.49 -0.08960124
|
||||||
|
137000 0.0006750775 0 0.00067501 0.55809563 103595.49 -0.090252473
|
||||||
|
138000 0.00068827043 0 0.0006882016 0.55806674 103595.49 -0.090238994
|
||||||
|
139000 0.00069748073 0 0.00069741098 0.55734587 103595.49 -0.090118549
|
||||||
|
140000 0.00071065284 0 0.00071058177 0.55711669 103595.49 -0.090336074
|
||||||
|
141000 0.00070994204 0 0.00070987104 0.55638115 103595.49 -0.089917062
|
||||||
|
142000 0.00071514386 0 0.00071507235 0.55614391 103595.49 -0.090392071
|
||||||
|
143000 0.00071334667 0 0.00071327533 0.55640687 103595.49 -0.091256718
|
||||||
|
144000 0.00069553102 0 0.00069546147 0.55705702 103595.49 -0.091761396
|
||||||
|
145000 0.00068849503 0 0.00068842618 0.55692035 103595.49 -0.091895738
|
||||||
|
146000 0.00068407816 0 0.00068400975 0.55660026 103595.49 -0.092191588
|
||||||
|
147000 0.00069521557 0 0.00069514605 0.55556456 103595.49 -0.092354739
|
||||||
|
148000 0.00068349281 0 0.00068342446 0.55537498 103595.49 -0.092914636
|
||||||
|
149000 0.00067959644 0 0.00067952848 0.55537695 103595.49 -0.093738463
|
||||||
|
150000 0.00067100566 0 0.00067093856 0.55544851 103595.49 -0.094104003
|
||||||
|
151000 0.00068044722 0 0.00068037917 0.5554655 103595.49 -0.094943239
|
||||||
|
152000 0.00068109012 0 0.00068102201 0.55585405 103595.49 -0.095355111
|
||||||
|
153000 0.00068666181 0 0.00068659314 0.55501583 103595.49 -0.095234652
|
||||||
|
154000 0.00068283406 0 0.00068276578 0.55644996 103595.49 -0.095902623
|
||||||
|
155000 0.00069836346 0 0.00069829363 0.55747472 103595.49 -0.096978444
|
||||||
|
156000 0.00072807264 0 0.00072799984 0.55807332 103595.49 -0.097415305
|
||||||
|
157000 0.00077300609 0 0.00077292879 0.55871196 103595.49 -0.098034508
|
||||||
|
158000 0.00081631408 0 0.00081623245 0.558479 103595.49 -0.09825722
|
||||||
|
159000 0.00079291984 0 0.00079284054 0.55784788 103595.49 -0.097758094
|
||||||
|
160000 0.0008203256 0 0.00082024357 0.55700259 103595.49 -0.097519328
|
||||||
|
161000 0.00081471235 0 0.00081463087 0.556622 103595.49 -0.097787992
|
||||||
|
162000 0.00080692462 0 0.00080684393 0.5566795 103595.49 -0.097210216
|
||||||
|
163000 0.00081149678 0 0.00081141564 0.55596697 103595.49 -0.097517476
|
||||||
|
164000 0.00081577795 0 0.00081569637 0.55569684 103595.49 -0.096908869
|
||||||
|
165000 0.00084604988 0 0.00084596528 0.55492052 103595.49 -0.095481627
|
||||||
|
166000 0.00082198923 0 0.00082190703 0.5552628 103595.49 -0.09477531
|
||||||
|
167000 0.00084903108 0 0.00084894618 0.55477991 103595.49 -0.094758799
|
||||||
|
168000 0.00081613582 0 0.00081605421 0.55508416 103595.49 -0.094804088
|
||||||
|
169000 0.00083341061 0 0.00083332727 0.55476794 103595.49 -0.094519882
|
||||||
|
170000 0.00077835092 0 0.00077827308 0.55516626 103595.49 -0.094843673
|
||||||
|
171000 0.00074843733 0 0.00074836249 0.55417469 103595.49 -0.094731356
|
||||||
|
172000 0.0007425125 0 0.00074243825 0.55431854 103595.49 -0.095174333
|
||||||
|
173000 0.00074144093 0 0.00074136678 0.55429464 103595.49 -0.094982598
|
||||||
|
174000 0.00072375323 0 0.00072368086 0.55421045 103595.49 -0.09489531
|
||||||
|
175000 0.0007270779 0 0.00072700519 0.55413607 103595.49 -0.094197685
|
||||||
|
176000 0.00071114682 0 0.00071107571 0.55342226 103595.49 -0.093083865
|
||||||
|
177000 0.00069325125 0 0.00069318193 0.55441386 103595.49 -0.093289572
|
||||||
|
178000 0.00067686202 0 0.00067679434 0.55504892 103595.49 -0.093512587
|
||||||
|
179000 0.00068326039 0 0.00068319206 0.55519365 103595.49 -0.093974329
|
||||||
|
180000 0.00075070045 0 0.00075062538 0.55415541 103595.49 -0.09327459
|
||||||
|
181000 0.00077670344 0 0.00077662577 0.55328725 103595.49 -0.092373689
|
||||||
|
182000 0.00077422781 0 0.00077415038 0.553131 103595.49 -0.092353979
|
||||||
|
183000 0.00080250542 0 0.00080242517 0.5519122 103595.49 -0.091897169
|
||||||
|
184000 0.00081235214 0 0.00081227091 0.55172769 103595.49 -0.091906209
|
||||||
|
185000 0.00078879443 0 0.00078871555 0.55145488 103595.49 -0.091198506
|
||||||
|
186000 0.00078497746 0 0.00078489896 0.55202944 103595.49 -0.091674987
|
||||||
|
187000 0.00079483049 0 0.000794751 0.55278073 103595.49 -0.092508295
|
||||||
|
188000 0.00079056756 0 0.0007904885 0.55362903 103595.49 -0.092801369
|
||||||
|
189000 0.00079162262 0 0.00079154346 0.55429061 103595.49 -0.092964781
|
||||||
|
190000 0.00078121133 0 0.00078113321 0.55386716 103595.49 -0.092689851
|
||||||
|
191000 0.00076574893 0 0.00076567235 0.5546533 103595.49 -0.093414672
|
||||||
|
192000 0.00076215201 0 0.0007620758 0.55503049 103595.49 -0.093986391
|
||||||
|
193000 0.00075652635 0 0.0007564507 0.55477696 103595.49 -0.094417347
|
||||||
|
194000 0.00075725781 0 0.00075718208 0.55457687 103595.49 -0.094241721
|
||||||
|
195000 0.0007434693 0 0.00074339496 0.55471575 103595.49 -0.094102015
|
||||||
|
196000 0.00073792493 0 0.00073785114 0.55463671 103595.49 -0.094452279
|
||||||
|
197000 0.00074673445 0 0.00074665978 0.55459327 103595.49 -0.09463863
|
||||||
|
198000 0.00072734835 0 0.00072727561 0.55514628 103595.49 -0.094622434
|
||||||
|
199000 0.00071846919 0 0.00071839734 0.55501969 103595.49 -0.094414887
|
||||||
|
200000 0.00072384651 0 0.00072377412 0.55533335 103595.49 -0.094159469
|
||||||
|
Loop time of 443.321 on 1 procs for 200000 steps with 10000 atoms
|
||||||
|
|
||||||
|
Performance: 194892.839 tau/day, 451.141 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 | 362.28 | 362.28 | 362.28 | 0.0 | 81.72
|
||||||
|
Neigh | 1.737 | 1.737 | 1.737 | 0.0 | 0.39
|
||||||
|
Comm | 5.0082 | 5.0082 | 5.0082 | 0.0 | 1.13
|
||||||
|
Output | 0.01774 | 0.01774 | 0.01774 | 0.0 | 0.00
|
||||||
|
Modify | 64.992 | 64.992 | 64.992 | 0.0 | 14.66
|
||||||
|
Other | | 9.286 | | | 2.09
|
||||||
|
|
||||||
|
Nlocal: 10000.0 ave 10000 max 10000 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 487.000 ave 487 max 487 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 34427.0 ave 34427 max 34427 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 34427
|
||||||
|
Ave neighs/atom = 3.4427000
|
||||||
|
Neighbor list builds = 244
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Please see the log.cite file for references relevant to this simulation
|
||||||
|
|
||||||
|
Total wall time: 0:07:23
|
||||||
291
examples/multi/log.30Nov20.powerlaw.intel.4
Normal file
291
examples/multi/log.30Nov20.powerlaw.intel.4
Normal file
@ -0,0 +1,291 @@
|
|||||||
|
LAMMPS (24 Dec 2020)
|
||||||
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97)
|
||||||
|
using 1 OpenMP thread(s) per MPI task
|
||||||
|
# Shear power-law distributed granular particles
|
||||||
|
|
||||||
|
units lj
|
||||||
|
atom_style sphere
|
||||||
|
dimension 2
|
||||||
|
read_data data.powerlaw
|
||||||
|
Reading data file ...
|
||||||
|
triclinic box = (9.9514336 9.9514336 0.0000000) to (331.81396 331.81396 1.0000000) with tilt (0.0000000 0.0000000 0.0000000)
|
||||||
|
2 by 2 by 1 MPI processor grid
|
||||||
|
reading atoms ...
|
||||||
|
10000 atoms
|
||||||
|
reading velocities ...
|
||||||
|
10000 velocities
|
||||||
|
read_data CPU = 0.114 seconds
|
||||||
|
change_box all triclinic
|
||||||
|
Changing box ...
|
||||||
|
triclinic box = (9.9514336 9.9514336 0.0000000) to (331.81396 331.81396 1.0000000) with tilt (0.0000000 0.0000000 0.0000000)
|
||||||
|
|
||||||
|
# multi neighbor and comm for efficiency
|
||||||
|
|
||||||
|
neighbor 1 multi
|
||||||
|
neigh_modify delay 0 collection/interval 6 1.5 3 10 30 100 200
|
||||||
|
comm_modify mode multi vel yes reduce/multi
|
||||||
|
|
||||||
|
# granular potential
|
||||||
|
|
||||||
|
pair_style granular
|
||||||
|
pair_coeff * * hooke 20.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity
|
||||||
|
|
||||||
|
# fixes
|
||||||
|
|
||||||
|
fix 1 all nve/sphere
|
||||||
|
fix 2 all enforce2d
|
||||||
|
fix 3 all deform 1 xy erate 1e-4
|
||||||
|
|
||||||
|
# dump 1 all custom 20000 dump.granular id x y z radius
|
||||||
|
|
||||||
|
thermo_style custom step temp epair etotal press vol pxy
|
||||||
|
thermo 1000
|
||||||
|
|
||||||
|
timestep 0.005
|
||||||
|
|
||||||
|
run 200000
|
||||||
|
Neighbor list info ...
|
||||||
|
update every 1 steps, delay 0 steps, check yes
|
||||||
|
max neighbors/atom: 2000, page size: 100000
|
||||||
|
master list distance cutoff = 164.7888
|
||||||
|
ghost atom cutoff = 164.7888
|
||||||
|
binsize = 82.3944, bins = 4 4 1
|
||||||
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||||
|
(1) pair granular, perpetual
|
||||||
|
attributes: half, newton on, size, history
|
||||||
|
pair build: half/size/multi/newton/tri
|
||||||
|
stencil: half/multi/2d/tri
|
||||||
|
bin: multi
|
||||||
|
Per MPI rank memory allocation (min/avg/max) = 12.65 | 12.67 | 12.68 Mbytes
|
||||||
|
Step Temp E_pair TotEng Press Volume Pxy
|
||||||
|
0 4.9204851e-05 0 4.9199931e-05 0.61204991 103595.49 -0.00083309917
|
||||||
|
1000 0.00038076464 0 0.00038072657 0.58694623 103595.49 -0.0066712806
|
||||||
|
2000 0.00027986478 0 0.00027983679 0.5845274 103595.49 -0.008880933
|
||||||
|
3000 0.00022105227 0 0.00022103017 0.58295464 103595.49 -0.011327442
|
||||||
|
4000 0.00020888366 0 0.00020886277 0.5826542 103595.49 -0.014147424
|
||||||
|
5000 0.00019912663 0 0.00019910672 0.58175837 103595.49 -0.015685634
|
||||||
|
6000 0.0001989441 0 0.00019892421 0.58170841 103595.49 -0.017379973
|
||||||
|
7000 0.00019307783 0 0.00019305852 0.58133913 103595.49 -0.019556709
|
||||||
|
8000 0.00018132444 0 0.00018130631 0.58134077 103595.49 -0.021609399
|
||||||
|
9000 0.00017909088 0 0.00017907297 0.58117179 103595.49 -0.023603514
|
||||||
|
10000 0.00018391928 0 0.00018390089 0.58070675 103595.49 -0.026026784
|
||||||
|
11000 0.00018985439 0 0.00018983541 0.58006086 103595.49 -0.028574238
|
||||||
|
12000 0.00018903569 0 0.00018901678 0.5794232 103595.49 -0.031151884
|
||||||
|
13000 0.00019070382 0 0.00019068475 0.57890243 103595.49 -0.033469404
|
||||||
|
14000 0.00019371625 0 0.00019369688 0.5787389 103595.49 -0.035646526
|
||||||
|
15000 0.00019833475 0 0.00019831492 0.57883166 103595.49 -0.037709788
|
||||||
|
16000 0.0002011729 0 0.00020115278 0.57875606 103595.49 -0.039452453
|
||||||
|
17000 0.00020285197 0 0.00020283168 0.5786311 103595.49 -0.040960671
|
||||||
|
18000 0.00020319173 0 0.00020317141 0.57842387 103595.49 -0.042257076
|
||||||
|
19000 0.00020290253 0 0.00020288224 0.57795043 103595.49 -0.043364149
|
||||||
|
20000 0.00020509847 0 0.00020507796 0.57714779 103595.49 -0.04439226
|
||||||
|
21000 0.0002180326 0 0.0002180108 0.57569003 103595.49 -0.044749042
|
||||||
|
22000 0.00020751218 0 0.00020749143 0.57477071 103595.49 -0.045719595
|
||||||
|
23000 0.0002205328 0 0.00022051075 0.57409228 103595.49 -0.047332145
|
||||||
|
24000 0.00022689643 0 0.00022687374 0.57325004 103595.49 -0.048717593
|
||||||
|
25000 0.00025224797 0 0.00025222275 0.57283728 103595.49 -0.050255013
|
||||||
|
26000 0.00025343192 0 0.00025340657 0.5723866 103595.49 -0.051604294
|
||||||
|
27000 0.0002668981 0 0.00026687141 0.57221051 103595.49 -0.052915314
|
||||||
|
28000 0.00027867942 0 0.00027865155 0.57197889 103595.49 -0.053831415
|
||||||
|
29000 0.00028697868 0 0.00028694998 0.57177287 103595.49 -0.054693262
|
||||||
|
30000 0.00028857623 0 0.00028854737 0.5714545 103595.49 -0.055559583
|
||||||
|
31000 0.00029228526 0 0.00029225603 0.57110328 103595.49 -0.056491646
|
||||||
|
32000 0.00029648479 0 0.00029645514 0.57060242 103595.49 -0.057299367
|
||||||
|
33000 0.00030524226 0 0.00030521174 0.57003089 103595.49 -0.058207205
|
||||||
|
34000 0.00031725278 0 0.00031722106 0.56920179 103595.49 -0.059123522
|
||||||
|
35000 0.00032273715 0 0.00032270488 0.56844806 103595.49 -0.06001074
|
||||||
|
36000 0.00033013214 0 0.00033009912 0.56795631 103595.49 -0.06107304
|
||||||
|
37000 0.00033942364 0 0.00033938969 0.56749308 103595.49 -0.062060209
|
||||||
|
38000 0.00035140856 0 0.00035137342 0.56682754 103595.49 -0.062954063
|
||||||
|
39000 0.00036125739 0 0.00036122126 0.56654839 103595.49 -0.063755554
|
||||||
|
40000 0.00037765404 0 0.00037761628 0.56619876 103595.49 -0.064535888
|
||||||
|
41000 0.00040833154 0 0.00040829071 0.56554179 103595.49 -0.064688901
|
||||||
|
42000 0.0004285629 0 0.00042852004 0.56474124 103595.49 -0.06526276
|
||||||
|
43000 0.00042691211 0 0.00042686942 0.56362219 103595.49 -0.065275494
|
||||||
|
44000 0.00040296803 0 0.00040292773 0.56310053 103595.49 -0.065625772
|
||||||
|
45000 0.00040933842 0 0.00040929749 0.56291338 103595.49 -0.066164396
|
||||||
|
46000 0.00040202229 0 0.00040198209 0.56273845 103595.49 -0.066541045
|
||||||
|
47000 0.00038914157 0 0.00038910266 0.562658 103595.49 -0.067357923
|
||||||
|
48000 0.00038428678 0 0.00038424835 0.5627468 103595.49 -0.068230972
|
||||||
|
49000 0.00036912501 0 0.0003690881 0.56261857 103595.49 -0.068794933
|
||||||
|
50000 0.00035203987 0 0.00035200467 0.56258099 103595.49 -0.069290362
|
||||||
|
51000 0.00034400774 0 0.00034397334 0.56237066 103595.49 -0.070274303
|
||||||
|
52000 0.00034126666 0 0.00034123253 0.56221436 103595.49 -0.071744779
|
||||||
|
53000 0.00033563205 0 0.00033559849 0.56195218 103595.49 -0.072836324
|
||||||
|
54000 0.0003304406 0 0.00033040756 0.5623187 103595.49 -0.073999087
|
||||||
|
55000 0.00032742828 0 0.00032739553 0.56225383 103595.49 -0.075066978
|
||||||
|
56000 0.00032696921 0 0.00032693651 0.56285643 103595.49 -0.076445225
|
||||||
|
57000 0.0003316388 0 0.00033160564 0.56354513 103595.49 -0.077683955
|
||||||
|
58000 0.00034325202 0 0.0003432177 0.56416895 103595.49 -0.078839054
|
||||||
|
59000 0.0003433584 0 0.00034332406 0.56490343 103595.49 -0.079658776
|
||||||
|
60000 0.00034732721 0 0.00034729247 0.5651932 103595.49 -0.080573609
|
||||||
|
61000 0.00034978913 0 0.00034975415 0.56517379 103595.49 -0.081109788
|
||||||
|
62000 0.00034995232 0 0.00034991733 0.56534537 103595.49 -0.081491908
|
||||||
|
63000 0.00033854315 0 0.00033850929 0.56582246 103595.49 -0.081894953
|
||||||
|
64000 0.0003260452 0 0.00032601259 0.56583259 103595.49 -0.082790811
|
||||||
|
65000 0.00031763096 0 0.0003175992 0.56576947 103595.49 -0.083707224
|
||||||
|
66000 0.00031761371 0 0.00031758194 0.56548785 103595.49 -0.084243042
|
||||||
|
67000 0.00031503681 0 0.0003150053 0.56483862 103595.49 -0.08451056
|
||||||
|
68000 0.0003036386 0 0.00030360824 0.56444755 103595.49 -0.084967521
|
||||||
|
69000 0.00030398979 0 0.00030395939 0.56436362 103595.49 -0.085541879
|
||||||
|
70000 0.0003281569 0 0.00032812409 0.56372598 103595.49 -0.085287975
|
||||||
|
71000 0.00035614631 0 0.0003561107 0.56322133 103595.49 -0.084970215
|
||||||
|
72000 0.00032709207 0 0.00032705936 0.56231837 103595.49 -0.085540239
|
||||||
|
73000 0.00032545048 0 0.00032541793 0.56278947 103595.49 -0.085940822
|
||||||
|
74000 0.00033285331 0 0.00033282002 0.56288405 103595.49 -0.08695227
|
||||||
|
75000 0.00034622589 0 0.00034619127 0.56198219 103595.49 -0.086349357
|
||||||
|
76000 0.00033654825 0 0.0003365146 0.56183659 103595.49 -0.086892729
|
||||||
|
77000 0.00033550364 0 0.00033547009 0.56197292 103595.49 -0.087018641
|
||||||
|
78000 0.00032680247 0 0.00032676979 0.56183307 103595.49 -0.087097072
|
||||||
|
79000 0.00031624495 0 0.00031621333 0.56161689 103595.49 -0.087358849
|
||||||
|
80000 0.0003124879 0 0.00031245665 0.5618608 103595.49 -0.087165611
|
||||||
|
81000 0.00029451552 0 0.00029448606 0.56211081 103595.49 -0.087652479
|
||||||
|
82000 0.00029588468 0 0.00029585509 0.5628096 103595.49 -0.08832193
|
||||||
|
83000 0.00030483225 0 0.00030480177 0.56261673 103595.49 -0.088586937
|
||||||
|
84000 0.00029556003 0 0.00029553047 0.56272654 103595.49 -0.089434209
|
||||||
|
85000 0.00030506369 0 0.00030503319 0.5627918 103595.49 -0.089830152
|
||||||
|
86000 0.00030015302 0 0.00030012301 0.56240656 103595.49 -0.090100219
|
||||||
|
87000 0.00030322942 0 0.0003031991 0.56243997 103595.49 -0.090327187
|
||||||
|
88000 0.00030569181 0 0.00030566124 0.56236256 103595.49 -0.090734148
|
||||||
|
89000 0.00031220625 0 0.00031217503 0.5621542 103595.49 -0.090898044
|
||||||
|
90000 0.00032214966 0 0.00032211744 0.56209534 103595.49 -0.090909986
|
||||||
|
91000 0.00033884101 0 0.00033880712 0.56191673 103595.49 -0.090818046
|
||||||
|
92000 0.00033260559 0 0.00033257233 0.56172194 103595.49 -0.090647169
|
||||||
|
93000 0.00032732547 0 0.00032729274 0.5619652 103595.49 -0.090575176
|
||||||
|
94000 0.00033817734 0 0.00033814352 0.56155436 103595.49 -0.090700379
|
||||||
|
95000 0.00033009649 0 0.00033006348 0.56147407 103595.49 -0.090940641
|
||||||
|
96000 0.00032882782 0 0.00032879494 0.56191577 103595.49 -0.091469188
|
||||||
|
97000 0.00032856078 0 0.00032852793 0.56271585 103595.49 -0.092256803
|
||||||
|
98000 0.00033030749 0 0.00033027446 0.56340097 103595.49 -0.093188128
|
||||||
|
99000 0.00033611507 0 0.00033608146 0.56375754 103595.49 -0.093539699
|
||||||
|
100000 0.00034990568 0 0.00034987069 0.56450225 103595.49 -0.093951624
|
||||||
|
101000 0.00044441478 0 0.00044437034 0.56437908 103595.49 -0.094161976
|
||||||
|
102000 0.00045403284 0 0.00045398743 0.56433013 103595.49 -0.093900071
|
||||||
|
103000 0.00045412317 0 0.00045407776 0.56468095 103595.49 -0.093670567
|
||||||
|
104000 0.00046494637 0 0.00046489988 0.56478442 103595.49 -0.093397211
|
||||||
|
105000 0.00047962271 0 0.00047957475 0.56482329 103595.49 -0.093141318
|
||||||
|
106000 0.00046840864 0 0.0004683618 0.56494359 103595.49 -0.092994704
|
||||||
|
107000 0.00046432422 0 0.00046427779 0.56543377 103595.49 -0.093135897
|
||||||
|
108000 0.0004655443 0 0.00046549774 0.5656898 103595.49 -0.093383926
|
||||||
|
109000 0.0004863785 0 0.00048632986 0.5657434 103595.49 -0.093328929
|
||||||
|
110000 0.00048804324 0 0.00048799443 0.5656147 103595.49 -0.09302382
|
||||||
|
111000 0.00050352097 0 0.00050347062 0.56529279 103595.49 -0.092461373
|
||||||
|
112000 0.00050474509 0 0.00050469461 0.56537494 103595.49 -0.092212501
|
||||||
|
113000 0.0005125299 0 0.00051247865 0.56547326 103595.49 -0.092304578
|
||||||
|
114000 0.00052700168 0 0.00052694898 0.56568076 103595.49 -0.092013613
|
||||||
|
115000 0.00054217865 0 0.00054212444 0.56526328 103595.49 -0.091011537
|
||||||
|
116000 0.00055122699 0 0.00055117186 0.56489606 103595.49 -0.090688925
|
||||||
|
117000 0.00055802701 0 0.00055797121 0.56458767 103595.49 -0.090385903
|
||||||
|
118000 0.00055416633 0 0.00055411091 0.56433528 103595.49 -0.090454192
|
||||||
|
119000 0.00055519395 0 0.00055513843 0.56411926 103595.49 -0.090495063
|
||||||
|
120000 0.0005535194 0 0.00055346405 0.56424847 103595.49 -0.090915789
|
||||||
|
121000 0.00054781097 0 0.00054775619 0.56443756 103595.49 -0.090687173
|
||||||
|
122000 0.00054528815 0 0.00054523362 0.56401103 103595.49 -0.090443168
|
||||||
|
123000 0.0005456223 0 0.00054556773 0.56376875 103595.49 -0.090277114
|
||||||
|
124000 0.00054080131 0 0.00054074723 0.563306 103595.49 -0.091297668
|
||||||
|
125000 0.00054597 0 0.0005459154 0.56387718 103595.49 -0.091522394
|
||||||
|
126000 0.000544669 0 0.00054461453 0.56318185 103595.49 -0.091100523
|
||||||
|
127000 0.00054592361 0 0.00054586902 0.56328758 103595.49 -0.091299714
|
||||||
|
128000 0.00056246325 0 0.000562407 0.56296852 103595.49 -0.091491356
|
||||||
|
129000 0.00057655488 0 0.00057649723 0.56242057 103595.49 -0.091474584
|
||||||
|
130000 0.00060363901 0 0.00060357864 0.56182729 103595.49 -0.091367782
|
||||||
|
131000 0.00060590757 0 0.00060584698 0.56115572 103595.49 -0.090594163
|
||||||
|
132000 0.00061689139 0 0.0006168297 0.56029248 103595.49 -0.089857939
|
||||||
|
133000 0.00063288773 0 0.00063282444 0.55971427 103595.49 -0.08954619
|
||||||
|
134000 0.00064153654 0 0.00064147238 0.55929877 103595.49 -0.089860563
|
||||||
|
135000 0.00065473169 0 0.00065466622 0.5590797 103595.49 -0.089932375
|
||||||
|
136000 0.0006814182 0 0.00068135006 0.55797116 103595.49 -0.08929097
|
||||||
|
137000 0.00068344911 0 0.00068338077 0.55796657 103595.49 -0.089644888
|
||||||
|
138000 0.00071510067 0 0.00071502916 0.55752379 103595.49 -0.089734088
|
||||||
|
139000 0.00074772787 0 0.0007476531 0.55740054 103595.49 -0.089968295
|
||||||
|
140000 0.00072706311 0 0.0007269904 0.55659113 103595.49 -0.090370844
|
||||||
|
141000 0.0007179286 0 0.00071785681 0.55659012 103595.49 -0.089976688
|
||||||
|
142000 0.00072587657 0 0.00072580399 0.55589037 103595.49 -0.090532153
|
||||||
|
143000 0.00074470967 0 0.0007446352 0.55553128 103595.49 -0.091019969
|
||||||
|
144000 0.00071737422 0 0.00071730248 0.55555994 103595.49 -0.090926005
|
||||||
|
145000 0.00070363824 0 0.00070356787 0.55548936 103595.49 -0.0912353
|
||||||
|
146000 0.00069604487 0 0.00069597527 0.55540516 103595.49 -0.091656715
|
||||||
|
147000 0.00070047196 0 0.00070040191 0.55466746 103595.49 -0.092101291
|
||||||
|
148000 0.00069764904 0 0.00069757927 0.55460283 103595.49 -0.092334573
|
||||||
|
149000 0.00068884707 0 0.00068877819 0.55462796 103595.49 -0.0928736
|
||||||
|
150000 0.00067704593 0 0.00067697823 0.55520015 103595.49 -0.093512131
|
||||||
|
151000 0.00067702275 0 0.00067695505 0.55530068 103595.49 -0.094127311
|
||||||
|
152000 0.000690717 0 0.00069064792 0.55432538 103595.49 -0.094248615
|
||||||
|
153000 0.00067758953 0 0.00067752177 0.55460446 103595.49 -0.094839924
|
||||||
|
154000 0.00067748542 0 0.00067741767 0.55532529 103595.49 -0.095832411
|
||||||
|
155000 0.00068723442 0 0.0006871657 0.55637763 103595.49 -0.096838207
|
||||||
|
156000 0.00071590663 0 0.00071583504 0.5569485 103595.49 -0.097686166
|
||||||
|
157000 0.00078378647 0 0.0007837081 0.55755381 103595.49 -0.097968527
|
||||||
|
158000 0.00080144334 0 0.00080136319 0.55741023 103595.49 -0.098119361
|
||||||
|
159000 0.00079183165 0 0.00079175247 0.55756142 103595.49 -0.097925888
|
||||||
|
160000 0.00081212358 0 0.00081204237 0.55669124 103595.49 -0.098171108
|
||||||
|
161000 0.00082903843 0 0.00082895553 0.55608918 103595.49 -0.097827206
|
||||||
|
162000 0.00084257416 0 0.0008424899 0.5560239 103595.49 -0.096775743
|
||||||
|
163000 0.00086279615 0 0.00086270987 0.55550215 103595.49 -0.095981927
|
||||||
|
164000 0.00092139657 0 0.00092130443 0.55395137 103595.49 -0.095215338
|
||||||
|
165000 0.00095519936 0 0.00095510384 0.55376787 103595.49 -0.0945666
|
||||||
|
166000 0.00092201276 0 0.00092192056 0.55373794 103595.49 -0.093531233
|
||||||
|
167000 0.0008525194 0 0.00085243415 0.55375862 103595.49 -0.09389901
|
||||||
|
168000 0.00081977785 0 0.00081969587 0.5536646 103595.49 -0.093829746
|
||||||
|
169000 0.00079692467 0 0.00079684497 0.55416599 103595.49 -0.094433271
|
||||||
|
170000 0.00077787798 0 0.0007778002 0.55416629 103595.49 -0.095043413
|
||||||
|
171000 0.0007651362 0 0.00076505969 0.55418872 103595.49 -0.095212376
|
||||||
|
172000 0.00074631438 0 0.00074623975 0.55403881 103595.49 -0.095463949
|
||||||
|
173000 0.00074431288 0 0.00074423845 0.55415801 103595.49 -0.095319615
|
||||||
|
174000 0.00073924649 0 0.00073917257 0.55373682 103595.49 -0.094724272
|
||||||
|
175000 0.00070973165 0 0.00070966068 0.55393569 103595.49 -0.094201112
|
||||||
|
176000 0.00069820766 0 0.00069813784 0.55341229 103595.49 -0.093530469
|
||||||
|
177000 0.00070922657 0 0.00070915564 0.55282781 103595.49 -0.093282587
|
||||||
|
178000 0.00073688566 0 0.00073681197 0.55223248 103595.49 -0.092190554
|
||||||
|
179000 0.00072455886 0 0.0007244864 0.55244288 103595.49 -0.09182393
|
||||||
|
180000 0.00071894558 0 0.00071887369 0.55281517 103595.49 -0.092177032
|
||||||
|
181000 0.00071752475 0 0.000717453 0.55297293 103595.49 -0.09230934
|
||||||
|
182000 0.00072247421 0 0.00072240196 0.55287294 103595.49 -0.092465908
|
||||||
|
183000 0.00070596821 0 0.00070589761 0.5526242 103595.49 -0.092013313
|
||||||
|
184000 0.00072460909 0 0.00072453663 0.55230817 103595.49 -0.092211243
|
||||||
|
185000 0.00072499917 0 0.00072492667 0.55273387 103595.49 -0.092920761
|
||||||
|
186000 0.00072852698 0 0.00072845413 0.55358929 103595.49 -0.093428623
|
||||||
|
187000 0.00072515668 0 0.00072508417 0.55336733 103595.49 -0.093440126
|
||||||
|
188000 0.00071355728 0 0.00071348593 0.55408468 103595.49 -0.094819333
|
||||||
|
189000 0.00071703212 0 0.00071696042 0.55424355 103595.49 -0.096198144
|
||||||
|
190000 0.00071808849 0 0.00071801668 0.55504118 103595.49 -0.097199842
|
||||||
|
191000 0.00072458142 0 0.00072450896 0.55493515 103595.49 -0.097564772
|
||||||
|
192000 0.00071472504 0 0.00071465357 0.55572657 103595.49 -0.097663072
|
||||||
|
193000 0.00070803966 0 0.00070796886 0.55546116 103595.49 -0.097306162
|
||||||
|
194000 0.00068236077 0 0.00068229254 0.55581155 103595.49 -0.097141594
|
||||||
|
195000 0.00067304613 0 0.00067297882 0.55559507 103595.49 -0.096646489
|
||||||
|
196000 0.00066680808 0 0.0006667414 0.55512029 103595.49 -0.096241456
|
||||||
|
197000 0.00065829161 0 0.00065822578 0.55545375 103595.49 -0.095808778
|
||||||
|
198000 0.0006617611 0 0.00066169492 0.55551074 103595.49 -0.095423531
|
||||||
|
199000 0.00066805655 0 0.00066798975 0.55581298 103595.49 -0.095287337
|
||||||
|
200000 0.00067263902 0 0.00067257175 0.55601669 103595.49 -0.095551006
|
||||||
|
Loop time of 145.127 on 4 procs for 200000 steps with 10000 atoms
|
||||||
|
|
||||||
|
Performance: 595339.507 tau/day, 1378.101 timesteps/s
|
||||||
|
100.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||||
|
|
||||||
|
MPI task timing breakdown:
|
||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 57.89 | 91.946 | 113.82 | 229.7 | 63.36
|
||||||
|
Neigh | 0.34276 | 0.48607 | 0.56708 | 13.1 | 0.33
|
||||||
|
Comm | 6.569 | 28.916 | 63.505 | 417.0 | 19.92
|
||||||
|
Output | 0.0087178 | 0.011935 | 0.01563 | 2.3 | 0.01
|
||||||
|
Modify | 10.432 | 16.495 | 20.378 | 97.7 | 11.37
|
||||||
|
Other | | 7.272 | | | 5.01
|
||||||
|
|
||||||
|
Nlocal: 2500.00 ave 2990 max 1652 min
|
||||||
|
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||||
|
Nghost: 228.000 ave 254 max 198 min
|
||||||
|
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||||
|
Neighs: 8611.25 ave 10364 max 5676 min
|
||||||
|
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||||
|
|
||||||
|
Total # of neighbors = 34445
|
||||||
|
Ave neighs/atom = 3.4445000
|
||||||
|
Neighbor list builds = 241
|
||||||
|
Dangerous builds = 0
|
||||||
|
|
||||||
|
Please see the log.cite file for references relevant to this simulation
|
||||||
|
|
||||||
|
Total wall time: 0:02:25
|
||||||
@ -62,7 +62,7 @@ delete_atoms overlap 0.5 small big
|
|||||||
|
|
||||||
reset_timestep 0
|
reset_timestep 0
|
||||||
|
|
||||||
neighbor 0.3 bin
|
neighbor 0.3 multi
|
||||||
neigh_modify delay 0 every 1 check yes
|
neigh_modify delay 0 every 1 check yes
|
||||||
|
|
||||||
comm_modify mode multi group big vel yes
|
comm_modify mode multi group big vel yes
|
||||||
|
|||||||
@ -911,14 +911,14 @@ class lammps(object):
|
|||||||
else: return None
|
else: return None
|
||||||
|
|
||||||
if ctype == LMP_TYPE_SCALAR:
|
if ctype == LMP_TYPE_SCALAR:
|
||||||
if style == LMP_STYLE_GLOBAL:
|
if cstyle == LMP_STYLE_GLOBAL:
|
||||||
self.lib.lammps_extract_compute.restype = POINTER(c_double)
|
self.lib.lammps_extract_compute.restype = POINTER(c_double)
|
||||||
with ExceptionCheck(self):
|
with ExceptionCheck(self):
|
||||||
ptr = self.lib.lammps_extract_compute(self.lmp,cid,cstyle,ctype)
|
ptr = self.lib.lammps_extract_compute(self.lmp,cid,cstyle,ctype)
|
||||||
return ptr[0]
|
return ptr[0]
|
||||||
elif style == LMP_STYLE_ATOM:
|
elif cstyle == LMP_STYLE_ATOM:
|
||||||
return None
|
return None
|
||||||
elif style == LMP_STYLE_LOCAL:
|
elif cstyle == LMP_STYLE_LOCAL:
|
||||||
self.lib.lammps_extract_compute.restype = POINTER(c_int)
|
self.lib.lammps_extract_compute.restype = POINTER(c_int)
|
||||||
with ExceptionCheck(self):
|
with ExceptionCheck(self):
|
||||||
ptr = self.lib.lammps_extract_compute(self.lmp,cid,cstyle,ctype)
|
ptr = self.lib.lammps_extract_compute(self.lmp,cid,cstyle,ctype)
|
||||||
|
|||||||
@ -43,6 +43,7 @@ PairGranHookeHistory::PairGranHookeHistory(LAMMPS *lmp) : Pair(lmp)
|
|||||||
single_enable = 1;
|
single_enable = 1;
|
||||||
no_virial_fdotr_compute = 1;
|
no_virial_fdotr_compute = 1;
|
||||||
centroidstressflag = CENTROID_NOTAVAIL;
|
centroidstressflag = CENTROID_NOTAVAIL;
|
||||||
|
finitecutflag = 1;
|
||||||
history = 1;
|
history = 1;
|
||||||
size_history = 3;
|
size_history = 3;
|
||||||
|
|
||||||
@ -798,3 +799,23 @@ double PairGranHookeHistory::memory_usage()
|
|||||||
double bytes = (double)nmax * sizeof(double);
|
double bytes = (double)nmax * sizeof(double);
|
||||||
return bytes;
|
return bytes;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
self-interaction range of particle
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
double PairGranHookeHistory::atom2cut(int i)
|
||||||
|
{
|
||||||
|
double cut = atom->radius[i]*2;
|
||||||
|
return cut;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
maximum interaction range for two finite particles
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
double PairGranHookeHistory::radii2cut(double r1, double r2)
|
||||||
|
{
|
||||||
|
double cut = r1+r2;
|
||||||
|
return cut;
|
||||||
|
}
|
||||||
|
|||||||
@ -42,6 +42,8 @@ class PairGranHookeHistory : public Pair {
|
|||||||
int pack_forward_comm(int, int *, double *, int, int *);
|
int pack_forward_comm(int, int *, double *, int, int *);
|
||||||
void unpack_forward_comm(int, int, double *);
|
void unpack_forward_comm(int, int, double *);
|
||||||
double memory_usage();
|
double memory_usage();
|
||||||
|
double atom2cut(int);
|
||||||
|
double radii2cut(double,double);
|
||||||
|
|
||||||
protected:
|
protected:
|
||||||
double kn,kt,gamman,gammat,xmu;
|
double kn,kt,gamman,gammat,xmu;
|
||||||
|
|||||||
@ -67,6 +67,7 @@ PairGranular::PairGranular(LAMMPS *lmp) : Pair(lmp)
|
|||||||
single_enable = 1;
|
single_enable = 1;
|
||||||
no_virial_fdotr_compute = 1;
|
no_virial_fdotr_compute = 1;
|
||||||
centroidstressflag = CENTROID_NOTAVAIL;
|
centroidstressflag = CENTROID_NOTAVAIL;
|
||||||
|
finitecutflag = 1;
|
||||||
|
|
||||||
single_extra = 12;
|
single_extra = 12;
|
||||||
svector = new double[single_extra];
|
svector = new double[single_extra];
|
||||||
@ -1837,3 +1838,50 @@ void PairGranular::transfer_history(double* source, double* target)
|
|||||||
for (int i = 0; i < size_history; i++)
|
for (int i = 0; i < size_history; i++)
|
||||||
target[i] = history_transfer_factors[i]*source[i];
|
target[i] = history_transfer_factors[i]*source[i];
|
||||||
}
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
self-interaction range of particle
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
double PairGranular::atom2cut(int i)
|
||||||
|
{
|
||||||
|
double cut;
|
||||||
|
|
||||||
|
cut = atom->radius[i]*2;
|
||||||
|
if(beyond_contact) {
|
||||||
|
int itype = atom->type[i];
|
||||||
|
if(normal_model[itype][itype] == JKR) {
|
||||||
|
cut += pulloff_distance(cut, cut, itype, itype);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
return cut;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
maximum interaction range for two finite particles
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
double PairGranular::radii2cut(double r1, double r2)
|
||||||
|
{
|
||||||
|
double cut = 0.0;
|
||||||
|
|
||||||
|
if(beyond_contact) {
|
||||||
|
int n = atom->ntypes;
|
||||||
|
double temp;
|
||||||
|
|
||||||
|
// Check all combinations of i and j to find theoretical maximum pull off distance
|
||||||
|
for(int i = 0; i < n; i++){
|
||||||
|
for(int j = 0; j < n; j++){
|
||||||
|
if(normal_model[i][j] == JKR) {
|
||||||
|
temp = pulloff_distance(r1, r2, i, j);
|
||||||
|
if(temp > cut) cut = temp;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
cut += r1 + r2;
|
||||||
|
|
||||||
|
return cut;
|
||||||
|
}
|
||||||
|
|||||||
@ -40,6 +40,8 @@ class PairGranular : public Pair {
|
|||||||
int pack_forward_comm(int, int *, double *, int, int *);
|
int pack_forward_comm(int, int *, double *, int, int *);
|
||||||
void unpack_forward_comm(int, int, double *);
|
void unpack_forward_comm(int, int, double *);
|
||||||
double memory_usage();
|
double memory_usage();
|
||||||
|
double atom2cut(int);
|
||||||
|
double radii2cut(double,double);
|
||||||
|
|
||||||
protected:
|
protected:
|
||||||
double dt;
|
double dt;
|
||||||
|
|||||||
@ -15,11 +15,11 @@
|
|||||||
|
|
||||||
NBinStyle(kk/host,
|
NBinStyle(kk/host,
|
||||||
NBinKokkos<LMPHostType>,
|
NBinKokkos<LMPHostType>,
|
||||||
NB_KOKKOS_HOST)
|
NB_STANDARD | NB_KOKKOS_HOST)
|
||||||
|
|
||||||
NBinStyle(kk/device,
|
NBinStyle(kk/device,
|
||||||
NBinKokkos<LMPDeviceType>,
|
NBinKokkos<LMPDeviceType>,
|
||||||
NB_KOKKOS_DEVICE)
|
NB_STANDARD | NB_KOKKOS_DEVICE)
|
||||||
|
|
||||||
#else
|
#else
|
||||||
|
|
||||||
|
|||||||
@ -15,11 +15,11 @@
|
|||||||
|
|
||||||
NBinStyle(ssa/kk/host,
|
NBinStyle(ssa/kk/host,
|
||||||
NBinSSAKokkos<LMPHostType>,
|
NBinSSAKokkos<LMPHostType>,
|
||||||
NB_SSA | NB_KOKKOS_HOST)
|
NB_STANDARD | NB_SSA | NB_KOKKOS_HOST)
|
||||||
|
|
||||||
NBinStyle(ssa/kk/device,
|
NBinStyle(ssa/kk/device,
|
||||||
NBinSSAKokkos<LMPDeviceType>,
|
NBinSSAKokkos<LMPDeviceType>,
|
||||||
NB_SSA | NB_KOKKOS_DEVICE)
|
NB_STANDARD | NB_SSA | NB_KOKKOS_DEVICE)
|
||||||
|
|
||||||
#else
|
#else
|
||||||
|
|
||||||
|
|||||||
@ -15,7 +15,7 @@
|
|||||||
|
|
||||||
NBinStyle(ssa,
|
NBinStyle(ssa,
|
||||||
NBinSSA,
|
NBinSSA,
|
||||||
NB_SSA)
|
NB_STANDARD | NB_SSA)
|
||||||
|
|
||||||
#else
|
#else
|
||||||
|
|
||||||
|
|||||||
@ -16,13 +16,13 @@
|
|||||||
James Larentzos and Timothy I. Mattox (Engility Corporation)
|
James Larentzos and Timothy I. Mattox (Engility Corporation)
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
#include "nstencil_half_bin_2d_newton_ssa.h"
|
#include "nstencil_half_bin_2d_ssa.h"
|
||||||
|
|
||||||
using namespace LAMMPS_NS;
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
NStencilHalfBin2dNewtonSSA::NStencilHalfBin2dNewtonSSA(LAMMPS *lmp) :
|
NStencilHalfBin2dSSA::NStencilHalfBin2dSSA(LAMMPS *lmp) :
|
||||||
NStencilSSA(lmp) {}
|
NStencilSSA(lmp) {}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
@ -37,7 +37,7 @@ NStencilHalfBin2dNewtonSSA::NStencilHalfBin2dNewtonSSA(LAMMPS *lmp) :
|
|||||||
to locate all the Active Interaction Region (AIR) ghosts for SSA
|
to locate all the Active Interaction Region (AIR) ghosts for SSA
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
void NStencilHalfBin2dNewtonSSA::create()
|
void NStencilHalfBin2dSSA::create()
|
||||||
{
|
{
|
||||||
int i,j,pos = 0;
|
int i,j,pos = 0;
|
||||||
nstencil_ssa[0] = 0; // redundant info, but saves a conditional
|
nstencil_ssa[0] = 0; // redundant info, but saves a conditional
|
||||||
@ -13,23 +13,23 @@
|
|||||||
|
|
||||||
#ifdef NSTENCIL_CLASS
|
#ifdef NSTENCIL_CLASS
|
||||||
|
|
||||||
NStencilStyle(half/bin/2d/newton/ssa,
|
NStencilStyle(half/bin/2d/ssa,
|
||||||
NStencilHalfBin2dNewtonSSA,
|
NStencilHalfBin2dSSA,
|
||||||
NS_HALF | NS_BIN | NS_2D | NS_NEWTON | NS_SSA | NS_ORTHO | NS_GHOST)
|
NS_HALF | NS_BIN | NS_2D | NS_SSA | NS_ORTHO | NS_GHOST)
|
||||||
|
|
||||||
#else
|
#else
|
||||||
|
|
||||||
#ifndef LMP_NSTENCIL_HALF_BIN_2D_NEWTON_SSA_H
|
#ifndef LMP_NSTENCIL_HALF_BIN_2D_SSA_H
|
||||||
#define LMP_NSTENCIL_HALF_BIN_2D_NEWTON_SSA_H
|
#define LMP_NSTENCIL_HALF_BIN_2D_SSA_H
|
||||||
|
|
||||||
#include "nstencil_ssa.h"
|
#include "nstencil_ssa.h"
|
||||||
|
|
||||||
namespace LAMMPS_NS {
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
class NStencilHalfBin2dNewtonSSA : public NStencilSSA {
|
class NStencilHalfBin2dSSA : public NStencilSSA {
|
||||||
public:
|
public:
|
||||||
NStencilHalfBin2dNewtonSSA(class LAMMPS *);
|
NStencilHalfBin2dSSA(class LAMMPS *);
|
||||||
~NStencilHalfBin2dNewtonSSA() {}
|
~NStencilHalfBin2dSSA() {}
|
||||||
void create();
|
void create();
|
||||||
};
|
};
|
||||||
|
|
||||||
@ -16,13 +16,13 @@
|
|||||||
James Larentzos and Timothy I. Mattox (Engility Corporation)
|
James Larentzos and Timothy I. Mattox (Engility Corporation)
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
#include "nstencil_half_bin_3d_newton_ssa.h"
|
#include "nstencil_half_bin_3d_ssa.h"
|
||||||
|
|
||||||
using namespace LAMMPS_NS;
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
NStencilHalfBin3dNewtonSSA::NStencilHalfBin3dNewtonSSA(LAMMPS *lmp) :
|
NStencilHalfBin3dSSA::NStencilHalfBin3dSSA(LAMMPS *lmp) :
|
||||||
NStencilSSA(lmp) {}
|
NStencilSSA(lmp) {}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
@ -37,7 +37,7 @@ NStencilHalfBin3dNewtonSSA::NStencilHalfBin3dNewtonSSA(LAMMPS *lmp) :
|
|||||||
to locate all the Active Interaction Region (AIR) ghosts for SSA
|
to locate all the Active Interaction Region (AIR) ghosts for SSA
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
void NStencilHalfBin3dNewtonSSA::create()
|
void NStencilHalfBin3dSSA::create()
|
||||||
{
|
{
|
||||||
int i,j,k,pos = 0;
|
int i,j,k,pos = 0;
|
||||||
nstencil_ssa[0] = 0; // redundant info, but saves a conditional
|
nstencil_ssa[0] = 0; // redundant info, but saves a conditional
|
||||||
@ -13,23 +13,23 @@
|
|||||||
|
|
||||||
#ifdef NSTENCIL_CLASS
|
#ifdef NSTENCIL_CLASS
|
||||||
|
|
||||||
NStencilStyle(half/bin/3d/newton/ssa,
|
NStencilStyle(half/bin/3d/ssa,
|
||||||
NStencilHalfBin3dNewtonSSA,
|
NStencilHalfBin3dSSA,
|
||||||
NS_HALF | NS_BIN | NS_3D | NS_NEWTON | NS_SSA | NS_ORTHO | NS_GHOST)
|
NS_HALF | NS_BIN | NS_3D | NS_SSA | NS_ORTHO | NS_GHOST)
|
||||||
|
|
||||||
#else
|
#else
|
||||||
|
|
||||||
#ifndef LMP_NSTENCIL_HALF_BIN_3D_NEWTON_SSA_H
|
#ifndef LMP_NSTENCIL_HALF_BIN_3D_SSA_H
|
||||||
#define LMP_NSTENCIL_HALF_BIN_3D_NEWTON_SSA_H
|
#define LMP_NSTENCIL_HALF_BIN_3D_SSA_H
|
||||||
|
|
||||||
#include "nstencil_ssa.h"
|
#include "nstencil_ssa.h"
|
||||||
|
|
||||||
namespace LAMMPS_NS {
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
class NStencilHalfBin3dNewtonSSA : public NStencilSSA {
|
class NStencilHalfBin3dSSA : public NStencilSSA {
|
||||||
public:
|
public:
|
||||||
NStencilHalfBin3dNewtonSSA(class LAMMPS *);
|
NStencilHalfBin3dSSA(class LAMMPS *);
|
||||||
~NStencilHalfBin3dNewtonSSA() {}
|
~NStencilHalfBin3dSSA() {}
|
||||||
void create();
|
void create();
|
||||||
};
|
};
|
||||||
|
|
||||||
@ -15,7 +15,7 @@
|
|||||||
|
|
||||||
NBinStyle(intel,
|
NBinStyle(intel,
|
||||||
NBinIntel,
|
NBinIntel,
|
||||||
NB_INTEL)
|
NB_STANDARD | NB_INTEL)
|
||||||
|
|
||||||
#else
|
#else
|
||||||
|
|
||||||
|
|||||||
142
src/USER-OMP/npair_full_multi_old_omp.cpp
Normal file
142
src/USER-OMP/npair_full_multi_old_omp.cpp
Normal file
@ -0,0 +1,142 @@
|
|||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
https://lammps.sandia.gov/, 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 "omp_compat.h"
|
||||||
|
#include "npair_full_multi_old_omp.h"
|
||||||
|
#include "npair_omp.h"
|
||||||
|
#include "neigh_list.h"
|
||||||
|
#include "atom.h"
|
||||||
|
#include "atom_vec.h"
|
||||||
|
#include "molecule.h"
|
||||||
|
#include "domain.h"
|
||||||
|
#include "my_page.h"
|
||||||
|
#include "error.h"
|
||||||
|
|
||||||
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
NPairFullMultiOldOmp::NPairFullMultiOldOmp(LAMMPS *lmp) : NPair(lmp) {}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
binned neighbor list construction for all neighbors
|
||||||
|
multi-type stencil is itype dependent and is distance checked
|
||||||
|
every neighbor pair appears in list of both atoms i and j
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void NPairFullMultiOldOmp::build(NeighList *list)
|
||||||
|
{
|
||||||
|
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
|
||||||
|
const int molecular = atom->molecular;
|
||||||
|
const int moltemplate = (molecular == Atom::TEMPLATE) ? 1 : 0;
|
||||||
|
|
||||||
|
NPAIR_OMP_INIT;
|
||||||
|
#if defined(_OPENMP)
|
||||||
|
#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(list)
|
||||||
|
#endif
|
||||||
|
NPAIR_OMP_SETUP(nlocal);
|
||||||
|
|
||||||
|
int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom;
|
||||||
|
tagint tagprev;
|
||||||
|
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
||||||
|
int *neighptr,*s;
|
||||||
|
double *cutsq,*distsq;
|
||||||
|
|
||||||
|
// loop over each atom, storing neighbors
|
||||||
|
|
||||||
|
double **x = atom->x;
|
||||||
|
int *type = atom->type;
|
||||||
|
int *mask = atom->mask;
|
||||||
|
tagint *tag = atom->tag;
|
||||||
|
tagint *molecule = atom->molecule;
|
||||||
|
tagint **special = atom->special;
|
||||||
|
int **nspecial = atom->nspecial;
|
||||||
|
|
||||||
|
int *molindex = atom->molindex;
|
||||||
|
int *molatom = atom->molatom;
|
||||||
|
Molecule **onemols = atom->avec->onemols;
|
||||||
|
|
||||||
|
int *ilist = list->ilist;
|
||||||
|
int *numneigh = list->numneigh;
|
||||||
|
int **firstneigh = list->firstneigh;
|
||||||
|
|
||||||
|
// each thread has its own page allocator
|
||||||
|
MyPage<int> &ipage = list->ipage[tid];
|
||||||
|
ipage.reset();
|
||||||
|
|
||||||
|
for (i = ifrom; i < ito; i++) {
|
||||||
|
|
||||||
|
n = 0;
|
||||||
|
neighptr = ipage.vget();
|
||||||
|
|
||||||
|
itype = type[i];
|
||||||
|
xtmp = x[i][0];
|
||||||
|
ytmp = x[i][1];
|
||||||
|
ztmp = x[i][2];
|
||||||
|
if (moltemplate) {
|
||||||
|
imol = molindex[i];
|
||||||
|
iatom = molatom[i];
|
||||||
|
tagprev = tag[i] - iatom - 1;
|
||||||
|
}
|
||||||
|
|
||||||
|
// loop over all atoms in other bins in stencil, including self
|
||||||
|
// skip if i,j neighbor cutoff is less than bin distance
|
||||||
|
// skip i = j
|
||||||
|
|
||||||
|
ibin = atom2bin[i];
|
||||||
|
s = stencil_multi_old[itype];
|
||||||
|
distsq = distsq_multi_old[itype];
|
||||||
|
cutsq = cutneighsq[itype];
|
||||||
|
ns = nstencil_multi_old[itype];
|
||||||
|
for (k = 0; k < ns; k++) {
|
||||||
|
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
|
||||||
|
jtype = type[j];
|
||||||
|
if (cutsq[jtype] < distsq[k]) continue;
|
||||||
|
if (i == j) continue;
|
||||||
|
|
||||||
|
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
||||||
|
|
||||||
|
delx = xtmp - x[j][0];
|
||||||
|
dely = ytmp - x[j][1];
|
||||||
|
delz = ztmp - x[j][2];
|
||||||
|
rsq = delx*delx + dely*dely + delz*delz;
|
||||||
|
|
||||||
|
if (rsq <= cutneighsq[itype][jtype]) {
|
||||||
|
if (molecular != Atom::ATOMIC) {
|
||||||
|
if (!moltemplate)
|
||||||
|
which = find_special(special[i],nspecial[i],tag[j]);
|
||||||
|
else if (imol >=0)
|
||||||
|
which = find_special(onemols[imol]->special[iatom],
|
||||||
|
onemols[imol]->nspecial[iatom],
|
||||||
|
tag[j]-tagprev);
|
||||||
|
else which = 0;
|
||||||
|
if (which == 0) neighptr[n++] = j;
|
||||||
|
else if (domain->minimum_image_check(delx,dely,delz))
|
||||||
|
neighptr[n++] = j;
|
||||||
|
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
|
||||||
|
} else neighptr[n++] = j;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
ilist[i] = i;
|
||||||
|
firstneigh[i] = neighptr;
|
||||||
|
numneigh[i] = n;
|
||||||
|
ipage.vgot(n);
|
||||||
|
if (ipage.status())
|
||||||
|
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
|
||||||
|
}
|
||||||
|
NPAIR_OMP_CLOSE;
|
||||||
|
list->inum = nlocal;
|
||||||
|
list->gnum = 0;
|
||||||
|
}
|
||||||
@ -11,26 +11,27 @@
|
|||||||
See the README file in the top-level LAMMPS directory.
|
See the README file in the top-level LAMMPS directory.
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
#ifdef NSTENCIL_CLASS
|
#ifdef NPAIR_CLASS
|
||||||
|
|
||||||
NStencilStyle(half/bin/2d/newtoff,
|
NPairStyle(full/multi/old/omp,
|
||||||
NStencilHalfBin2dNewtoff,
|
NPairFullMultiOldOmp,
|
||||||
NS_HALF | NS_BIN | NS_2D | NS_NEWTOFF | NS_ORTHO | NS_TRI)
|
NP_FULL | NP_MULTI_OLD | NP_OMP |
|
||||||
|
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI)
|
||||||
|
|
||||||
#else
|
#else
|
||||||
|
|
||||||
#ifndef LMP_NSTENCIL_HALF_BIN_2D_NEWTOFF_H
|
#ifndef LMP_NPAIR_FULL_MULTI_OLD_OMP_H
|
||||||
#define LMP_NSTENCIL_HALF_BIN_2D_NEWTOFF_H
|
#define LMP_NPAIR_FULL_MULTI_OLD_OMP_H
|
||||||
|
|
||||||
#include "nstencil.h"
|
#include "npair.h"
|
||||||
|
|
||||||
namespace LAMMPS_NS {
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
class NStencilHalfBin2dNewtoff : public NStencil {
|
class NPairFullMultiOldOmp : public NPair {
|
||||||
public:
|
public:
|
||||||
NStencilHalfBin2dNewtoff(class LAMMPS *);
|
NPairFullMultiOldOmp(class LAMMPS *);
|
||||||
~NStencilHalfBin2dNewtoff() {}
|
~NPairFullMultiOldOmp() {}
|
||||||
void create();
|
void build(class NeighList *);
|
||||||
};
|
};
|
||||||
|
|
||||||
}
|
}
|
||||||
@ -14,6 +14,7 @@
|
|||||||
#include "omp_compat.h"
|
#include "omp_compat.h"
|
||||||
#include "npair_full_multi_omp.h"
|
#include "npair_full_multi_omp.h"
|
||||||
#include "npair_omp.h"
|
#include "npair_omp.h"
|
||||||
|
#include "neighbor.h"
|
||||||
#include "neigh_list.h"
|
#include "neigh_list.h"
|
||||||
#include "atom.h"
|
#include "atom.h"
|
||||||
#include "atom_vec.h"
|
#include "atom_vec.h"
|
||||||
@ -30,7 +31,7 @@ NPairFullMultiOmp::NPairFullMultiOmp(LAMMPS *lmp) : NPair(lmp) {}
|
|||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
binned neighbor list construction for all neighbors
|
binned neighbor list construction for all neighbors
|
||||||
multi-type stencil is itype dependent and is distance checked
|
multi stencil is icollection-jcollection dependent
|
||||||
every neighbor pair appears in list of both atoms i and j
|
every neighbor pair appears in list of both atoms i and j
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
@ -46,14 +47,15 @@ void NPairFullMultiOmp::build(NeighList *list)
|
|||||||
#endif
|
#endif
|
||||||
NPAIR_OMP_SETUP(nlocal);
|
NPAIR_OMP_SETUP(nlocal);
|
||||||
|
|
||||||
int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom;
|
int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,which,ns,imol,iatom;
|
||||||
tagint tagprev;
|
tagint tagprev;
|
||||||
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
||||||
int *neighptr,*s;
|
int *neighptr,*s;
|
||||||
double *cutsq,*distsq;
|
int js;
|
||||||
|
|
||||||
// loop over each atom, storing neighbors
|
// loop over each atom, storing neighbors
|
||||||
|
|
||||||
|
int *collection = neighbor->collection;
|
||||||
double **x = atom->x;
|
double **x = atom->x;
|
||||||
int *type = atom->type;
|
int *type = atom->type;
|
||||||
int *mask = atom->mask;
|
int *mask = atom->mask;
|
||||||
@ -80,6 +82,7 @@ void NPairFullMultiOmp::build(NeighList *list)
|
|||||||
neighptr = ipage.vget();
|
neighptr = ipage.vget();
|
||||||
|
|
||||||
itype = type[i];
|
itype = type[i];
|
||||||
|
icollection = collection[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];
|
||||||
@ -89,43 +92,51 @@ void NPairFullMultiOmp::build(NeighList *list)
|
|||||||
tagprev = tag[i] - iatom - 1;
|
tagprev = tag[i] - iatom - 1;
|
||||||
}
|
}
|
||||||
|
|
||||||
// loop over all atoms in other bins in stencil, including self
|
|
||||||
// skip if i,j neighbor cutoff is less than bin distance
|
|
||||||
// skip i = j
|
|
||||||
|
|
||||||
ibin = atom2bin[i];
|
ibin = atom2bin[i];
|
||||||
s = stencil_multi[itype];
|
|
||||||
distsq = distsq_multi[itype];
|
|
||||||
cutsq = cutneighsq[itype];
|
|
||||||
ns = nstencil_multi[itype];
|
|
||||||
for (k = 0; k < ns; k++) {
|
|
||||||
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
|
|
||||||
jtype = type[j];
|
|
||||||
if (cutsq[jtype] < distsq[k]) continue;
|
|
||||||
if (i == j) continue;
|
|
||||||
|
|
||||||
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
// loop through stencils for all collections
|
||||||
|
for (jcollection = 0; jcollection < ncollections; jcollection++) {
|
||||||
|
|
||||||
delx = xtmp - x[j][0];
|
// if same collection use own bin
|
||||||
dely = ytmp - x[j][1];
|
if (icollection == jcollection) jbin = ibin;
|
||||||
delz = ztmp - x[j][2];
|
else jbin = coord2bin(x[i], jcollection);
|
||||||
rsq = delx*delx + dely*dely + delz*delz;
|
|
||||||
|
|
||||||
if (rsq <= cutneighsq[itype][jtype]) {
|
// loop over all atoms in surrounding bins in stencil including self
|
||||||
if (molecular != Atom::ATOMIC) {
|
// skip i = j
|
||||||
if (!moltemplate)
|
// use full stencil for all collection combinations
|
||||||
which = find_special(special[i],nspecial[i],tag[j]);
|
|
||||||
else if (imol >=0)
|
s = stencil_multi[icollection][jcollection];
|
||||||
which = find_special(onemols[imol]->special[iatom],
|
ns = nstencil_multi[icollection][jcollection];
|
||||||
onemols[imol]->nspecial[iatom],
|
|
||||||
tag[j]-tagprev);
|
for (k = 0; k < ns; k++) {
|
||||||
else which = 0;
|
js = binhead_multi[jcollection][jbin + s[k]];
|
||||||
if (which == 0) neighptr[n++] = j;
|
for (j = js; j >= 0; j = bins[j]) {
|
||||||
else if (domain->minimum_image_check(delx,dely,delz))
|
if (i == j) continue;
|
||||||
neighptr[n++] = j;
|
|
||||||
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
|
jtype = type[j];
|
||||||
} else neighptr[n++] = j;
|
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
||||||
}
|
|
||||||
|
delx = xtmp - x[j][0];
|
||||||
|
dely = ytmp - x[j][1];
|
||||||
|
delz = ztmp - x[j][2];
|
||||||
|
rsq = delx*delx + dely*dely + delz*delz;
|
||||||
|
|
||||||
|
if (rsq <= cutneighsq[itype][jtype]) {
|
||||||
|
if (molecular != Atom::ATOMIC) {
|
||||||
|
if (!moltemplate)
|
||||||
|
which = find_special(special[i],nspecial[i],tag[j]);
|
||||||
|
else if (imol >= 0)
|
||||||
|
which = find_special(onemols[imol]->special[iatom],
|
||||||
|
onemols[imol]->nspecial[iatom],
|
||||||
|
tag[j]-tagprev);
|
||||||
|
else which = 0;
|
||||||
|
if (which == 0) neighptr[n++] = j;
|
||||||
|
else if (domain->minimum_image_check(delx,dely,delz))
|
||||||
|
neighptr[n++] = j;
|
||||||
|
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
|
||||||
|
} else neighptr[n++] = j;
|
||||||
|
}
|
||||||
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|||||||
@ -14,6 +14,7 @@
|
|||||||
#include "omp_compat.h"
|
#include "omp_compat.h"
|
||||||
#include "npair_half_multi_newtoff_omp.h"
|
#include "npair_half_multi_newtoff_omp.h"
|
||||||
#include "npair_omp.h"
|
#include "npair_omp.h"
|
||||||
|
#include "neighbor.h"
|
||||||
#include "neigh_list.h"
|
#include "neigh_list.h"
|
||||||
#include "atom.h"
|
#include "atom.h"
|
||||||
#include "atom_vec.h"
|
#include "atom_vec.h"
|
||||||
@ -30,8 +31,8 @@ NPairHalfMultiNewtoffOmp::NPairHalfMultiNewtoffOmp(LAMMPS *lmp) : NPair(lmp) {}
|
|||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
binned neighbor list construction with partial Newton's 3rd law
|
binned neighbor list construction with partial Newton's 3rd law
|
||||||
|
multi stencil is icollection-jcollection dependent
|
||||||
each owned atom i checks own bin and other bins in stencil
|
each owned atom i checks own bin and other bins in stencil
|
||||||
multi-type stencil is itype dependent and is distance checked
|
|
||||||
pair stored once if i,j are both owned and i < j
|
pair stored once if i,j are both owned and i < j
|
||||||
pair stored by me if j is ghost (also stored by proc owning j)
|
pair stored by me if j is ghost (also stored by proc owning j)
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
@ -48,14 +49,15 @@ void NPairHalfMultiNewtoffOmp::build(NeighList *list)
|
|||||||
#endif
|
#endif
|
||||||
NPAIR_OMP_SETUP(nlocal);
|
NPAIR_OMP_SETUP(nlocal);
|
||||||
|
|
||||||
int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom;
|
int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,which,ns,imol,iatom;
|
||||||
tagint tagprev;
|
tagint tagprev;
|
||||||
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
||||||
int *neighptr,*s;
|
int *neighptr,*s;
|
||||||
double *cutsq,*distsq;
|
int js;
|
||||||
|
|
||||||
// loop over each atom, storing neighbors
|
// loop over each atom, storing neighbors
|
||||||
|
|
||||||
|
int *collection = neighbor->collection;
|
||||||
double **x = atom->x;
|
double **x = atom->x;
|
||||||
int *type = atom->type;
|
int *type = atom->type;
|
||||||
int *mask = atom->mask;
|
int *mask = atom->mask;
|
||||||
@ -82,6 +84,7 @@ void NPairHalfMultiNewtoffOmp::build(NeighList *list)
|
|||||||
neighptr = ipage.vget();
|
neighptr = ipage.vget();
|
||||||
|
|
||||||
itype = type[i];
|
itype = type[i];
|
||||||
|
icollection = collection[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];
|
||||||
@ -91,44 +94,52 @@ void NPairHalfMultiNewtoffOmp::build(NeighList *list)
|
|||||||
tagprev = tag[i] - iatom - 1;
|
tagprev = tag[i] - iatom - 1;
|
||||||
}
|
}
|
||||||
|
|
||||||
// loop over all atoms in other bins in stencil including self
|
|
||||||
// only store pair if i < j
|
|
||||||
// skip if i,j neighbor cutoff is less than bin distance
|
|
||||||
// stores own/own pairs only once
|
|
||||||
// stores own/ghost pairs on both procs
|
|
||||||
|
|
||||||
ibin = atom2bin[i];
|
ibin = atom2bin[i];
|
||||||
s = stencil_multi[itype];
|
|
||||||
distsq = distsq_multi[itype];
|
|
||||||
cutsq = cutneighsq[itype];
|
|
||||||
ns = nstencil_multi[itype];
|
|
||||||
for (k = 0; k < ns; k++) {
|
|
||||||
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
|
|
||||||
if (j <= i) continue;
|
|
||||||
jtype = type[j];
|
|
||||||
if (cutsq[jtype] < distsq[k]) continue;
|
|
||||||
|
|
||||||
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
// loop through stencils for all collections
|
||||||
|
for (jcollection = 0; jcollection < ncollections; jcollection++) {
|
||||||
|
|
||||||
delx = xtmp - x[j][0];
|
// if same collection use own bin
|
||||||
dely = ytmp - x[j][1];
|
if (icollection == jcollection) jbin = ibin;
|
||||||
delz = ztmp - x[j][2];
|
else jbin = coord2bin(x[i], jcollection);
|
||||||
rsq = delx*delx + dely*dely + delz*delz;
|
|
||||||
|
|
||||||
if (rsq <= cutneighsq[itype][jtype]) {
|
// loop over all atoms in other bins in stencil including self
|
||||||
if (molecular != Atom::ATOMIC) {
|
// only store pair if i < j
|
||||||
if (!moltemplate)
|
// stores own/own pairs only once
|
||||||
which = find_special(special[i],nspecial[i],tag[j]);
|
// stores own/ghost pairs on both procs
|
||||||
else if (imol >=0)
|
// use full stencil for all collection combinations
|
||||||
which = find_special(onemols[imol]->special[iatom],
|
|
||||||
onemols[imol]->nspecial[iatom],
|
s = stencil_multi[icollection][jcollection];
|
||||||
tag[j]-tagprev);
|
ns = nstencil_multi[icollection][jcollection];
|
||||||
else which = 0;
|
|
||||||
if (which == 0) neighptr[n++] = j;
|
for (k = 0; k < ns; k++) {
|
||||||
else if (domain->minimum_image_check(delx,dely,delz))
|
js = binhead_multi[jcollection][jbin + s[k]];
|
||||||
neighptr[n++] = j;
|
for (j = js; j >= 0; j = bins[j]) {
|
||||||
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
|
if (j <= i) continue;
|
||||||
} else neighptr[n++] = j;
|
|
||||||
|
jtype = type[j];
|
||||||
|
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
||||||
|
|
||||||
|
delx = xtmp - x[j][0];
|
||||||
|
dely = ytmp - x[j][1];
|
||||||
|
delz = ztmp - x[j][2];
|
||||||
|
rsq = delx*delx + dely*dely + delz*delz;
|
||||||
|
|
||||||
|
if (rsq <= cutneighsq[itype][jtype]) {
|
||||||
|
if (molecular != Atom::ATOMIC) {
|
||||||
|
if (!moltemplate)
|
||||||
|
which = find_special(special[i],nspecial[i],tag[j]);
|
||||||
|
else if (imol >= 0)
|
||||||
|
which = find_special(onemols[imol]->special[iatom],
|
||||||
|
onemols[imol]->nspecial[iatom],
|
||||||
|
tag[j]-tagprev);
|
||||||
|
else which = 0;
|
||||||
|
if (which == 0) neighptr[n++] = j;
|
||||||
|
else if (domain->minimum_image_check(delx,dely,delz))
|
||||||
|
neighptr[n++] = j;
|
||||||
|
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
|
||||||
|
} else neighptr[n++] = j;
|
||||||
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|||||||
@ -14,6 +14,7 @@
|
|||||||
#include "omp_compat.h"
|
#include "omp_compat.h"
|
||||||
#include "npair_half_multi_newton_omp.h"
|
#include "npair_half_multi_newton_omp.h"
|
||||||
#include "npair_omp.h"
|
#include "npair_omp.h"
|
||||||
|
#include "neighbor.h"
|
||||||
#include "neigh_list.h"
|
#include "neigh_list.h"
|
||||||
#include "atom.h"
|
#include "atom.h"
|
||||||
#include "atom_vec.h"
|
#include "atom_vec.h"
|
||||||
@ -30,8 +31,8 @@ NPairHalfMultiNewtonOmp::NPairHalfMultiNewtonOmp(LAMMPS *lmp) : NPair(lmp) {}
|
|||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
binned neighbor list construction with full Newton's 3rd law
|
binned neighbor list construction with full Newton's 3rd law
|
||||||
|
multi stencil is icollection-jcollection dependent
|
||||||
each owned atom i checks its own bin and other bins in Newton stencil
|
each owned atom i checks its own bin and other bins in Newton stencil
|
||||||
multi-type stencil is itype dependent and is distance checked
|
|
||||||
every pair stored exactly once by some processor
|
every pair stored exactly once by some processor
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
@ -47,14 +48,15 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list)
|
|||||||
#endif
|
#endif
|
||||||
NPAIR_OMP_SETUP(nlocal);
|
NPAIR_OMP_SETUP(nlocal);
|
||||||
|
|
||||||
int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom;
|
int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,which,ns,imol,iatom;
|
||||||
tagint tagprev;
|
tagint tagprev;
|
||||||
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
||||||
int *neighptr,*s;
|
int *neighptr,*s;
|
||||||
double *cutsq,*distsq;
|
int js;
|
||||||
|
|
||||||
// loop over each atom, storing neighbors
|
// loop over each atom, storing neighbors
|
||||||
|
|
||||||
|
int *collection = neighbor->collection;
|
||||||
double **x = atom->x;
|
double **x = atom->x;
|
||||||
int *type = atom->type;
|
int *type = atom->type;
|
||||||
int *mask = atom->mask;
|
int *mask = atom->mask;
|
||||||
@ -81,6 +83,7 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list)
|
|||||||
neighptr = ipage.vget();
|
neighptr = ipage.vget();
|
||||||
|
|
||||||
itype = type[i];
|
itype = type[i];
|
||||||
|
icollection = collection[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];
|
||||||
@ -90,80 +93,103 @@ void NPairHalfMultiNewtonOmp::build(NeighList *list)
|
|||||||
tagprev = tag[i] - iatom - 1;
|
tagprev = tag[i] - iatom - 1;
|
||||||
}
|
}
|
||||||
|
|
||||||
// loop over rest of atoms in i's bin, ghosts are at end of linked list
|
|
||||||
// if j is owned atom, store it, since j is beyond i in linked list
|
|
||||||
// if j is ghost, only store if j coords are "above and to the right" of i
|
|
||||||
|
|
||||||
for (j = bins[i]; j >= 0; j = bins[j]) {
|
|
||||||
if (j >= nlocal) {
|
|
||||||
if (x[j][2] < ztmp) continue;
|
|
||||||
if (x[j][2] == ztmp) {
|
|
||||||
if (x[j][1] < ytmp) continue;
|
|
||||||
if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
jtype = type[j];
|
|
||||||
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
|
||||||
|
|
||||||
delx = xtmp - x[j][0];
|
|
||||||
dely = ytmp - x[j][1];
|
|
||||||
delz = ztmp - x[j][2];
|
|
||||||
rsq = delx*delx + dely*dely + delz*delz;
|
|
||||||
|
|
||||||
if (rsq <= cutneighsq[itype][jtype]) {
|
|
||||||
if (molecular != Atom::ATOMIC) {
|
|
||||||
if (!moltemplate)
|
|
||||||
which = find_special(special[i],nspecial[i],tag[j]);
|
|
||||||
else if (imol >=0)
|
|
||||||
which = find_special(onemols[imol]->special[iatom],
|
|
||||||
onemols[imol]->nspecial[iatom],
|
|
||||||
tag[j]-tagprev);
|
|
||||||
else which = 0;
|
|
||||||
if (which == 0) neighptr[n++] = j;
|
|
||||||
else if (domain->minimum_image_check(delx,dely,delz))
|
|
||||||
neighptr[n++] = j;
|
|
||||||
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
|
|
||||||
} else neighptr[n++] = j;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
// loop over all atoms in other bins in stencil, store every pair
|
|
||||||
// skip if i,j neighbor cutoff is less than bin distance
|
|
||||||
|
|
||||||
ibin = atom2bin[i];
|
ibin = atom2bin[i];
|
||||||
s = stencil_multi[itype];
|
|
||||||
distsq = distsq_multi[itype];
|
|
||||||
cutsq = cutneighsq[itype];
|
|
||||||
ns = nstencil_multi[itype];
|
|
||||||
for (k = 0; k < ns; k++) {
|
|
||||||
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
|
|
||||||
jtype = type[j];
|
|
||||||
if (cutsq[jtype] < distsq[k]) continue;
|
|
||||||
|
|
||||||
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
// loop through stencils for all collections
|
||||||
|
for (jcollection = 0; jcollection < ncollections; jcollection++) {
|
||||||
|
|
||||||
delx = xtmp - x[j][0];
|
// if same collection use own bin
|
||||||
dely = ytmp - x[j][1];
|
if (icollection == jcollection) jbin = ibin;
|
||||||
delz = ztmp - x[j][2];
|
else jbin = coord2bin(x[i], jcollection);
|
||||||
rsq = delx*delx + dely*dely + delz*delz;
|
|
||||||
|
|
||||||
if (rsq <= cutneighsq[itype][jtype]) {
|
// if same size: uses half stencil so check central bin
|
||||||
if (molecular != Atom::ATOMIC) {
|
if (cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){
|
||||||
if (!moltemplate)
|
|
||||||
which = find_special(special[i],nspecial[i],tag[j]);
|
if (icollection == jcollection) js = bins[i];
|
||||||
else if (imol >=0)
|
else js = binhead_multi[jcollection][jbin];
|
||||||
which = find_special(onemols[imol]->special[iatom],
|
|
||||||
onemols[imol]->nspecial[iatom],
|
// if same collection,
|
||||||
tag[j]-tagprev);
|
// if j is owned atom, store it, since j is beyond i in linked list
|
||||||
else which = 0;
|
// if j is ghost, only store if j coords are "above and to the right" of i
|
||||||
if (which == 0) neighptr[n++] = j;
|
|
||||||
else if (domain->minimum_image_check(delx,dely,delz))
|
// if different collections,
|
||||||
neighptr[n++] = j;
|
// if j is owned atom, store it if j > i
|
||||||
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
|
// if j is ghost, only store if j coords are "above and to the right" of i
|
||||||
} else neighptr[n++] = j;
|
|
||||||
}
|
for (j = js; j >= 0; j = bins[j]) {
|
||||||
|
if ((icollection != jcollection) && (j < i)) continue;
|
||||||
|
|
||||||
|
if (j >= nlocal) {
|
||||||
|
if (x[j][2] < ztmp) continue;
|
||||||
|
if (x[j][2] == ztmp) {
|
||||||
|
if (x[j][1] < ytmp) continue;
|
||||||
|
if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
jtype = type[j];
|
||||||
|
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
||||||
|
|
||||||
|
delx = xtmp - x[j][0];
|
||||||
|
dely = ytmp - x[j][1];
|
||||||
|
delz = ztmp - x[j][2];
|
||||||
|
rsq = delx*delx + dely*dely + delz*delz;
|
||||||
|
|
||||||
|
if (rsq <= cutneighsq[itype][jtype]) {
|
||||||
|
if (molecular) {
|
||||||
|
if (!moltemplate)
|
||||||
|
which = find_special(special[i],nspecial[i],tag[j]);
|
||||||
|
else if (imol >= 0)
|
||||||
|
which = find_special(onemols[imol]->special[iatom],
|
||||||
|
onemols[imol]->nspecial[iatom],
|
||||||
|
tag[j]-tagprev);
|
||||||
|
else which = 0;
|
||||||
|
if (which == 0) neighptr[n++] = j;
|
||||||
|
else if (domain->minimum_image_check(delx,dely,delz))
|
||||||
|
neighptr[n++] = j;
|
||||||
|
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
|
||||||
|
} else neighptr[n++] = j;
|
||||||
|
}
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
// for all collections, loop over all atoms in other bins in stencil, store every pair
|
||||||
|
// stencil is empty if i larger than j
|
||||||
|
// stencil is half if i same size as j
|
||||||
|
// stencil is full if i smaller than j
|
||||||
|
|
||||||
|
s = stencil_multi[icollection][jcollection];
|
||||||
|
ns = nstencil_multi[icollection][jcollection];
|
||||||
|
|
||||||
|
for (k = 0; k < ns; k++) {
|
||||||
|
js = binhead_multi[jcollection][jbin + s[k]];
|
||||||
|
for (j = js; j >= 0; j = bins[j]) {
|
||||||
|
|
||||||
|
jtype = type[j];
|
||||||
|
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
||||||
|
|
||||||
|
delx = xtmp - x[j][0];
|
||||||
|
dely = ytmp - x[j][1];
|
||||||
|
delz = ztmp - x[j][2];
|
||||||
|
rsq = delx*delx + dely*dely + delz*delz;
|
||||||
|
|
||||||
|
if (rsq <= cutneighsq[itype][jtype]) {
|
||||||
|
if (molecular != Atom::ATOMIC) {
|
||||||
|
if (!moltemplate)
|
||||||
|
which = find_special(special[i],nspecial[i],tag[j]);
|
||||||
|
else if (imol >= 0)
|
||||||
|
which = find_special(onemols[imol]->special[iatom],
|
||||||
|
onemols[imol]->nspecial[iatom],
|
||||||
|
tag[j]-tagprev);
|
||||||
|
else which = 0;
|
||||||
|
if (which == 0) neighptr[n++] = j;
|
||||||
|
else if (domain->minimum_image_check(delx,dely,delz))
|
||||||
|
neighptr[n++] = j;
|
||||||
|
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
|
||||||
|
} else neighptr[n++] = j;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
ilist[i] = i;
|
ilist[i] = i;
|
||||||
|
|||||||
@ -14,6 +14,7 @@
|
|||||||
#include "omp_compat.h"
|
#include "omp_compat.h"
|
||||||
#include "npair_half_multi_newton_tri_omp.h"
|
#include "npair_half_multi_newton_tri_omp.h"
|
||||||
#include "npair_omp.h"
|
#include "npair_omp.h"
|
||||||
|
#include "neighbor.h"
|
||||||
#include "neigh_list.h"
|
#include "neigh_list.h"
|
||||||
#include "atom.h"
|
#include "atom.h"
|
||||||
#include "atom_vec.h"
|
#include "atom_vec.h"
|
||||||
@ -31,8 +32,8 @@ NPairHalfMultiNewtonTriOmp::NPairHalfMultiNewtonTriOmp(LAMMPS *lmp) :
|
|||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
binned neighbor list construction with Newton's 3rd law for triclinic
|
binned neighbor list construction with Newton's 3rd law for triclinic
|
||||||
|
multi stencil is icollection-jcollection dependent
|
||||||
each owned atom i checks its own bin and other bins in triclinic stencil
|
each owned atom i checks its own bin and other bins in triclinic stencil
|
||||||
multi-type stencil is itype dependent and is distance checked
|
|
||||||
every pair stored exactly once by some processor
|
every pair stored exactly once by some processor
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
@ -48,14 +49,15 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list)
|
|||||||
#endif
|
#endif
|
||||||
NPAIR_OMP_SETUP(nlocal);
|
NPAIR_OMP_SETUP(nlocal);
|
||||||
|
|
||||||
int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom;
|
int i,j,k,n,itype,jtype,ibin,jbin,icollection,jcollection,which,ns,imol,iatom;
|
||||||
tagint tagprev;
|
tagint tagprev;
|
||||||
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
||||||
int *neighptr,*s;
|
int *neighptr,*s;
|
||||||
double *cutsq,*distsq;
|
int js;
|
||||||
|
|
||||||
// loop over each atom, storing neighbors
|
// loop over each atom, storing neighbors
|
||||||
|
|
||||||
|
int *collection = neighbor->collection;
|
||||||
double **x = atom->x;
|
double **x = atom->x;
|
||||||
int *type = atom->type;
|
int *type = atom->type;
|
||||||
int *mask = atom->mask;
|
int *mask = atom->mask;
|
||||||
@ -82,6 +84,7 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list)
|
|||||||
neighptr = ipage.vget();
|
neighptr = ipage.vget();
|
||||||
|
|
||||||
itype = type[i];
|
itype = type[i];
|
||||||
|
icollection = collection[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];
|
||||||
@ -91,55 +94,68 @@ void NPairHalfMultiNewtonTriOmp::build(NeighList *list)
|
|||||||
tagprev = tag[i] - iatom - 1;
|
tagprev = tag[i] - iatom - 1;
|
||||||
}
|
}
|
||||||
|
|
||||||
// loop over all atoms in bins, including self, in stencil
|
|
||||||
// skip if i,j neighbor cutoff is less than bin distance
|
|
||||||
// bins below self are excluded from stencil
|
|
||||||
// pairs for atoms j "below" i are excluded
|
|
||||||
// below = lower z or (equal z and lower y) or (equal zy and lower x)
|
|
||||||
// (equal zyx and j <= i)
|
|
||||||
// latter excludes self-self interaction but allows superposed atoms
|
|
||||||
|
|
||||||
ibin = atom2bin[i];
|
ibin = atom2bin[i];
|
||||||
s = stencil_multi[itype];
|
|
||||||
distsq = distsq_multi[itype];
|
// loop through stencils for all collections
|
||||||
cutsq = cutneighsq[itype];
|
for (jcollection = 0; jcollection < ncollections; jcollection++) {
|
||||||
ns = nstencil_multi[itype];
|
|
||||||
for (k = 0; k < ns; k++) {
|
// if same collection use own bin
|
||||||
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
|
if (icollection == jcollection) jbin = ibin;
|
||||||
jtype = type[j];
|
else jbin = coord2bin(x[i], jcollection);
|
||||||
if (cutsq[jtype] < distsq[k]) continue;
|
|
||||||
if (x[j][2] < ztmp) continue;
|
// loop over all atoms in bins in stencil
|
||||||
if (x[j][2] == ztmp) {
|
// stencil is empty if i larger than j
|
||||||
if (x[j][1] < ytmp) continue;
|
// stencil is half if i same size as j
|
||||||
if (x[j][1] == ytmp) {
|
// stencil is full if i smaller than j
|
||||||
if (x[j][0] < xtmp) continue;
|
// if half: pairs for atoms j "below" i are excluded
|
||||||
if (x[j][0] == xtmp && j <= i) continue;
|
// below = lower z or (equal z and lower y) or (equal zy and lower x)
|
||||||
|
// (equal zyx and j <= i)
|
||||||
|
// latter excludes self-self interaction but allows superposed atoms
|
||||||
|
|
||||||
|
s = stencil_multi[icollection][jcollection];
|
||||||
|
ns = nstencil_multi[icollection][jcollection];
|
||||||
|
|
||||||
|
for (k = 0; k < ns; k++) {
|
||||||
|
js = binhead_multi[jcollection][jbin + s[k]];
|
||||||
|
for (j = js; j >= 0; j = bins[j]) {
|
||||||
|
|
||||||
|
// if same size (same collection), use half stencil
|
||||||
|
if (cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){
|
||||||
|
if (x[j][2] < ztmp) continue;
|
||||||
|
if (x[j][2] == ztmp) {
|
||||||
|
if (x[j][1] < ytmp) continue;
|
||||||
|
if (x[j][1] == ytmp) {
|
||||||
|
if (x[j][0] < xtmp) continue;
|
||||||
|
if (x[j][0] == xtmp && j <= i) continue;
|
||||||
|
}
|
||||||
|
}
|
||||||
}
|
}
|
||||||
}
|
|
||||||
|
|
||||||
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
jtype = type[j];
|
||||||
|
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
||||||
|
|
||||||
delx = xtmp - x[j][0];
|
delx = xtmp - x[j][0];
|
||||||
dely = ytmp - x[j][1];
|
dely = ytmp - x[j][1];
|
||||||
delz = ztmp - x[j][2];
|
delz = ztmp - x[j][2];
|
||||||
rsq = delx*delx + dely*dely + delz*delz;
|
rsq = delx*delx + dely*dely + delz*delz;
|
||||||
|
|
||||||
if (rsq <= cutneighsq[itype][jtype]) {
|
if (rsq <= cutneighsq[itype][jtype]) {
|
||||||
if (molecular != Atom::ATOMIC) {
|
if (molecular != Atom::ATOMIC) {
|
||||||
if (!moltemplate)
|
if (!moltemplate)
|
||||||
which = find_special(special[i],nspecial[i],tag[j]);
|
which = find_special(special[i],nspecial[i],tag[j]);
|
||||||
else if (imol >=0)
|
else if (imol >= 0)
|
||||||
which = find_special(onemols[imol]->special[iatom],
|
which = find_special(onemols[imol]->special[iatom],
|
||||||
onemols[imol]->nspecial[iatom],
|
onemols[imol]->nspecial[iatom],
|
||||||
tag[j]-tagprev);
|
tag[j]-tagprev);
|
||||||
else which = 0;
|
else which = 0;
|
||||||
if (which == 0) neighptr[n++] = j;
|
if (which == 0) neighptr[n++] = j;
|
||||||
else if (domain->minimum_image_check(delx,dely,delz))
|
else if (domain->minimum_image_check(delx,dely,delz))
|
||||||
neighptr[n++] = j;
|
neighptr[n++] = j;
|
||||||
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
|
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
|
||||||
} else neighptr[n++] = j;
|
} else neighptr[n++] = j;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
ilist[i] = i;
|
ilist[i] = i;
|
||||||
|
|||||||
145
src/USER-OMP/npair_half_multi_old_newtoff_omp.cpp
Normal file
145
src/USER-OMP/npair_half_multi_old_newtoff_omp.cpp
Normal file
@ -0,0 +1,145 @@
|
|||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
https://lammps.sandia.gov/, 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 "omp_compat.h"
|
||||||
|
#include "npair_half_multi_old_newtoff_omp.h"
|
||||||
|
#include "npair_omp.h"
|
||||||
|
#include "neigh_list.h"
|
||||||
|
#include "atom.h"
|
||||||
|
#include "atom_vec.h"
|
||||||
|
#include "molecule.h"
|
||||||
|
#include "domain.h"
|
||||||
|
#include "my_page.h"
|
||||||
|
#include "error.h"
|
||||||
|
|
||||||
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
NPairHalfMultiOldNewtoffOmp::NPairHalfMultiOldNewtoffOmp(LAMMPS *lmp) : NPair(lmp) {}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
binned neighbor list construction with partial Newton's 3rd law
|
||||||
|
each owned atom i checks own bin and other bins in stencil
|
||||||
|
multi-type stencil is itype dependent and is distance checked
|
||||||
|
pair stored once if i,j are both owned and i < j
|
||||||
|
pair stored by me if j is ghost (also stored by proc owning j)
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void NPairHalfMultiOldNewtoffOmp::build(NeighList *list)
|
||||||
|
{
|
||||||
|
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
|
||||||
|
const int molecular = atom->molecular;
|
||||||
|
const int moltemplate = (molecular == Atom::TEMPLATE) ? 1 : 0;
|
||||||
|
|
||||||
|
NPAIR_OMP_INIT;
|
||||||
|
#if defined(_OPENMP)
|
||||||
|
#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(list)
|
||||||
|
#endif
|
||||||
|
NPAIR_OMP_SETUP(nlocal);
|
||||||
|
|
||||||
|
int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom;
|
||||||
|
tagint tagprev;
|
||||||
|
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
||||||
|
int *neighptr,*s;
|
||||||
|
double *cutsq,*distsq;
|
||||||
|
|
||||||
|
// loop over each atom, storing neighbors
|
||||||
|
|
||||||
|
double **x = atom->x;
|
||||||
|
int *type = atom->type;
|
||||||
|
int *mask = atom->mask;
|
||||||
|
tagint *tag = atom->tag;
|
||||||
|
tagint *molecule = atom->molecule;
|
||||||
|
tagint **special = atom->special;
|
||||||
|
int **nspecial = atom->nspecial;
|
||||||
|
|
||||||
|
int *molindex = atom->molindex;
|
||||||
|
int *molatom = atom->molatom;
|
||||||
|
Molecule **onemols = atom->avec->onemols;
|
||||||
|
|
||||||
|
int *ilist = list->ilist;
|
||||||
|
int *numneigh = list->numneigh;
|
||||||
|
int **firstneigh = list->firstneigh;
|
||||||
|
|
||||||
|
// each thread has its own page allocator
|
||||||
|
MyPage<int> &ipage = list->ipage[tid];
|
||||||
|
ipage.reset();
|
||||||
|
|
||||||
|
for (i = ifrom; i < ito; i++) {
|
||||||
|
|
||||||
|
n = 0;
|
||||||
|
neighptr = ipage.vget();
|
||||||
|
|
||||||
|
itype = type[i];
|
||||||
|
xtmp = x[i][0];
|
||||||
|
ytmp = x[i][1];
|
||||||
|
ztmp = x[i][2];
|
||||||
|
if (moltemplate) {
|
||||||
|
imol = molindex[i];
|
||||||
|
iatom = molatom[i];
|
||||||
|
tagprev = tag[i] - iatom - 1;
|
||||||
|
}
|
||||||
|
|
||||||
|
// loop over all atoms in other bins in stencil including self
|
||||||
|
// only store pair if i < j
|
||||||
|
// skip if i,j neighbor cutoff is less than bin distance
|
||||||
|
// stores own/own pairs only once
|
||||||
|
// stores own/ghost pairs on both procs
|
||||||
|
|
||||||
|
ibin = atom2bin[i];
|
||||||
|
s = stencil_multi_old[itype];
|
||||||
|
distsq = distsq_multi_old[itype];
|
||||||
|
cutsq = cutneighsq[itype];
|
||||||
|
ns = nstencil_multi_old[itype];
|
||||||
|
for (k = 0; k < ns; k++) {
|
||||||
|
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
|
||||||
|
if (j <= i) continue;
|
||||||
|
jtype = type[j];
|
||||||
|
if (cutsq[jtype] < distsq[k]) continue;
|
||||||
|
|
||||||
|
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
||||||
|
|
||||||
|
delx = xtmp - x[j][0];
|
||||||
|
dely = ytmp - x[j][1];
|
||||||
|
delz = ztmp - x[j][2];
|
||||||
|
rsq = delx*delx + dely*dely + delz*delz;
|
||||||
|
|
||||||
|
if (rsq <= cutneighsq[itype][jtype]) {
|
||||||
|
if (molecular != Atom::ATOMIC) {
|
||||||
|
if (!moltemplate)
|
||||||
|
which = find_special(special[i],nspecial[i],tag[j]);
|
||||||
|
else if (imol >=0)
|
||||||
|
which = find_special(onemols[imol]->special[iatom],
|
||||||
|
onemols[imol]->nspecial[iatom],
|
||||||
|
tag[j]-tagprev);
|
||||||
|
else which = 0;
|
||||||
|
if (which == 0) neighptr[n++] = j;
|
||||||
|
else if (domain->minimum_image_check(delx,dely,delz))
|
||||||
|
neighptr[n++] = j;
|
||||||
|
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
|
||||||
|
} else neighptr[n++] = j;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
ilist[i] = i;
|
||||||
|
firstneigh[i] = neighptr;
|
||||||
|
numneigh[i] = n;
|
||||||
|
ipage.vgot(n);
|
||||||
|
if (ipage.status())
|
||||||
|
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
|
||||||
|
}
|
||||||
|
NPAIR_OMP_CLOSE;
|
||||||
|
list->inum = nlocal;
|
||||||
|
}
|
||||||
43
src/USER-OMP/npair_half_multi_old_newtoff_omp.h
Normal file
43
src/USER-OMP/npair_half_multi_old_newtoff_omp.h
Normal file
@ -0,0 +1,43 @@
|
|||||||
|
/* -*- c++ -*- ----------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
https://lammps.sandia.gov/, 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.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#ifdef NPAIR_CLASS
|
||||||
|
|
||||||
|
NPairStyle(half/multi/old/newtoff/omp,
|
||||||
|
NPairHalfMultiOldNewtoffOmp,
|
||||||
|
NP_HALF | NP_MULTI_OLD | NP_NEWTOFF | NP_OMP | NP_ORTHO | NP_TRI)
|
||||||
|
|
||||||
|
#else
|
||||||
|
|
||||||
|
#ifndef LMP_NPAIR_HALF_MULTI_OLD_NEWTOFF_OMP_H
|
||||||
|
#define LMP_NPAIR_HALF_MULTI_OLD_NEWTOFF_OMP_H
|
||||||
|
|
||||||
|
#include "npair.h"
|
||||||
|
|
||||||
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
|
class NPairHalfMultiOldNewtoffOmp : public NPair {
|
||||||
|
public:
|
||||||
|
NPairHalfMultiOldNewtoffOmp(class LAMMPS *);
|
||||||
|
~NPairHalfMultiOldNewtoffOmp() {}
|
||||||
|
void build(class NeighList *);
|
||||||
|
};
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
#endif
|
||||||
|
#endif
|
||||||
|
|
||||||
|
/* ERROR/WARNING messages:
|
||||||
|
|
||||||
|
*/
|
||||||
178
src/USER-OMP/npair_half_multi_old_newton_omp.cpp
Normal file
178
src/USER-OMP/npair_half_multi_old_newton_omp.cpp
Normal file
@ -0,0 +1,178 @@
|
|||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
https://lammps.sandia.gov/, 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 "omp_compat.h"
|
||||||
|
#include "npair_half_multi_old_newton_omp.h"
|
||||||
|
#include "npair_omp.h"
|
||||||
|
#include "neigh_list.h"
|
||||||
|
#include "atom.h"
|
||||||
|
#include "atom_vec.h"
|
||||||
|
#include "molecule.h"
|
||||||
|
#include "domain.h"
|
||||||
|
#include "my_page.h"
|
||||||
|
#include "error.h"
|
||||||
|
|
||||||
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
NPairHalfMultiOldNewtonOmp::NPairHalfMultiOldNewtonOmp(LAMMPS *lmp) : NPair(lmp) {}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
binned neighbor list construction with full Newton's 3rd law
|
||||||
|
each owned atom i checks its own bin and other bins in Newton stencil
|
||||||
|
multi-type stencil is itype dependent and is distance checked
|
||||||
|
every pair stored exactly once by some processor
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void NPairHalfMultiOldNewtonOmp::build(NeighList *list)
|
||||||
|
{
|
||||||
|
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
|
||||||
|
const int molecular = atom->molecular;
|
||||||
|
const int moltemplate = (molecular == Atom::TEMPLATE) ? 1 : 0;
|
||||||
|
|
||||||
|
NPAIR_OMP_INIT;
|
||||||
|
#if defined(_OPENMP)
|
||||||
|
#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(list)
|
||||||
|
#endif
|
||||||
|
NPAIR_OMP_SETUP(nlocal);
|
||||||
|
|
||||||
|
int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom;
|
||||||
|
tagint tagprev;
|
||||||
|
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
||||||
|
int *neighptr,*s;
|
||||||
|
double *cutsq,*distsq;
|
||||||
|
|
||||||
|
// loop over each atom, storing neighbors
|
||||||
|
|
||||||
|
double **x = atom->x;
|
||||||
|
int *type = atom->type;
|
||||||
|
int *mask = atom->mask;
|
||||||
|
tagint *tag = atom->tag;
|
||||||
|
tagint *molecule = atom->molecule;
|
||||||
|
tagint **special = atom->special;
|
||||||
|
int **nspecial = atom->nspecial;
|
||||||
|
|
||||||
|
int *molindex = atom->molindex;
|
||||||
|
int *molatom = atom->molatom;
|
||||||
|
Molecule **onemols = atom->avec->onemols;
|
||||||
|
|
||||||
|
int *ilist = list->ilist;
|
||||||
|
int *numneigh = list->numneigh;
|
||||||
|
int **firstneigh = list->firstneigh;
|
||||||
|
|
||||||
|
// each thread has its own page allocator
|
||||||
|
MyPage<int> &ipage = list->ipage[tid];
|
||||||
|
ipage.reset();
|
||||||
|
|
||||||
|
for (i = ifrom; i < ito; i++) {
|
||||||
|
|
||||||
|
n = 0;
|
||||||
|
neighptr = ipage.vget();
|
||||||
|
|
||||||
|
itype = type[i];
|
||||||
|
xtmp = x[i][0];
|
||||||
|
ytmp = x[i][1];
|
||||||
|
ztmp = x[i][2];
|
||||||
|
if (moltemplate) {
|
||||||
|
imol = molindex[i];
|
||||||
|
iatom = molatom[i];
|
||||||
|
tagprev = tag[i] - iatom - 1;
|
||||||
|
}
|
||||||
|
|
||||||
|
// loop over rest of atoms in i's bin, ghosts are at end of linked list
|
||||||
|
// if j is owned atom, store it, since j is beyond i in linked list
|
||||||
|
// if j is ghost, only store if j coords are "above and to the right" of i
|
||||||
|
|
||||||
|
for (j = bins[i]; j >= 0; j = bins[j]) {
|
||||||
|
if (j >= nlocal) {
|
||||||
|
if (x[j][2] < ztmp) continue;
|
||||||
|
if (x[j][2] == ztmp) {
|
||||||
|
if (x[j][1] < ytmp) continue;
|
||||||
|
if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
jtype = type[j];
|
||||||
|
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
||||||
|
|
||||||
|
delx = xtmp - x[j][0];
|
||||||
|
dely = ytmp - x[j][1];
|
||||||
|
delz = ztmp - x[j][2];
|
||||||
|
rsq = delx*delx + dely*dely + delz*delz;
|
||||||
|
|
||||||
|
if (rsq <= cutneighsq[itype][jtype]) {
|
||||||
|
if (molecular != Atom::ATOMIC) {
|
||||||
|
if (!moltemplate)
|
||||||
|
which = find_special(special[i],nspecial[i],tag[j]);
|
||||||
|
else if (imol >=0)
|
||||||
|
which = find_special(onemols[imol]->special[iatom],
|
||||||
|
onemols[imol]->nspecial[iatom],
|
||||||
|
tag[j]-tagprev);
|
||||||
|
else which = 0;
|
||||||
|
if (which == 0) neighptr[n++] = j;
|
||||||
|
else if (domain->minimum_image_check(delx,dely,delz))
|
||||||
|
neighptr[n++] = j;
|
||||||
|
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
|
||||||
|
} else neighptr[n++] = j;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
// loop over all atoms in other bins in stencil, store every pair
|
||||||
|
// skip if i,j neighbor cutoff is less than bin distance
|
||||||
|
|
||||||
|
ibin = atom2bin[i];
|
||||||
|
s = stencil_multi_old[itype];
|
||||||
|
distsq = distsq_multi_old[itype];
|
||||||
|
cutsq = cutneighsq[itype];
|
||||||
|
ns = nstencil_multi_old[itype];
|
||||||
|
for (k = 0; k < ns; k++) {
|
||||||
|
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
|
||||||
|
jtype = type[j];
|
||||||
|
if (cutsq[jtype] < distsq[k]) continue;
|
||||||
|
|
||||||
|
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
||||||
|
|
||||||
|
delx = xtmp - x[j][0];
|
||||||
|
dely = ytmp - x[j][1];
|
||||||
|
delz = ztmp - x[j][2];
|
||||||
|
rsq = delx*delx + dely*dely + delz*delz;
|
||||||
|
|
||||||
|
if (rsq <= cutneighsq[itype][jtype]) {
|
||||||
|
if (molecular != Atom::ATOMIC) {
|
||||||
|
if (!moltemplate)
|
||||||
|
which = find_special(special[i],nspecial[i],tag[j]);
|
||||||
|
else if (imol >=0)
|
||||||
|
which = find_special(onemols[imol]->special[iatom],
|
||||||
|
onemols[imol]->nspecial[iatom],
|
||||||
|
tag[j]-tagprev);
|
||||||
|
else which = 0;
|
||||||
|
if (which == 0) neighptr[n++] = j;
|
||||||
|
else if (domain->minimum_image_check(delx,dely,delz))
|
||||||
|
neighptr[n++] = j;
|
||||||
|
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
|
||||||
|
} else neighptr[n++] = j;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
ilist[i] = i;
|
||||||
|
firstneigh[i] = neighptr;
|
||||||
|
numneigh[i] = n;
|
||||||
|
ipage.vgot(n);
|
||||||
|
if (ipage.status())
|
||||||
|
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
|
||||||
|
}
|
||||||
|
NPAIR_OMP_CLOSE;
|
||||||
|
list->inum = nlocal;
|
||||||
|
}
|
||||||
@ -11,26 +11,26 @@
|
|||||||
See the README file in the top-level LAMMPS directory.
|
See the README file in the top-level LAMMPS directory.
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
#ifdef NSTENCIL_CLASS
|
#ifdef NPAIR_CLASS
|
||||||
|
|
||||||
NStencilStyle(half/bin/2d/newton/tri,
|
NPairStyle(half/multi/old/newton/omp,
|
||||||
NStencilHalfBin2dNewtonTri,
|
NPairHalfMultiOldNewtonOmp,
|
||||||
NS_HALF | NS_BIN | NS_2D | NS_NEWTON | NS_TRI)
|
NP_HALF | NP_MULTI_OLD | NP_NEWTON | NP_OMP | NP_ORTHO)
|
||||||
|
|
||||||
#else
|
#else
|
||||||
|
|
||||||
#ifndef LMP_NSTENCIL_HALF_BIN_2D_NEWTON_TRI_H
|
#ifndef LMP_NPAIR_HALF_MULTI_OLD_NEWTON_OMP_H
|
||||||
#define LMP_NSTENCIL_HALF_BIN_2D_NEWTON_TRI_H
|
#define LMP_NPAIR_HALF_MULTI_OLD_NEWTON_OMP_H
|
||||||
|
|
||||||
#include "nstencil.h"
|
#include "npair.h"
|
||||||
|
|
||||||
namespace LAMMPS_NS {
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
class NStencilHalfBin2dNewtonTri : public NStencil {
|
class NPairHalfMultiOldNewtonOmp : public NPair {
|
||||||
public:
|
public:
|
||||||
NStencilHalfBin2dNewtonTri(class LAMMPS *);
|
NPairHalfMultiOldNewtonOmp(class LAMMPS *);
|
||||||
~NStencilHalfBin2dNewtonTri() {}
|
~NPairHalfMultiOldNewtonOmp() {}
|
||||||
void create();
|
void build(class NeighList *);
|
||||||
};
|
};
|
||||||
|
|
||||||
}
|
}
|
||||||
154
src/USER-OMP/npair_half_multi_old_newton_tri_omp.cpp
Normal file
154
src/USER-OMP/npair_half_multi_old_newton_tri_omp.cpp
Normal file
@ -0,0 +1,154 @@
|
|||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
https://lammps.sandia.gov/, 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 "omp_compat.h"
|
||||||
|
#include "npair_half_multi_old_newton_tri_omp.h"
|
||||||
|
#include "npair_omp.h"
|
||||||
|
#include "neigh_list.h"
|
||||||
|
#include "atom.h"
|
||||||
|
#include "atom_vec.h"
|
||||||
|
#include "molecule.h"
|
||||||
|
#include "domain.h"
|
||||||
|
#include "my_page.h"
|
||||||
|
#include "error.h"
|
||||||
|
|
||||||
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
NPairHalfMultiOldNewtonTriOmp::NPairHalfMultiOldNewtonTriOmp(LAMMPS *lmp) :
|
||||||
|
NPair(lmp) {}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
binned neighbor list construction with Newton's 3rd law for triclinic
|
||||||
|
each owned atom i checks its own bin and other bins in triclinic stencil
|
||||||
|
multi-type stencil is itype dependent and is distance checked
|
||||||
|
every pair stored exactly once by some processor
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void NPairHalfMultiOldNewtonTriOmp::build(NeighList *list)
|
||||||
|
{
|
||||||
|
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
|
||||||
|
const int molecular = atom->molecular;
|
||||||
|
const int moltemplate = (molecular == Atom::TEMPLATE) ? 1 : 0;
|
||||||
|
|
||||||
|
NPAIR_OMP_INIT;
|
||||||
|
#if defined(_OPENMP)
|
||||||
|
#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(list)
|
||||||
|
#endif
|
||||||
|
NPAIR_OMP_SETUP(nlocal);
|
||||||
|
|
||||||
|
int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom;
|
||||||
|
tagint tagprev;
|
||||||
|
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
||||||
|
int *neighptr,*s;
|
||||||
|
double *cutsq,*distsq;
|
||||||
|
|
||||||
|
// loop over each atom, storing neighbors
|
||||||
|
|
||||||
|
double **x = atom->x;
|
||||||
|
int *type = atom->type;
|
||||||
|
int *mask = atom->mask;
|
||||||
|
tagint *tag = atom->tag;
|
||||||
|
tagint *molecule = atom->molecule;
|
||||||
|
tagint **special = atom->special;
|
||||||
|
int **nspecial = atom->nspecial;
|
||||||
|
|
||||||
|
int *molindex = atom->molindex;
|
||||||
|
int *molatom = atom->molatom;
|
||||||
|
Molecule **onemols = atom->avec->onemols;
|
||||||
|
|
||||||
|
int *ilist = list->ilist;
|
||||||
|
int *numneigh = list->numneigh;
|
||||||
|
int **firstneigh = list->firstneigh;
|
||||||
|
|
||||||
|
// each thread has its own page allocator
|
||||||
|
MyPage<int> &ipage = list->ipage[tid];
|
||||||
|
ipage.reset();
|
||||||
|
|
||||||
|
for (i = ifrom; i < ito; i++) {
|
||||||
|
|
||||||
|
n = 0;
|
||||||
|
neighptr = ipage.vget();
|
||||||
|
|
||||||
|
itype = type[i];
|
||||||
|
xtmp = x[i][0];
|
||||||
|
ytmp = x[i][1];
|
||||||
|
ztmp = x[i][2];
|
||||||
|
if (moltemplate) {
|
||||||
|
imol = molindex[i];
|
||||||
|
iatom = molatom[i];
|
||||||
|
tagprev = tag[i] - iatom - 1;
|
||||||
|
}
|
||||||
|
|
||||||
|
// loop over all atoms in bins, including self, in stencil
|
||||||
|
// skip if i,j neighbor cutoff is less than bin distance
|
||||||
|
// bins below self are excluded from stencil
|
||||||
|
// pairs for atoms j "below" i are excluded
|
||||||
|
// below = lower z or (equal z and lower y) or (equal zy and lower x)
|
||||||
|
// (equal zyx and j <= i)
|
||||||
|
// latter excludes self-self interaction but allows superposed atoms
|
||||||
|
|
||||||
|
ibin = atom2bin[i];
|
||||||
|
s = stencil_multi_old[itype];
|
||||||
|
distsq = distsq_multi_old[itype];
|
||||||
|
cutsq = cutneighsq[itype];
|
||||||
|
ns = nstencil_multi_old[itype];
|
||||||
|
for (k = 0; k < ns; k++) {
|
||||||
|
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
|
||||||
|
jtype = type[j];
|
||||||
|
if (cutsq[jtype] < distsq[k]) continue;
|
||||||
|
if (x[j][2] < ztmp) continue;
|
||||||
|
if (x[j][2] == ztmp) {
|
||||||
|
if (x[j][1] < ytmp) continue;
|
||||||
|
if (x[j][1] == ytmp) {
|
||||||
|
if (x[j][0] < xtmp) continue;
|
||||||
|
if (x[j][0] == xtmp && j <= i) continue;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
||||||
|
|
||||||
|
delx = xtmp - x[j][0];
|
||||||
|
dely = ytmp - x[j][1];
|
||||||
|
delz = ztmp - x[j][2];
|
||||||
|
rsq = delx*delx + dely*dely + delz*delz;
|
||||||
|
|
||||||
|
if (rsq <= cutneighsq[itype][jtype]) {
|
||||||
|
if (molecular != Atom::ATOMIC) {
|
||||||
|
if (!moltemplate)
|
||||||
|
which = find_special(special[i],nspecial[i],tag[j]);
|
||||||
|
else if (imol >=0)
|
||||||
|
which = find_special(onemols[imol]->special[iatom],
|
||||||
|
onemols[imol]->nspecial[iatom],
|
||||||
|
tag[j]-tagprev);
|
||||||
|
else which = 0;
|
||||||
|
if (which == 0) neighptr[n++] = j;
|
||||||
|
else if (domain->minimum_image_check(delx,dely,delz))
|
||||||
|
neighptr[n++] = j;
|
||||||
|
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
|
||||||
|
} else neighptr[n++] = j;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
ilist[i] = i;
|
||||||
|
firstneigh[i] = neighptr;
|
||||||
|
numneigh[i] = n;
|
||||||
|
ipage.vgot(n);
|
||||||
|
if (ipage.status())
|
||||||
|
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
|
||||||
|
}
|
||||||
|
NPAIR_OMP_CLOSE;
|
||||||
|
list->inum = nlocal;
|
||||||
|
}
|
||||||
43
src/USER-OMP/npair_half_multi_old_newton_tri_omp.h
Normal file
43
src/USER-OMP/npair_half_multi_old_newton_tri_omp.h
Normal file
@ -0,0 +1,43 @@
|
|||||||
|
/* -*- c++ -*- ----------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
https://lammps.sandia.gov/, 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.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#ifdef NPAIR_CLASS
|
||||||
|
|
||||||
|
NPairStyle(half/multi/old/newton/tri/omp,
|
||||||
|
NPairHalfMultiOldNewtonTriOmp,
|
||||||
|
NP_HALF | NP_MULTI_OLD | NP_NEWTON | NP_TRI | NP_OMP)
|
||||||
|
|
||||||
|
#else
|
||||||
|
|
||||||
|
#ifndef LMP_NPAIR_HALF_MULTI_OLD_NEWTON_TRI_OMP_H
|
||||||
|
#define LMP_NPAIR_HALF_MULTI_OLD_NEWTON_TRI_OMP_H
|
||||||
|
|
||||||
|
#include "npair.h"
|
||||||
|
|
||||||
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
|
class NPairHalfMultiOldNewtonTriOmp : public NPair {
|
||||||
|
public:
|
||||||
|
NPairHalfMultiOldNewtonTriOmp(class LAMMPS *);
|
||||||
|
~NPairHalfMultiOldNewtonTriOmp() {}
|
||||||
|
void build(class NeighList *);
|
||||||
|
};
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
#endif
|
||||||
|
#endif
|
||||||
|
|
||||||
|
/* ERROR/WARNING messages:
|
||||||
|
|
||||||
|
*/
|
||||||
@ -16,6 +16,7 @@
|
|||||||
#include "atom.h"
|
#include "atom.h"
|
||||||
#include "error.h"
|
#include "error.h"
|
||||||
#include "my_page.h"
|
#include "my_page.h"
|
||||||
|
#include "neighbor.h"
|
||||||
#include "neigh_list.h"
|
#include "neigh_list.h"
|
||||||
#include "npair_omp.h"
|
#include "npair_omp.h"
|
||||||
|
|
||||||
@ -25,14 +26,13 @@ using namespace LAMMPS_NS;
|
|||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
NPairHalfSizeMultiNewtoffOmp::NPairHalfSizeMultiNewtoffOmp(LAMMPS *lmp) :
|
NPairHalfSizeMultiNewtoffOmp::NPairHalfSizeMultiNewtoffOmp(LAMMPS *lmp) : NPair(lmp) {}
|
||||||
NPair(lmp) {}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
size particles
|
size particles
|
||||||
binned neighbor list construction with partial Newton's 3rd law
|
binned neighbor list construction with partial Newton's 3rd law
|
||||||
|
multi stencil is icollection-jcollection dependent
|
||||||
each owned atom i checks own bin and other bins in stencil
|
each owned atom i checks own bin and other bins in stencil
|
||||||
multi-type stencil is itype dependent and is distance checked
|
|
||||||
pair stored once if i,j are both owned and i < j
|
pair stored once if i,j are both owned and i < j
|
||||||
pair stored by me if j is ghost (also stored by proc owning j)
|
pair stored by me if j is ghost (also stored by proc owning j)
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
@ -49,12 +49,15 @@ void NPairHalfSizeMultiNewtoffOmp::build(NeighList *list)
|
|||||||
#endif
|
#endif
|
||||||
NPAIR_OMP_SETUP(nlocal);
|
NPAIR_OMP_SETUP(nlocal);
|
||||||
|
|
||||||
int i,j,k,n,itype,jtype,ibin,ns;
|
int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,ns;
|
||||||
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
||||||
double radi,radsum,cutdistsq;
|
double radi,radsum,cutdistsq;
|
||||||
int *neighptr,*s;
|
int *neighptr,*s;
|
||||||
double *cutsq,*distsq;
|
int js;
|
||||||
|
|
||||||
|
// loop over each atom, storing neighbors
|
||||||
|
|
||||||
|
int *collection = neighbor->collection;
|
||||||
double **x = atom->x;
|
double **x = atom->x;
|
||||||
double *radius = atom->radius;
|
double *radius = atom->radius;
|
||||||
int *type = atom->type;
|
int *type = atom->type;
|
||||||
@ -75,43 +78,52 @@ void NPairHalfSizeMultiNewtoffOmp::build(NeighList *list)
|
|||||||
neighptr = ipage.vget();
|
neighptr = ipage.vget();
|
||||||
|
|
||||||
itype = type[i];
|
itype = type[i];
|
||||||
|
icollection = collection[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];
|
||||||
radi = radius[i];
|
radi = radius[i];
|
||||||
|
|
||||||
// loop over all atoms in other bins in stencil including self
|
|
||||||
// only store pair if i < j
|
|
||||||
// skip if i,j neighbor cutoff is less than bin distance
|
|
||||||
// stores own/own pairs only once
|
|
||||||
// stores own/ghost pairs on both procs
|
|
||||||
|
|
||||||
ibin = atom2bin[i];
|
ibin = atom2bin[i];
|
||||||
s = stencil_multi[itype];
|
|
||||||
distsq = distsq_multi[itype];
|
|
||||||
cutsq = cutneighsq[itype];
|
|
||||||
ns = nstencil_multi[itype];
|
|
||||||
for (k = 0; k < ns; k++) {
|
|
||||||
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
|
|
||||||
if (j <= i) continue;
|
|
||||||
jtype = type[j];
|
|
||||||
if (cutsq[jtype] < distsq[k]) continue;
|
|
||||||
|
|
||||||
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
// loop through stencils for all collections
|
||||||
|
for (jcollection = 0; jcollection < ncollections; jcollection++) {
|
||||||
|
|
||||||
delx = xtmp - x[j][0];
|
// if same collection use own bin
|
||||||
dely = ytmp - x[j][1];
|
if(icollection == jcollection) jbin = ibin;
|
||||||
delz = ztmp - x[j][2];
|
else jbin = coord2bin(x[i], jcollection);
|
||||||
rsq = delx*delx + dely*dely + delz*delz;
|
|
||||||
radsum = radi + radius[j];
|
|
||||||
cutdistsq = (radsum+skin) * (radsum+skin);
|
|
||||||
|
|
||||||
if (rsq <= cutdistsq) {
|
// loop over all atoms in other bins in stencil including self
|
||||||
if (history && rsq < radsum*radsum)
|
// only store pair if i < j
|
||||||
neighptr[n++] = j ^ mask_history;
|
// stores own/own pairs only once
|
||||||
else
|
// stores own/ghost pairs on both procs
|
||||||
neighptr[n++] = j;
|
// use full stencil for all collection combinations
|
||||||
}
|
|
||||||
|
s = stencil_multi[icollection][jcollection];
|
||||||
|
ns = nstencil_multi[icollection][jcollection];
|
||||||
|
|
||||||
|
for (k = 0; k < ns; k++) {
|
||||||
|
js = binhead_multi[jcollection][jbin + s[k]];
|
||||||
|
for (j = js; j >=0; j = bins[j]) {
|
||||||
|
if (j <= i) continue;
|
||||||
|
|
||||||
|
jtype = type[j];
|
||||||
|
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
||||||
|
|
||||||
|
delx = xtmp - x[j][0];
|
||||||
|
dely = ytmp - x[j][1];
|
||||||
|
delz = ztmp - x[j][2];
|
||||||
|
rsq = delx*delx + dely*dely + delz*delz;
|
||||||
|
radsum = radi + radius[j];
|
||||||
|
cutdistsq = (radsum+skin) * (radsum+skin);
|
||||||
|
|
||||||
|
if (rsq <= cutdistsq) {
|
||||||
|
if (history && rsq < radsum*radsum)
|
||||||
|
neighptr[n++] = j ^ mask_history;
|
||||||
|
else
|
||||||
|
neighptr[n++] = j;
|
||||||
|
}
|
||||||
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|||||||
@ -15,8 +15,7 @@
|
|||||||
|
|
||||||
NPairStyle(half/size/multi/newtoff/omp,
|
NPairStyle(half/size/multi/newtoff/omp,
|
||||||
NPairHalfSizeMultiNewtoffOmp,
|
NPairHalfSizeMultiNewtoffOmp,
|
||||||
NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTOFF | NP_OMP |
|
NP_HALF | NP_SIZE | NP_MULTI | NP_NEWTOFF | NP_OMP | NP_ORTHO | NP_TRI)
|
||||||
NP_ORTHO | NP_TRI)
|
|
||||||
|
|
||||||
#else
|
#else
|
||||||
|
|
||||||
|
|||||||
@ -16,6 +16,7 @@
|
|||||||
#include "atom.h"
|
#include "atom.h"
|
||||||
#include "error.h"
|
#include "error.h"
|
||||||
#include "my_page.h"
|
#include "my_page.h"
|
||||||
|
#include "neighbor.h"
|
||||||
#include "neigh_list.h"
|
#include "neigh_list.h"
|
||||||
#include "npair_omp.h"
|
#include "npair_omp.h"
|
||||||
|
|
||||||
@ -25,14 +26,13 @@ using namespace LAMMPS_NS;
|
|||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
NPairHalfSizeMultiNewtonOmp::NPairHalfSizeMultiNewtonOmp(LAMMPS *lmp) :
|
NPairHalfSizeMultiNewtonOmp::NPairHalfSizeMultiNewtonOmp(LAMMPS *lmp) : NPair(lmp) {}
|
||||||
NPair(lmp) {}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
size particles
|
size particles
|
||||||
binned neighbor list construction with full Newton's 3rd law
|
binned neighbor list construction with full Newton's 3rd law
|
||||||
|
multi stencil is icollection-jcollection dependent
|
||||||
each owned atom i checks its own bin and other bins in Newton stencil
|
each owned atom i checks its own bin and other bins in Newton stencil
|
||||||
multi-type stencil is itype dependent and is distance checked
|
|
||||||
every pair stored exactly once by some processor
|
every pair stored exactly once by some processor
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
@ -48,12 +48,15 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list)
|
|||||||
#endif
|
#endif
|
||||||
NPAIR_OMP_SETUP(nlocal);
|
NPAIR_OMP_SETUP(nlocal);
|
||||||
|
|
||||||
int i,j,k,n,itype,jtype,ibin,ns;
|
int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,ns;
|
||||||
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
||||||
double radi,radsum,cutdistsq;
|
double radi,radsum,cutdistsq;
|
||||||
int *neighptr,*s;
|
int *neighptr,*s;
|
||||||
double *cutsq,*distsq;
|
int js;
|
||||||
|
|
||||||
|
// loop over each atom, storing neighbors
|
||||||
|
|
||||||
|
int *collection = neighbor->collection;
|
||||||
double **x = atom->x;
|
double **x = atom->x;
|
||||||
double *radius = atom->radius;
|
double *radius = atom->radius;
|
||||||
int *type = atom->type;
|
int *type = atom->type;
|
||||||
@ -74,70 +77,95 @@ void NPairHalfSizeMultiNewtonOmp::build(NeighList *list)
|
|||||||
neighptr = ipage.vget();
|
neighptr = ipage.vget();
|
||||||
|
|
||||||
itype = type[i];
|
itype = type[i];
|
||||||
|
icollection = collection[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];
|
||||||
radi = radius[i];
|
radi = radius[i];
|
||||||
|
|
||||||
// loop over rest of atoms in i's bin, ghosts are at end of linked list
|
|
||||||
// if j is owned atom, store it, since j is beyond i in linked list
|
|
||||||
// if j is ghost, only store if j coords are "above and to the right" of i
|
|
||||||
|
|
||||||
for (j = bins[i]; j >= 0; j = bins[j]) {
|
|
||||||
if (j >= nlocal) {
|
|
||||||
if (x[j][2] < ztmp) continue;
|
|
||||||
if (x[j][2] == ztmp) {
|
|
||||||
if (x[j][1] < ytmp) continue;
|
|
||||||
if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
jtype = type[j];
|
|
||||||
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
|
||||||
delx = xtmp - x[j][0];
|
|
||||||
dely = ytmp - x[j][1];
|
|
||||||
delz = ztmp - x[j][2];
|
|
||||||
rsq = delx*delx + dely*dely + delz*delz;
|
|
||||||
radsum = radi + radius[j];
|
|
||||||
cutdistsq = (radsum+skin) * (radsum+skin);
|
|
||||||
|
|
||||||
if (rsq <= cutdistsq) {
|
|
||||||
if (history && rsq < radsum*radsum)
|
|
||||||
neighptr[n++] = j ^ mask_history;
|
|
||||||
else
|
|
||||||
neighptr[n++] = j;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
// loop over all atoms in other bins in stencil, store every pair
|
|
||||||
// skip if i,j neighbor cutoff is less than bin distance
|
|
||||||
|
|
||||||
ibin = atom2bin[i];
|
ibin = atom2bin[i];
|
||||||
s = stencil_multi[itype];
|
|
||||||
distsq = distsq_multi[itype];
|
|
||||||
cutsq = cutneighsq[itype];
|
|
||||||
ns = nstencil_multi[itype];
|
|
||||||
for (k = 0; k < ns; k++) {
|
|
||||||
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
|
|
||||||
jtype = type[j];
|
|
||||||
if (cutsq[jtype] < distsq[k]) continue;
|
|
||||||
|
|
||||||
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
// loop through stencils for all collections
|
||||||
|
for (jcollection = 0; jcollection < ncollections; jcollection++) {
|
||||||
|
|
||||||
delx = xtmp - x[j][0];
|
// if same collection use own bin
|
||||||
dely = ytmp - x[j][1];
|
if(icollection == jcollection) jbin = ibin;
|
||||||
delz = ztmp - x[j][2];
|
else jbin = coord2bin(x[i], jcollection);
|
||||||
rsq = delx*delx + dely*dely + delz*delz;
|
|
||||||
radsum = radi + radius[j];
|
|
||||||
cutdistsq = (radsum+skin) * (radsum+skin);
|
|
||||||
|
|
||||||
if (rsq <= cutdistsq) {
|
// if same size: uses half stencil so check central bin
|
||||||
if (history && rsq < radsum*radsum)
|
if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){
|
||||||
neighptr[n++] = j ^ mask_history;
|
|
||||||
else
|
if(icollection == jcollection) js = bins[i];
|
||||||
neighptr[n++] = j;
|
else js = binhead_multi[jcollection][jbin];
|
||||||
|
|
||||||
|
// if same collection,
|
||||||
|
// if j is owned atom, store it, since j is beyond i in linked list
|
||||||
|
// if j is ghost, only store if j coords are "above and to the right" of i
|
||||||
|
|
||||||
|
// if different collections,
|
||||||
|
// if j is owned atom, store it if j > i
|
||||||
|
// if j is ghost, only store if j coords are "above and to the right" of i
|
||||||
|
|
||||||
|
for (j = js; j >= 0; j = bins[j]) {
|
||||||
|
if(icollection != jcollection and j < i) continue;
|
||||||
|
|
||||||
|
if (j >= nlocal) {
|
||||||
|
if (x[j][2] < ztmp) continue;
|
||||||
|
if (x[j][2] == ztmp) {
|
||||||
|
if (x[j][1] < ytmp) continue;
|
||||||
|
if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
jtype = type[j];
|
||||||
|
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
||||||
|
|
||||||
|
delx = xtmp - x[j][0];
|
||||||
|
dely = ytmp - x[j][1];
|
||||||
|
delz = ztmp - x[j][2];
|
||||||
|
rsq = delx*delx + dely*dely + delz*delz;
|
||||||
|
radsum = radi + radius[j];
|
||||||
|
cutdistsq = (radsum+skin) * (radsum+skin);
|
||||||
|
|
||||||
|
if (rsq <= cutdistsq) {
|
||||||
|
if (history && rsq < radsum*radsum)
|
||||||
|
neighptr[n++] = j ^ mask_history;
|
||||||
|
else
|
||||||
|
neighptr[n++] = j;
|
||||||
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
// for all collections, loop over all atoms in other bins in stencil, store every pair
|
||||||
|
// stencil is empty if i larger than j
|
||||||
|
// stencil is half if i same size as j
|
||||||
|
// stencil is full if i smaller than j
|
||||||
|
|
||||||
|
s = stencil_multi[icollection][jcollection];
|
||||||
|
ns = nstencil_multi[icollection][jcollection];
|
||||||
|
|
||||||
|
for (k = 0; k < ns; k++) {
|
||||||
|
js = binhead_multi[jcollection][jbin + s[k]];
|
||||||
|
for (j = js; j >= 0; j = bins[j]) {
|
||||||
|
|
||||||
|
jtype = type[j];
|
||||||
|
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
||||||
|
|
||||||
|
delx = xtmp - x[j][0];
|
||||||
|
dely = ytmp - x[j][1];
|
||||||
|
delz = ztmp - x[j][2];
|
||||||
|
rsq = delx*delx + dely*dely + delz*delz;
|
||||||
|
radsum = radi + radius[j];
|
||||||
|
cutdistsq = (radsum+skin) * (radsum+skin);
|
||||||
|
|
||||||
|
if (rsq <= cutdistsq) {
|
||||||
|
if (history && rsq < radsum*radsum)
|
||||||
|
neighptr[n++] = j ^ mask_history;
|
||||||
|
else
|
||||||
|
neighptr[n++] = j;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
ilist[i] = i;
|
ilist[i] = i;
|
||||||
|
|||||||
@ -16,6 +16,7 @@
|
|||||||
#include "atom.h"
|
#include "atom.h"
|
||||||
#include "error.h"
|
#include "error.h"
|
||||||
#include "my_page.h"
|
#include "my_page.h"
|
||||||
|
#include "neighbor.h"
|
||||||
#include "neigh_list.h"
|
#include "neigh_list.h"
|
||||||
#include "npair_omp.h"
|
#include "npair_omp.h"
|
||||||
|
|
||||||
@ -31,8 +32,8 @@ NPairHalfSizeMultiNewtonTriOmp::NPairHalfSizeMultiNewtonTriOmp(LAMMPS *lmp) :
|
|||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
size particles
|
size particles
|
||||||
binned neighbor list construction with Newton's 3rd law for triclinic
|
binned neighbor list construction with Newton's 3rd law for triclinic
|
||||||
|
multi stencil is icollection-jcollection dependent
|
||||||
each owned atom i checks its own bin and other bins in triclinic stencil
|
each owned atom i checks its own bin and other bins in triclinic stencil
|
||||||
multi-type stencil is itype dependent and is distance checked
|
|
||||||
every pair stored exactly once by some processor
|
every pair stored exactly once by some processor
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
@ -48,12 +49,15 @@ void NPairHalfSizeMultiNewtonTriOmp::build(NeighList *list)
|
|||||||
#endif
|
#endif
|
||||||
NPAIR_OMP_SETUP(nlocal);
|
NPAIR_OMP_SETUP(nlocal);
|
||||||
|
|
||||||
int i,j,k,n,itype,jtype,ibin,ns;
|
int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,ns;
|
||||||
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
||||||
double radi,radsum,cutdistsq;
|
double radi,radsum,cutdistsq;
|
||||||
int *neighptr,*s;
|
int *neighptr,*s;
|
||||||
double *cutsq,*distsq;
|
int js;
|
||||||
|
|
||||||
|
// loop over each atom, storing neighbors
|
||||||
|
|
||||||
|
int *collection = neighbor->collection;
|
||||||
double **x = atom->x;
|
double **x = atom->x;
|
||||||
double *radius = atom->radius;
|
double *radius = atom->radius;
|
||||||
int *type = atom->type;
|
int *type = atom->type;
|
||||||
@ -74,53 +78,68 @@ void NPairHalfSizeMultiNewtonTriOmp::build(NeighList *list)
|
|||||||
neighptr = ipage.vget();
|
neighptr = ipage.vget();
|
||||||
|
|
||||||
itype = type[i];
|
itype = type[i];
|
||||||
|
icollection = collection[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];
|
||||||
radi = radius[i];
|
radi = radius[i];
|
||||||
|
|
||||||
// loop over all atoms in bins, including self, in stencil
|
|
||||||
// skip if i,j neighbor cutoff is less than bin distance
|
|
||||||
// bins below self are excluded from stencil
|
|
||||||
// pairs for atoms j "below" i are excluded
|
|
||||||
// below = lower z or (equal z and lower y) or (equal zy and lower x)
|
|
||||||
// (equal zyx and j <= i)
|
|
||||||
// latter excludes self-self interaction but allows superposed atoms
|
|
||||||
|
|
||||||
ibin = atom2bin[i];
|
ibin = atom2bin[i];
|
||||||
s = stencil_multi[itype];
|
|
||||||
distsq = distsq_multi[itype];
|
// loop through stencils for all collections
|
||||||
cutsq = cutneighsq[itype];
|
for (jcollection = 0; jcollection < ncollections; jcollection++) {
|
||||||
ns = nstencil_multi[itype];
|
|
||||||
for (k = 0; k < ns; k++) {
|
// if same collection use own bin
|
||||||
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
|
if(icollection == jcollection) jbin = ibin;
|
||||||
jtype = type[j];
|
else jbin = coord2bin(x[i], jcollection);
|
||||||
if (cutsq[jtype] < distsq[k]) continue;
|
|
||||||
if (x[j][2] < ztmp) continue;
|
|
||||||
if (x[j][2] == ztmp) {
|
// loop over all atoms in bins in stencil
|
||||||
if (x[j][1] < ytmp) continue;
|
// stencil is empty if i larger than j
|
||||||
if (x[j][1] == ytmp) {
|
// stencil is half if i same size as j
|
||||||
if (x[j][0] < xtmp) continue;
|
// stencil is full if i smaller than j
|
||||||
if (x[j][0] == xtmp && j <= i) continue;
|
// if half: pairs for atoms j "below" i are excluded
|
||||||
|
// below = lower z or (equal z and lower y) or (equal zy and lower x)
|
||||||
|
// (equal zyx and j <= i)
|
||||||
|
// latter excludes self-self interaction but allows superposed atoms
|
||||||
|
|
||||||
|
s = stencil_multi[icollection][jcollection];
|
||||||
|
ns = nstencil_multi[icollection][jcollection];
|
||||||
|
|
||||||
|
for (k = 0; k < ns; k++) {
|
||||||
|
js = binhead_multi[jcollection][jbin + s[k]];
|
||||||
|
for (j = js; j >= 0; j = bins[j]) {
|
||||||
|
|
||||||
|
// if same size (same collection), use half stencil
|
||||||
|
if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){
|
||||||
|
if (x[j][2] < ztmp) continue;
|
||||||
|
if (x[j][2] == ztmp) {
|
||||||
|
if (x[j][1] < ytmp) continue;
|
||||||
|
if (x[j][1] == ytmp) {
|
||||||
|
if (x[j][0] < xtmp) continue;
|
||||||
|
if (x[j][0] == xtmp && j <= i) continue;
|
||||||
|
}
|
||||||
|
}
|
||||||
}
|
}
|
||||||
}
|
|
||||||
|
|
||||||
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
jtype = type[j];
|
||||||
|
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
||||||
|
|
||||||
delx = xtmp - x[j][0];
|
delx = xtmp - x[j][0];
|
||||||
dely = ytmp - x[j][1];
|
dely = ytmp - x[j][1];
|
||||||
delz = ztmp - x[j][2];
|
delz = ztmp - x[j][2];
|
||||||
rsq = delx*delx + dely*dely + delz*delz;
|
rsq = delx*delx + dely*dely + delz*delz;
|
||||||
radsum = radi + radius[j];
|
radsum = radi + radius[j];
|
||||||
cutdistsq = (radsum+skin) * (radsum+skin);
|
cutdistsq = (radsum+skin) * (radsum+skin);
|
||||||
|
|
||||||
if (rsq <= cutdistsq) {
|
if (rsq <= cutdistsq) {
|
||||||
if (history && rsq < radsum*radsum)
|
if (history && rsq < radsum*radsum)
|
||||||
neighptr[n++] = j ^ mask_history;
|
neighptr[n++] = j ^ mask_history;
|
||||||
else
|
else
|
||||||
neighptr[n++] = j;
|
neighptr[n++] = j;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
ilist[i] = i;
|
ilist[i] = i;
|
||||||
|
|||||||
126
src/USER-OMP/npair_half_size_multi_old_newtoff_omp.cpp
Normal file
126
src/USER-OMP/npair_half_size_multi_old_newtoff_omp.cpp
Normal file
@ -0,0 +1,126 @@
|
|||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
https://lammps.sandia.gov/, 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 "omp_compat.h"
|
||||||
|
#include "npair_half_size_multi_old_newtoff_omp.h"
|
||||||
|
#include "npair_omp.h"
|
||||||
|
#include "neigh_list.h"
|
||||||
|
#include "atom.h"
|
||||||
|
#include "atom_vec.h"
|
||||||
|
#include "my_page.h"
|
||||||
|
#include "error.h"
|
||||||
|
|
||||||
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
NPairHalfSizeMultiOldNewtoffOmp::NPairHalfSizeMultiOldNewtoffOmp(LAMMPS *lmp) :
|
||||||
|
NPair(lmp) {}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
size particles
|
||||||
|
binned neighbor list construction with partial Newton's 3rd law
|
||||||
|
each owned atom i checks own bin and other bins in stencil
|
||||||
|
multi-type stencil is itype dependent and is distance checked
|
||||||
|
pair stored once if i,j are both owned and i < j
|
||||||
|
pair stored by me if j is ghost (also stored by proc owning j)
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void NPairHalfSizeMultiOldNewtoffOmp::build(NeighList *list)
|
||||||
|
{
|
||||||
|
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
|
||||||
|
const int history = list->history;
|
||||||
|
const int mask_history = 3 << SBBITS;
|
||||||
|
|
||||||
|
NPAIR_OMP_INIT;
|
||||||
|
#if defined(_OPENMP)
|
||||||
|
#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(list)
|
||||||
|
#endif
|
||||||
|
NPAIR_OMP_SETUP(nlocal);
|
||||||
|
|
||||||
|
int i,j,k,n,itype,jtype,ibin,ns;
|
||||||
|
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
||||||
|
double radi,radsum,cutdistsq;
|
||||||
|
int *neighptr,*s;
|
||||||
|
double *cutsq,*distsq;
|
||||||
|
|
||||||
|
double **x = atom->x;
|
||||||
|
double *radius = atom->radius;
|
||||||
|
int *type = atom->type;
|
||||||
|
int *mask = atom->mask;
|
||||||
|
tagint *molecule = atom->molecule;
|
||||||
|
|
||||||
|
int *ilist = list->ilist;
|
||||||
|
int *numneigh = list->numneigh;
|
||||||
|
int **firstneigh = list->firstneigh;
|
||||||
|
|
||||||
|
// each thread has its own page allocator
|
||||||
|
MyPage<int> &ipage = list->ipage[tid];
|
||||||
|
ipage.reset();
|
||||||
|
|
||||||
|
for (i = ifrom; i < ito; i++) {
|
||||||
|
|
||||||
|
n = 0;
|
||||||
|
neighptr = ipage.vget();
|
||||||
|
|
||||||
|
itype = type[i];
|
||||||
|
xtmp = x[i][0];
|
||||||
|
ytmp = x[i][1];
|
||||||
|
ztmp = x[i][2];
|
||||||
|
radi = radius[i];
|
||||||
|
|
||||||
|
// loop over all atoms in other bins in stencil including self
|
||||||
|
// only store pair if i < j
|
||||||
|
// skip if i,j neighbor cutoff is less than bin distance
|
||||||
|
// stores own/own pairs only once
|
||||||
|
// stores own/ghost pairs on both procs
|
||||||
|
|
||||||
|
ibin = atom2bin[i];
|
||||||
|
s = stencil_multi_old[itype];
|
||||||
|
distsq = distsq_multi_old[itype];
|
||||||
|
cutsq = cutneighsq[itype];
|
||||||
|
ns = nstencil_multi_old[itype];
|
||||||
|
for (k = 0; k < ns; k++) {
|
||||||
|
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
|
||||||
|
if (j <= i) continue;
|
||||||
|
jtype = type[j];
|
||||||
|
if (cutsq[jtype] < distsq[k]) continue;
|
||||||
|
|
||||||
|
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
||||||
|
|
||||||
|
delx = xtmp - x[j][0];
|
||||||
|
dely = ytmp - x[j][1];
|
||||||
|
delz = ztmp - x[j][2];
|
||||||
|
rsq = delx*delx + dely*dely + delz*delz;
|
||||||
|
radsum = radi + radius[j];
|
||||||
|
cutdistsq = (radsum+skin) * (radsum+skin);
|
||||||
|
|
||||||
|
if (rsq <= cutdistsq) {
|
||||||
|
if (history && rsq < radsum*radsum)
|
||||||
|
neighptr[n++] = j ^ mask_history;
|
||||||
|
else
|
||||||
|
neighptr[n++] = j;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
ilist[i] = i;
|
||||||
|
firstneigh[i] = neighptr;
|
||||||
|
numneigh[i] = n;
|
||||||
|
ipage.vgot(n);
|
||||||
|
if (ipage.status())
|
||||||
|
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
|
||||||
|
}
|
||||||
|
NPAIR_OMP_CLOSE;
|
||||||
|
list->inum = nlocal;
|
||||||
|
}
|
||||||
44
src/USER-OMP/npair_half_size_multi_old_newtoff_omp.h
Normal file
44
src/USER-OMP/npair_half_size_multi_old_newtoff_omp.h
Normal file
@ -0,0 +1,44 @@
|
|||||||
|
/* -*- c++ -*- ----------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
https://lammps.sandia.gov/, 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.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#ifdef NPAIR_CLASS
|
||||||
|
|
||||||
|
NPairStyle(half/size/multi/old/newtoff/omp,
|
||||||
|
NPairHalfSizeMultiOldNewtoffOmp,
|
||||||
|
NP_HALF | NP_SIZE | NP_MULTI_OLD | NP_NEWTOFF | NP_OMP |
|
||||||
|
NP_ORTHO | NP_TRI)
|
||||||
|
|
||||||
|
#else
|
||||||
|
|
||||||
|
#ifndef LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTOFF_OMP_H
|
||||||
|
#define LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTOFF_OMP_H
|
||||||
|
|
||||||
|
#include "npair.h"
|
||||||
|
|
||||||
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
|
class NPairHalfSizeMultiOldNewtoffOmp : public NPair {
|
||||||
|
public:
|
||||||
|
NPairHalfSizeMultiOldNewtoffOmp(class LAMMPS *);
|
||||||
|
~NPairHalfSizeMultiOldNewtoffOmp() {}
|
||||||
|
void build(class NeighList *);
|
||||||
|
};
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
#endif
|
||||||
|
#endif
|
||||||
|
|
||||||
|
/* ERROR/WARNING messages:
|
||||||
|
|
||||||
|
*/
|
||||||
151
src/USER-OMP/npair_half_size_multi_old_newton_omp.cpp
Normal file
151
src/USER-OMP/npair_half_size_multi_old_newton_omp.cpp
Normal file
@ -0,0 +1,151 @@
|
|||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
https://lammps.sandia.gov/, 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 "omp_compat.h"
|
||||||
|
#include "npair_half_size_multi_old_newton_omp.h"
|
||||||
|
#include "npair_omp.h"
|
||||||
|
#include "neigh_list.h"
|
||||||
|
#include "atom.h"
|
||||||
|
#include "atom_vec.h"
|
||||||
|
#include "my_page.h"
|
||||||
|
#include "error.h"
|
||||||
|
|
||||||
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
NPairHalfSizeMultiOldNewtonOmp::NPairHalfSizeMultiOldNewtonOmp(LAMMPS *lmp) :
|
||||||
|
NPair(lmp) {}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
size particles
|
||||||
|
binned neighbor list construction with full Newton's 3rd law
|
||||||
|
each owned atom i checks its own bin and other bins in Newton stencil
|
||||||
|
multi-type stencil is itype dependent and is distance checked
|
||||||
|
every pair stored exactly once by some processor
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void NPairHalfSizeMultiOldNewtonOmp::build(NeighList *list)
|
||||||
|
{
|
||||||
|
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
|
||||||
|
const int history = list->history;
|
||||||
|
const int mask_history = 3 << SBBITS;
|
||||||
|
|
||||||
|
NPAIR_OMP_INIT;
|
||||||
|
#if defined(_OPENMP)
|
||||||
|
#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(list)
|
||||||
|
#endif
|
||||||
|
NPAIR_OMP_SETUP(nlocal);
|
||||||
|
|
||||||
|
int i,j,k,n,itype,jtype,ibin,ns;
|
||||||
|
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
||||||
|
double radi,radsum,cutdistsq;
|
||||||
|
int *neighptr,*s;
|
||||||
|
double *cutsq,*distsq;
|
||||||
|
|
||||||
|
double **x = atom->x;
|
||||||
|
double *radius = atom->radius;
|
||||||
|
int *type = atom->type;
|
||||||
|
int *mask = atom->mask;
|
||||||
|
tagint *molecule = atom->molecule;
|
||||||
|
|
||||||
|
int *ilist = list->ilist;
|
||||||
|
int *numneigh = list->numneigh;
|
||||||
|
int **firstneigh = list->firstneigh;
|
||||||
|
|
||||||
|
// each thread has its own page allocator
|
||||||
|
MyPage<int> &ipage = list->ipage[tid];
|
||||||
|
ipage.reset();
|
||||||
|
|
||||||
|
for (i = ifrom; i < ito; i++) {
|
||||||
|
|
||||||
|
n = 0;
|
||||||
|
neighptr = ipage.vget();
|
||||||
|
|
||||||
|
itype = type[i];
|
||||||
|
xtmp = x[i][0];
|
||||||
|
ytmp = x[i][1];
|
||||||
|
ztmp = x[i][2];
|
||||||
|
radi = radius[i];
|
||||||
|
|
||||||
|
// loop over rest of atoms in i's bin, ghosts are at end of linked list
|
||||||
|
// if j is owned atom, store it, since j is beyond i in linked list
|
||||||
|
// if j is ghost, only store if j coords are "above and to the right" of i
|
||||||
|
|
||||||
|
for (j = bins[i]; j >= 0; j = bins[j]) {
|
||||||
|
if (j >= nlocal) {
|
||||||
|
if (x[j][2] < ztmp) continue;
|
||||||
|
if (x[j][2] == ztmp) {
|
||||||
|
if (x[j][1] < ytmp) continue;
|
||||||
|
if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
jtype = type[j];
|
||||||
|
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
||||||
|
delx = xtmp - x[j][0];
|
||||||
|
dely = ytmp - x[j][1];
|
||||||
|
delz = ztmp - x[j][2];
|
||||||
|
rsq = delx*delx + dely*dely + delz*delz;
|
||||||
|
radsum = radi + radius[j];
|
||||||
|
cutdistsq = (radsum+skin) * (radsum+skin);
|
||||||
|
|
||||||
|
if (rsq <= cutdistsq) {
|
||||||
|
if (history && rsq < radsum*radsum)
|
||||||
|
neighptr[n++] = j ^ mask_history;
|
||||||
|
else
|
||||||
|
neighptr[n++] = j;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
// loop over all atoms in other bins in stencil, store every pair
|
||||||
|
// skip if i,j neighbor cutoff is less than bin distance
|
||||||
|
|
||||||
|
ibin = atom2bin[i];
|
||||||
|
s = stencil_multi_old[itype];
|
||||||
|
distsq = distsq_multi_old[itype];
|
||||||
|
cutsq = cutneighsq[itype];
|
||||||
|
ns = nstencil_multi_old[itype];
|
||||||
|
for (k = 0; k < ns; k++) {
|
||||||
|
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
|
||||||
|
jtype = type[j];
|
||||||
|
if (cutsq[jtype] < distsq[k]) continue;
|
||||||
|
|
||||||
|
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
||||||
|
|
||||||
|
delx = xtmp - x[j][0];
|
||||||
|
dely = ytmp - x[j][1];
|
||||||
|
delz = ztmp - x[j][2];
|
||||||
|
rsq = delx*delx + dely*dely + delz*delz;
|
||||||
|
radsum = radi + radius[j];
|
||||||
|
cutdistsq = (radsum+skin) * (radsum+skin);
|
||||||
|
|
||||||
|
if (rsq <= cutdistsq) {
|
||||||
|
if (history && rsq < radsum*radsum)
|
||||||
|
neighptr[n++] = j ^ mask_history;
|
||||||
|
else
|
||||||
|
neighptr[n++] = j;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
ilist[i] = i;
|
||||||
|
firstneigh[i] = neighptr;
|
||||||
|
numneigh[i] = n;
|
||||||
|
ipage.vgot(n);
|
||||||
|
if (ipage.status())
|
||||||
|
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
|
||||||
|
}
|
||||||
|
NPAIR_OMP_CLOSE;
|
||||||
|
list->inum = nlocal;
|
||||||
|
}
|
||||||
43
src/USER-OMP/npair_half_size_multi_old_newton_omp.h
Normal file
43
src/USER-OMP/npair_half_size_multi_old_newton_omp.h
Normal file
@ -0,0 +1,43 @@
|
|||||||
|
/* -*- c++ -*- ----------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
https://lammps.sandia.gov/, 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.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#ifdef NPAIR_CLASS
|
||||||
|
|
||||||
|
NPairStyle(half/size/multi/old/newton/omp,
|
||||||
|
NPairHalfSizeMultiOldNewtonOmp,
|
||||||
|
NP_HALF | NP_SIZE | NP_MULTI_OLD | NP_NEWTON | NP_OMP | NP_ORTHO)
|
||||||
|
|
||||||
|
#else
|
||||||
|
|
||||||
|
#ifndef LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTON_OMP_H
|
||||||
|
#define LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTON_OMP_H
|
||||||
|
|
||||||
|
#include "npair.h"
|
||||||
|
|
||||||
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
|
class NPairHalfSizeMultiOldNewtonOmp : public NPair {
|
||||||
|
public:
|
||||||
|
NPairHalfSizeMultiOldNewtonOmp(class LAMMPS *);
|
||||||
|
~NPairHalfSizeMultiOldNewtonOmp() {}
|
||||||
|
void build(class NeighList *);
|
||||||
|
};
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
#endif
|
||||||
|
#endif
|
||||||
|
|
||||||
|
/* ERROR/WARNING messages:
|
||||||
|
|
||||||
|
*/
|
||||||
134
src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.cpp
Normal file
134
src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.cpp
Normal file
@ -0,0 +1,134 @@
|
|||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
https://lammps.sandia.gov/, 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 "omp_compat.h"
|
||||||
|
#include "npair_half_size_multi_old_newton_tri_omp.h"
|
||||||
|
#include "npair_omp.h"
|
||||||
|
#include "neigh_list.h"
|
||||||
|
#include "atom.h"
|
||||||
|
#include "atom_vec.h"
|
||||||
|
#include "my_page.h"
|
||||||
|
#include "error.h"
|
||||||
|
|
||||||
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
NPairHalfSizeMultiOldNewtonTriOmp::NPairHalfSizeMultiOldNewtonTriOmp(LAMMPS *lmp) :
|
||||||
|
NPair(lmp) {}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
size particles
|
||||||
|
binned neighbor list construction with Newton's 3rd law for triclinic
|
||||||
|
each owned atom i checks its own bin and other bins in triclinic stencil
|
||||||
|
multi-type stencil is itype dependent and is distance checked
|
||||||
|
every pair stored exactly once by some processor
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void NPairHalfSizeMultiOldNewtonTriOmp::build(NeighList *list)
|
||||||
|
{
|
||||||
|
const int nlocal = (includegroup) ? atom->nfirst : atom->nlocal;
|
||||||
|
const int history = list->history;
|
||||||
|
const int mask_history = 3 << SBBITS;
|
||||||
|
|
||||||
|
NPAIR_OMP_INIT;
|
||||||
|
#if defined(_OPENMP)
|
||||||
|
#pragma omp parallel LMP_DEFAULT_NONE LMP_SHARED(list)
|
||||||
|
#endif
|
||||||
|
NPAIR_OMP_SETUP(nlocal);
|
||||||
|
|
||||||
|
int i,j,k,n,itype,jtype,ibin,ns;
|
||||||
|
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
||||||
|
double radi,radsum,cutdistsq;
|
||||||
|
int *neighptr,*s;
|
||||||
|
double *cutsq,*distsq;
|
||||||
|
|
||||||
|
double **x = atom->x;
|
||||||
|
double *radius = atom->radius;
|
||||||
|
int *type = atom->type;
|
||||||
|
int *mask = atom->mask;
|
||||||
|
tagint *molecule = atom->molecule;
|
||||||
|
|
||||||
|
int *ilist = list->ilist;
|
||||||
|
int *numneigh = list->numneigh;
|
||||||
|
int **firstneigh = list->firstneigh;
|
||||||
|
|
||||||
|
// each thread has its own page allocator
|
||||||
|
MyPage<int> &ipage = list->ipage[tid];
|
||||||
|
ipage.reset();
|
||||||
|
|
||||||
|
for (i = ifrom; i < ito; i++) {
|
||||||
|
|
||||||
|
n = 0;
|
||||||
|
neighptr = ipage.vget();
|
||||||
|
|
||||||
|
itype = type[i];
|
||||||
|
xtmp = x[i][0];
|
||||||
|
ytmp = x[i][1];
|
||||||
|
ztmp = x[i][2];
|
||||||
|
radi = radius[i];
|
||||||
|
|
||||||
|
// loop over all atoms in bins, including self, in stencil
|
||||||
|
// skip if i,j neighbor cutoff is less than bin distance
|
||||||
|
// bins below self are excluded from stencil
|
||||||
|
// pairs for atoms j "below" i are excluded
|
||||||
|
// below = lower z or (equal z and lower y) or (equal zy and lower x)
|
||||||
|
// (equal zyx and j <= i)
|
||||||
|
// latter excludes self-self interaction but allows superposed atoms
|
||||||
|
|
||||||
|
ibin = atom2bin[i];
|
||||||
|
s = stencil_multi_old[itype];
|
||||||
|
distsq = distsq_multi_old[itype];
|
||||||
|
cutsq = cutneighsq[itype];
|
||||||
|
ns = nstencil_multi_old[itype];
|
||||||
|
for (k = 0; k < ns; k++) {
|
||||||
|
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
|
||||||
|
jtype = type[j];
|
||||||
|
if (cutsq[jtype] < distsq[k]) continue;
|
||||||
|
if (x[j][2] < ztmp) continue;
|
||||||
|
if (x[j][2] == ztmp) {
|
||||||
|
if (x[j][1] < ytmp) continue;
|
||||||
|
if (x[j][1] == ytmp) {
|
||||||
|
if (x[j][0] < xtmp) continue;
|
||||||
|
if (x[j][0] == xtmp && j <= i) continue;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
||||||
|
|
||||||
|
delx = xtmp - x[j][0];
|
||||||
|
dely = ytmp - x[j][1];
|
||||||
|
delz = ztmp - x[j][2];
|
||||||
|
rsq = delx*delx + dely*dely + delz*delz;
|
||||||
|
radsum = radi + radius[j];
|
||||||
|
cutdistsq = (radsum+skin) * (radsum+skin);
|
||||||
|
|
||||||
|
if (rsq <= cutdistsq) {
|
||||||
|
if (history && rsq < radsum*radsum)
|
||||||
|
neighptr[n++] = j ^ mask_history;
|
||||||
|
else
|
||||||
|
neighptr[n++] = j;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
ilist[i] = i;
|
||||||
|
firstneigh[i] = neighptr;
|
||||||
|
numneigh[i] = n;
|
||||||
|
ipage.vgot(n);
|
||||||
|
if (ipage.status())
|
||||||
|
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
|
||||||
|
}
|
||||||
|
NPAIR_OMP_CLOSE;
|
||||||
|
list->inum = nlocal;
|
||||||
|
}
|
||||||
43
src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.h
Normal file
43
src/USER-OMP/npair_half_size_multi_old_newton_tri_omp.h
Normal file
@ -0,0 +1,43 @@
|
|||||||
|
/* -*- c++ -*- ----------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
https://lammps.sandia.gov/, 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.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#ifdef NPAIR_CLASS
|
||||||
|
|
||||||
|
NPairStyle(half/size/multi/old/newton/tri/omp,
|
||||||
|
NPairHalfSizeMultiOldNewtonTriOmp,
|
||||||
|
NP_HALF | NP_SIZE | NP_MULTI_OLD | NP_NEWTON | NP_TRI | NP_OMP)
|
||||||
|
|
||||||
|
#else
|
||||||
|
|
||||||
|
#ifndef LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTON_TRI_OMP_H
|
||||||
|
#define LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTON_TRI_OMP_H
|
||||||
|
|
||||||
|
#include "npair.h"
|
||||||
|
|
||||||
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
|
class NPairHalfSizeMultiOldNewtonTriOmp : public NPair {
|
||||||
|
public:
|
||||||
|
NPairHalfSizeMultiOldNewtonTriOmp(class LAMMPS *);
|
||||||
|
~NPairHalfSizeMultiOldNewtonTriOmp() {}
|
||||||
|
void build(class NeighList *);
|
||||||
|
};
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
#endif
|
||||||
|
#endif
|
||||||
|
|
||||||
|
/* ERROR/WARNING messages:
|
||||||
|
|
||||||
|
*/
|
||||||
@ -15,12 +15,12 @@
|
|||||||
|
|
||||||
NPairStyle(halffull/newtoff/omp,
|
NPairStyle(halffull/newtoff/omp,
|
||||||
NPairHalffullNewtoffOmp,
|
NPairHalffullNewtoffOmp,
|
||||||
NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_HALF |
|
NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_HALF |
|
||||||
NP_ORTHO | NP_TRI |NP_OMP)
|
NP_ORTHO | NP_TRI |NP_OMP)
|
||||||
|
|
||||||
NPairStyle(halffull/newtoff/skip/omp,
|
NPairStyle(halffull/newtoff/skip/omp,
|
||||||
NPairHalffullNewtoffOmp,
|
NPairHalffullNewtoffOmp,
|
||||||
NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_HALF |
|
NP_HALF_FULL | NP_NEWTOFF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_HALF |
|
||||||
NP_ORTHO | NP_TRI | NP_SKIP | NP_OMP)
|
NP_ORTHO | NP_TRI | NP_SKIP | NP_OMP)
|
||||||
#else
|
#else
|
||||||
|
|
||||||
|
|||||||
@ -15,12 +15,12 @@
|
|||||||
|
|
||||||
NPairStyle(halffull/newton/omp,
|
NPairStyle(halffull/newton/omp,
|
||||||
NPairHalffullNewtonOmp,
|
NPairHalffullNewtonOmp,
|
||||||
NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
|
NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
|
||||||
NP_ORTHO | NP_TRI| NP_OMP)
|
NP_ORTHO | NP_TRI| NP_OMP)
|
||||||
|
|
||||||
NPairStyle(halffull/newton/skip/omp,
|
NPairStyle(halffull/newton/skip/omp,
|
||||||
NPairHalffullNewtonOmp,
|
NPairHalffullNewtonOmp,
|
||||||
NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI |
|
NP_HALF_FULL | NP_NEWTON | NP_HALF | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
|
||||||
NP_ORTHO | NP_TRI | NP_SKIP | NP_OMP)
|
NP_ORTHO | NP_TRI | NP_SKIP | NP_OMP)
|
||||||
|
|
||||||
#else
|
#else
|
||||||
|
|||||||
@ -19,36 +19,36 @@
|
|||||||
NPairStyle(skip/omp,
|
NPairStyle(skip/omp,
|
||||||
NPairSkip,
|
NPairSkip,
|
||||||
NP_SKIP | NP_HALF | NP_FULL |
|
NP_SKIP | NP_HALF | NP_FULL |
|
||||||
NP_NSQ | NP_BIN | NP_MULTI |
|
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
|
||||||
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP)
|
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP)
|
||||||
|
|
||||||
NPairStyle(skip/half/respa/omp,
|
NPairStyle(skip/half/respa/omp,
|
||||||
NPairSkipRespa,
|
NPairSkipRespa,
|
||||||
NP_SKIP | NP_RESPA | NP_HALF | NP_FULL |
|
NP_SKIP | NP_RESPA | NP_HALF | NP_FULL |
|
||||||
NP_NSQ | NP_BIN | NP_MULTI |
|
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
|
||||||
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP)
|
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP)
|
||||||
|
|
||||||
NPairStyle(skip/half/size/omp,
|
NPairStyle(skip/half/size/omp,
|
||||||
NPairSkipSize,
|
NPairSkipSize,
|
||||||
NP_SKIP | NP_SIZE | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI |
|
NP_SKIP | NP_SIZE | NP_HALF | NP_FULL | NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
|
||||||
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP)
|
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP)
|
||||||
|
|
||||||
NPairStyle(skip/size/off2on/omp,
|
NPairStyle(skip/size/off2on/omp,
|
||||||
NPairSkipSizeOff2on,
|
NPairSkipSizeOff2on,
|
||||||
NP_SKIP | NP_SIZE | NP_OFF2ON | NP_HALF |
|
NP_SKIP | NP_SIZE | NP_OFF2ON | NP_HALF |
|
||||||
NP_NSQ | NP_BIN | NP_MULTI |
|
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_MULTI_OLD |
|
||||||
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP)
|
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP)
|
||||||
|
|
||||||
NPairStyle(skip/size/off2on/oneside/omp,
|
NPairStyle(skip/size/off2on/oneside/omp,
|
||||||
NPairSkipSizeOff2onOneside,
|
NPairSkipSizeOff2onOneside,
|
||||||
NP_SKIP | NP_SIZE | NP_OFF2ON | NP_ONESIDE | NP_HALF |
|
NP_SKIP | NP_SIZE | NP_OFF2ON | NP_ONESIDE | NP_HALF |
|
||||||
NP_NSQ | NP_BIN | NP_MULTI | NP_NEWTON | NP_NEWTOFF |
|
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF |
|
||||||
NP_ORTHO | NP_TRI | NP_OMP)
|
NP_ORTHO | NP_TRI | NP_OMP)
|
||||||
|
|
||||||
NPairStyle(skip/ghost/omp,
|
NPairStyle(skip/ghost/omp,
|
||||||
NPairSkip,
|
NPairSkip,
|
||||||
NP_SKIP | NP_HALF | NP_FULL |
|
NP_SKIP | NP_HALF | NP_FULL |
|
||||||
NP_NSQ | NP_BIN | NP_MULTI |
|
NP_NSQ | NP_BIN | NP_MULTI | NP_MULTI_OLD |
|
||||||
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP | NP_GHOST)
|
NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI | NP_OMP | NP_GHOST)
|
||||||
|
|
||||||
#endif
|
#endif
|
||||||
|
|||||||
102
src/comm.cpp
102
src/comm.cpp
@ -35,7 +35,6 @@
|
|||||||
#include "update.h"
|
#include "update.h"
|
||||||
|
|
||||||
#include <cstring>
|
#include <cstring>
|
||||||
|
|
||||||
#ifdef _OPENMP
|
#ifdef _OPENMP
|
||||||
#include <omp.h>
|
#include <omp.h>
|
||||||
#endif
|
#endif
|
||||||
@ -58,6 +57,9 @@ Comm::Comm(LAMMPS *lmp) : Pointers(lmp)
|
|||||||
bordergroup = 0;
|
bordergroup = 0;
|
||||||
cutghostuser = 0.0;
|
cutghostuser = 0.0;
|
||||||
cutusermulti = nullptr;
|
cutusermulti = nullptr;
|
||||||
|
cutusermultiold = nullptr;
|
||||||
|
ncollections = 0;
|
||||||
|
ncollections_cutoff = 0;
|
||||||
ghost_velocity = 0;
|
ghost_velocity = 0;
|
||||||
|
|
||||||
user_procgrid[0] = user_procgrid[1] = user_procgrid[2] = 0;
|
user_procgrid[0] = user_procgrid[1] = user_procgrid[2] = 0;
|
||||||
@ -76,6 +78,7 @@ Comm::Comm(LAMMPS *lmp) : Pointers(lmp)
|
|||||||
grid2proc = nullptr;
|
grid2proc = nullptr;
|
||||||
xsplit = ysplit = zsplit = nullptr;
|
xsplit = ysplit = zsplit = nullptr;
|
||||||
rcbnew = 0;
|
rcbnew = 0;
|
||||||
|
multi_reduce = 0;
|
||||||
|
|
||||||
// use of OpenMP threads
|
// use of OpenMP threads
|
||||||
// query OpenMP for number of threads/process set by user at run-time
|
// query OpenMP for number of threads/process set by user at run-time
|
||||||
@ -117,6 +120,7 @@ Comm::~Comm()
|
|||||||
memory->destroy(ysplit);
|
memory->destroy(ysplit);
|
||||||
memory->destroy(zsplit);
|
memory->destroy(zsplit);
|
||||||
memory->destroy(cutusermulti);
|
memory->destroy(cutusermulti);
|
||||||
|
memory->destroy(cutusermultiold);
|
||||||
delete [] customfile;
|
delete [] customfile;
|
||||||
delete [] outfile;
|
delete [] outfile;
|
||||||
}
|
}
|
||||||
@ -144,9 +148,16 @@ void Comm::copy_arrays(Comm *oldcomm)
|
|||||||
memcpy(zsplit,oldcomm->zsplit,(procgrid[2]+1)*sizeof(double));
|
memcpy(zsplit,oldcomm->zsplit,(procgrid[2]+1)*sizeof(double));
|
||||||
}
|
}
|
||||||
|
|
||||||
|
ncollections = oldcomm->ncollections;
|
||||||
|
ncollections_cutoff = oldcomm->ncollections_cutoff;
|
||||||
if (oldcomm->cutusermulti) {
|
if (oldcomm->cutusermulti) {
|
||||||
memory->create(cutusermulti,atom->ntypes+1,"comm:cutusermulti");
|
memory->create(cutusermulti,ncollections_cutoff,"comm:cutusermulti");
|
||||||
memcpy(cutusermulti,oldcomm->cutusermulti,atom->ntypes+1);
|
memcpy(cutusermulti,oldcomm->cutusermulti,ncollections_cutoff);
|
||||||
|
}
|
||||||
|
|
||||||
|
if (oldcomm->cutusermultiold) {
|
||||||
|
memory->create(cutusermultiold,atom->ntypes+1,"comm:cutusermultiold");
|
||||||
|
memcpy(cutusermultiold,oldcomm->cutusermultiold,atom->ntypes+1);
|
||||||
}
|
}
|
||||||
|
|
||||||
if (customfile)
|
if (customfile)
|
||||||
@ -235,6 +246,18 @@ void Comm::init()
|
|||||||
maxexchange_fix_dynamic = 0;
|
maxexchange_fix_dynamic = 0;
|
||||||
for (int i = 0; i < nfix; i++)
|
for (int i = 0; i < nfix; i++)
|
||||||
if (fix[i]->maxexchange_dynamic) maxexchange_fix_dynamic = 1;
|
if (fix[i]->maxexchange_dynamic) maxexchange_fix_dynamic = 1;
|
||||||
|
|
||||||
|
if ((mode == Comm::MULTI) && (neighbor->style != Neighbor::MULTI))
|
||||||
|
error->all(FLERR,"Cannot use comm mode multi without multi-style neighbor lists");
|
||||||
|
|
||||||
|
if (multi_reduce) {
|
||||||
|
if (force->newton == 0)
|
||||||
|
error->all(FLERR,"Cannot use multi/reduce communication with Newton off");
|
||||||
|
if (neighbor->any_full())
|
||||||
|
error->all(FLERR,"Cannot use multi/reduce communication with a full neighbor list");
|
||||||
|
if (mode != Comm::MULTI)
|
||||||
|
error->all(FLERR,"Cannot use multi/reduce communication without mode multi");
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
@ -270,13 +293,26 @@ void Comm::modify_params(int narg, char **arg)
|
|||||||
if (strcmp(arg[iarg+1],"single") == 0) {
|
if (strcmp(arg[iarg+1],"single") == 0) {
|
||||||
// need to reset cutghostuser when switching comm mode
|
// need to reset cutghostuser when switching comm mode
|
||||||
if (mode == Comm::MULTI) cutghostuser = 0.0;
|
if (mode == Comm::MULTI) cutghostuser = 0.0;
|
||||||
|
if (mode == Comm::MULTIOLD) cutghostuser = 0.0;
|
||||||
memory->destroy(cutusermulti);
|
memory->destroy(cutusermulti);
|
||||||
cutusermulti = nullptr;
|
memory->destroy(cutusermultiold);
|
||||||
mode = Comm::SINGLE;
|
mode = Comm::SINGLE;
|
||||||
} else if (strcmp(arg[iarg+1],"multi") == 0) {
|
} else if (strcmp(arg[iarg+1],"multi") == 0) {
|
||||||
|
if (neighbor->style != Neighbor::MULTI)
|
||||||
|
error->all(FLERR,"Cannot use comm mode 'multi' without 'multi' style neighbor lists");
|
||||||
// need to reset cutghostuser when switching comm mode
|
// need to reset cutghostuser when switching comm mode
|
||||||
if (mode == Comm::SINGLE) cutghostuser = 0.0;
|
if (mode == Comm::SINGLE) cutghostuser = 0.0;
|
||||||
|
if (mode == Comm::MULTIOLD) cutghostuser = 0.0;
|
||||||
|
memory->destroy(cutusermultiold);
|
||||||
mode = Comm::MULTI;
|
mode = Comm::MULTI;
|
||||||
|
} else if (strcmp(arg[iarg+1],"multi/old") == 0) {
|
||||||
|
if (neighbor->style == Neighbor::MULTI)
|
||||||
|
error->all(FLERR,"Cannot use comm mode 'multi/old' with 'multi' style neighbor lists");
|
||||||
|
// need to reset cutghostuser when switching comm mode
|
||||||
|
if (mode == Comm::SINGLE) cutghostuser = 0.0;
|
||||||
|
if (mode == Comm::MULTI) cutghostuser = 0.0;
|
||||||
|
memory->destroy(cutusermulti);
|
||||||
|
mode = Comm::MULTIOLD;
|
||||||
} else error->all(FLERR,"Illegal comm_modify command");
|
} else error->all(FLERR,"Illegal comm_modify command");
|
||||||
iarg += 2;
|
iarg += 2;
|
||||||
} else if (strcmp(arg[iarg],"group") == 0) {
|
} else if (strcmp(arg[iarg],"group") == 0) {
|
||||||
@ -291,8 +327,9 @@ void Comm::modify_params(int narg, char **arg)
|
|||||||
} else if (strcmp(arg[iarg],"cutoff") == 0) {
|
} else if (strcmp(arg[iarg],"cutoff") == 0) {
|
||||||
if (iarg+2 > narg) error->all(FLERR,"Illegal comm_modify command");
|
if (iarg+2 > narg) error->all(FLERR,"Illegal comm_modify command");
|
||||||
if (mode == Comm::MULTI)
|
if (mode == Comm::MULTI)
|
||||||
error->all(FLERR,
|
error->all(FLERR, "Use cutoff/multi keyword to set cutoff in multi mode");
|
||||||
"Use cutoff/multi keyword to set cutoff in multi mode");
|
if (mode == Comm::MULTIOLD)
|
||||||
|
error->all(FLERR, "Use cutoff/multi/old keyword to set cutoff in multi mode");
|
||||||
cutghostuser = utils::numeric(FLERR,arg[iarg+1],false,lmp);
|
cutghostuser = utils::numeric(FLERR,arg[iarg+1],false,lmp);
|
||||||
if (cutghostuser < 0.0)
|
if (cutghostuser < 0.0)
|
||||||
error->all(FLERR,"Invalid cutoff in comm_modify command");
|
error->all(FLERR,"Invalid cutoff in comm_modify command");
|
||||||
@ -302,16 +339,45 @@ void Comm::modify_params(int narg, char **arg)
|
|||||||
double cut;
|
double cut;
|
||||||
if (mode == Comm::SINGLE)
|
if (mode == Comm::SINGLE)
|
||||||
error->all(FLERR,"Use cutoff keyword to set cutoff in single mode");
|
error->all(FLERR,"Use cutoff keyword to set cutoff in single mode");
|
||||||
|
if (mode == Comm::MULTIOLD)
|
||||||
|
error->all(FLERR,"Use cutoff/multi/old keyword to set cutoff in multi/old mode");
|
||||||
if (domain->box_exist == 0)
|
if (domain->box_exist == 0)
|
||||||
error->all(FLERR,
|
error->all(FLERR, "Cannot set cutoff/multi before simulation box is defined");
|
||||||
"Cannot set cutoff/multi before simulation box is defined");
|
|
||||||
|
// Check if # of collections has changed, if so erase any previously defined cutoffs
|
||||||
|
// Neighbor will reset ncollections if collections are redefined
|
||||||
|
if (! cutusermulti || ncollections_cutoff != neighbor->ncollections) {
|
||||||
|
ncollections_cutoff = neighbor->ncollections;
|
||||||
|
memory->destroy(cutusermulti);
|
||||||
|
memory->create(cutusermulti,ncollections_cutoff,"comm:cutusermulti");
|
||||||
|
for (i=0; i < ncollections_cutoff; ++i)
|
||||||
|
cutusermulti[i] = -1.0;
|
||||||
|
}
|
||||||
|
utils::bounds(FLERR,arg[iarg+1],1,ncollections_cutoff,nlo,nhi,error);
|
||||||
|
cut = utils::numeric(FLERR,arg[iarg+2],false,lmp);
|
||||||
|
cutghostuser = MAX(cutghostuser,cut);
|
||||||
|
if (cut < 0.0)
|
||||||
|
error->all(FLERR,"Invalid cutoff in comm_modify command");
|
||||||
|
// collections use 1-based indexing externally and 0-based indexing internally
|
||||||
|
for (i=nlo; i<=nhi; ++i)
|
||||||
|
cutusermulti[i-1] = cut;
|
||||||
|
iarg += 3;
|
||||||
|
} else if (strcmp(arg[iarg],"cutoff/multi/old") == 0) {
|
||||||
|
int i,nlo,nhi;
|
||||||
|
double cut;
|
||||||
|
if (mode == Comm::SINGLE)
|
||||||
|
error->all(FLERR,"Use cutoff keyword to set cutoff in single mode");
|
||||||
|
if (mode == Comm::MULTI)
|
||||||
|
error->all(FLERR,"Use cutoff/multi keyword to set cutoff in multi mode");
|
||||||
|
if (domain->box_exist == 0)
|
||||||
|
error->all(FLERR, "Cannot set cutoff/multi before simulation box is defined");
|
||||||
const int ntypes = atom->ntypes;
|
const int ntypes = atom->ntypes;
|
||||||
if (iarg+3 > narg)
|
if (iarg+3 > narg)
|
||||||
error->all(FLERR,"Illegal comm_modify command");
|
error->all(FLERR,"Illegal comm_modify command");
|
||||||
if (cutusermulti == nullptr) {
|
if (cutusermultiold == nullptr) {
|
||||||
memory->create(cutusermulti,ntypes+1,"comm:cutusermulti");
|
memory->create(cutusermultiold,ntypes+1,"comm:cutusermultiold");
|
||||||
for (i=0; i < ntypes+1; ++i)
|
for (i=0; i < ntypes+1; ++i)
|
||||||
cutusermulti[i] = -1.0;
|
cutusermultiold[i] = -1.0;
|
||||||
}
|
}
|
||||||
utils::bounds(FLERR,arg[iarg+1],1,ntypes,nlo,nhi,error);
|
utils::bounds(FLERR,arg[iarg+1],1,ntypes,nlo,nhi,error);
|
||||||
cut = utils::numeric(FLERR,arg[iarg+2],false,lmp);
|
cut = utils::numeric(FLERR,arg[iarg+2],false,lmp);
|
||||||
@ -319,8 +385,13 @@ void Comm::modify_params(int narg, char **arg)
|
|||||||
if (cut < 0.0)
|
if (cut < 0.0)
|
||||||
error->all(FLERR,"Invalid cutoff in comm_modify command");
|
error->all(FLERR,"Invalid cutoff in comm_modify command");
|
||||||
for (i=nlo; i<=nhi; ++i)
|
for (i=nlo; i<=nhi; ++i)
|
||||||
cutusermulti[i] = cut;
|
cutusermultiold[i] = cut;
|
||||||
iarg += 3;
|
iarg += 3;
|
||||||
|
} else if (strcmp(arg[iarg],"reduce/multi") == 0) {
|
||||||
|
if (mode == Comm::SINGLE)
|
||||||
|
error->all(FLERR,"Use reduce/multi in mode multi only");
|
||||||
|
multi_reduce = 1;
|
||||||
|
iarg += 1;
|
||||||
} else if (strcmp(arg[iarg],"vel") == 0) {
|
} else if (strcmp(arg[iarg],"vel") == 0) {
|
||||||
if (iarg+2 > narg) error->all(FLERR,"Illegal comm_modify command");
|
if (iarg+2 > narg) error->all(FLERR,"Illegal comm_modify command");
|
||||||
if (strcmp(arg[iarg+1],"yes") == 0) ghost_velocity = 1;
|
if (strcmp(arg[iarg+1],"yes") == 0) ghost_velocity = 1;
|
||||||
@ -667,6 +738,13 @@ double Comm::get_comm_cutoff()
|
|||||||
error->warning(FLERR,"Communication cutoff adjusted to {}",maxcommcutoff);
|
error->warning(FLERR,"Communication cutoff adjusted to {}",maxcommcutoff);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
// Check maximum interval size for neighbor multi
|
||||||
|
if (neighbor->interval_collection_flag) {
|
||||||
|
for (int i = 0; i < neighbor->ncollections; i++){
|
||||||
|
maxcommcutoff = MAX(maxcommcutoff, neighbor->collection2cut[i]);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
return maxcommcutoff;
|
return maxcommcutoff;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|||||||
20
src/comm.h
20
src/comm.h
@ -25,14 +25,17 @@ class Comm : protected Pointers {
|
|||||||
// LAYOUT_NONUNIFORM = logical bricks, but diff sizes via LB
|
// LAYOUT_NONUNIFORM = logical bricks, but diff sizes via LB
|
||||||
// LAYOUT_TILED = general tiling, due to RCB LB
|
// LAYOUT_TILED = general tiling, due to RCB LB
|
||||||
enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED};
|
enum{LAYOUT_UNIFORM,LAYOUT_NONUNIFORM,LAYOUT_TILED};
|
||||||
int mode; // 0 = single cutoff, 1 = multi-type cutoff
|
int mode; // 0 = single cutoff, 1 = multi-collection cutoff, 2 = multiold-type cutoff
|
||||||
enum{SINGLE,MULTI};
|
enum{SINGLE,MULTI,MULTIOLD};
|
||||||
|
|
||||||
int me,nprocs; // proc info
|
int me,nprocs; // proc info
|
||||||
int ghost_velocity; // 1 if ghost atoms have velocity, 0 if not
|
int ghost_velocity; // 1 if ghost atoms have velocity, 0 if not
|
||||||
double cutghost[3]; // cutoffs used for acquiring ghost atoms
|
double cutghost[3]; // cutoffs used for acquiring ghost atoms
|
||||||
double cutghostuser; // user-specified ghost cutoff (mode == 0)
|
double cutghostuser; // user-specified ghost cutoff (mode == SINGLE)
|
||||||
double *cutusermulti; // per type user ghost cutoff (mode == 1)
|
double *cutusermulti; // per collection user ghost cutoff (mode == MULTI)
|
||||||
|
double *cutusermultiold; // per type user ghost cutoff (mode == MULTIOLD)
|
||||||
|
int ncollections; // # of collections known by comm, used to test if # has changed
|
||||||
|
int ncollections_cutoff; // # of collections stored b cutoff/multi
|
||||||
int recv_from_partition; // recv proc layout from this partition
|
int recv_from_partition; // recv proc layout from this partition
|
||||||
int send_to_partition; // send my proc layout to this partition
|
int send_to_partition; // send my proc layout to this partition
|
||||||
// -1 if no recv or send
|
// -1 if no recv or send
|
||||||
@ -149,6 +152,7 @@ class Comm : protected Pointers {
|
|||||||
int ncores; // # of cores per node
|
int ncores; // # of cores per node
|
||||||
int coregrid[3]; // 3d grid of cores within a node
|
int coregrid[3]; // 3d grid of cores within a node
|
||||||
int user_coregrid[3]; // user request for cores in each dim
|
int user_coregrid[3]; // user request for cores in each dim
|
||||||
|
int multi_reduce; // 1 if multi cutoff is intra-collection cutoff
|
||||||
|
|
||||||
void init_exchange();
|
void init_exchange();
|
||||||
int rendezvous_irregular(int, char *, int, int, int *,
|
int rendezvous_irregular(int, char *, int, int, int *,
|
||||||
@ -195,6 +199,10 @@ E: Use cutoff keyword to set cutoff in single mode
|
|||||||
|
|
||||||
Mode is single so cutoff/multi keyword cannot be used.
|
Mode is single so cutoff/multi keyword cannot be used.
|
||||||
|
|
||||||
|
E: Use cutoff/bytype in mode multi only
|
||||||
|
|
||||||
|
Mode is single so cutoff/bytype keyword cannot be used.
|
||||||
|
|
||||||
E: Cannot set cutoff/multi before simulation box is defined
|
E: Cannot set cutoff/multi before simulation box is defined
|
||||||
|
|
||||||
Self-explanatory.
|
Self-explanatory.
|
||||||
@ -239,6 +247,10 @@ E: Processor count in z must be 1 for 2d simulation
|
|||||||
|
|
||||||
Self-explanatory.
|
Self-explanatory.
|
||||||
|
|
||||||
|
E: Cannot use multi/tiered communication with Newton off
|
||||||
|
|
||||||
|
Self-explanatory.
|
||||||
|
|
||||||
E: Cannot put data on ring from nullptr pointer
|
E: Cannot put data on ring from nullptr pointer
|
||||||
|
|
||||||
W: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost.
|
W: Communication cutoff is 0.0. No ghost atoms will be generated. Atoms may get lost.
|
||||||
|
|||||||
@ -30,6 +30,7 @@
|
|||||||
|
|
||||||
#include <cmath>
|
#include <cmath>
|
||||||
#include <cstring>
|
#include <cstring>
|
||||||
|
#include <vector>
|
||||||
|
|
||||||
using namespace LAMMPS_NS;
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
@ -42,12 +43,11 @@ using namespace LAMMPS_NS;
|
|||||||
CommBrick::CommBrick(LAMMPS *lmp) :
|
CommBrick::CommBrick(LAMMPS *lmp) :
|
||||||
Comm(lmp),
|
Comm(lmp),
|
||||||
sendnum(nullptr), recvnum(nullptr), sendproc(nullptr), recvproc(nullptr),
|
sendnum(nullptr), recvnum(nullptr), sendproc(nullptr), recvproc(nullptr),
|
||||||
size_forward_recv(nullptr),
|
size_forward_recv(nullptr), size_reverse_send(nullptr), size_reverse_recv(nullptr),
|
||||||
size_reverse_send(nullptr), size_reverse_recv(nullptr),
|
|
||||||
slablo(nullptr), slabhi(nullptr), multilo(nullptr), multihi(nullptr),
|
slablo(nullptr), slabhi(nullptr), multilo(nullptr), multihi(nullptr),
|
||||||
cutghostmulti(nullptr), pbc_flag(nullptr), pbc(nullptr), firstrecv(nullptr),
|
multioldlo(nullptr), multioldhi(nullptr), cutghostmulti(nullptr), cutghostmultiold(nullptr),
|
||||||
sendlist(nullptr), localsendlist(nullptr), maxsendlist(nullptr),
|
pbc_flag(nullptr), pbc(nullptr), firstrecv(nullptr), sendlist(nullptr),
|
||||||
buf_send(nullptr), buf_recv(nullptr)
|
localsendlist(nullptr), maxsendlist(nullptr), buf_send(nullptr), buf_recv(nullptr)
|
||||||
{
|
{
|
||||||
style = 0;
|
style = 0;
|
||||||
layout = Comm::LAYOUT_UNIFORM;
|
layout = Comm::LAYOUT_UNIFORM;
|
||||||
@ -65,6 +65,11 @@ CommBrick::~CommBrick()
|
|||||||
memory->destroy(cutghostmulti);
|
memory->destroy(cutghostmulti);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
if (mode == Comm::MULTIOLD) {
|
||||||
|
free_multiold();
|
||||||
|
memory->destroy(cutghostmultiold);
|
||||||
|
}
|
||||||
|
|
||||||
if (sendlist) for (int i = 0; i < maxswap; i++) memory->destroy(sendlist[i]);
|
if (sendlist) for (int i = 0; i < maxswap; i++) memory->destroy(sendlist[i]);
|
||||||
if (localsendlist) memory->destroy(localsendlist);
|
if (localsendlist) memory->destroy(localsendlist);
|
||||||
memory->sfree(sendlist);
|
memory->sfree(sendlist);
|
||||||
@ -101,6 +106,9 @@ void CommBrick::init_buffers()
|
|||||||
multilo = multihi = nullptr;
|
multilo = multihi = nullptr;
|
||||||
cutghostmulti = nullptr;
|
cutghostmulti = nullptr;
|
||||||
|
|
||||||
|
multioldlo = multioldhi = nullptr;
|
||||||
|
cutghostmultiold = nullptr;
|
||||||
|
|
||||||
buf_send = buf_recv = nullptr;
|
buf_send = buf_recv = nullptr;
|
||||||
maxsend = maxrecv = BUFMIN;
|
maxsend = maxrecv = BUFMIN;
|
||||||
grow_send(maxsend,2);
|
grow_send(maxsend,2);
|
||||||
@ -128,23 +136,55 @@ void CommBrick::init()
|
|||||||
init_exchange();
|
init_exchange();
|
||||||
if (bufextra > bufextra_old) grow_send(maxsend+bufextra,2);
|
if (bufextra > bufextra_old) grow_send(maxsend+bufextra,2);
|
||||||
|
|
||||||
// memory for multi-style communication
|
// memory for multi style communication
|
||||||
|
// allocate in setup
|
||||||
|
|
||||||
if (mode == Comm::MULTI && multilo == nullptr) {
|
if (mode == Comm::MULTI) {
|
||||||
allocate_multi(maxswap);
|
// If inconsitent # of collections, destroy any preexisting arrays (may be missized)
|
||||||
memory->create(cutghostmulti,atom->ntypes+1,3,"comm:cutghostmulti");
|
if (ncollections != neighbor->ncollections) {
|
||||||
|
ncollections = neighbor->ncollections;
|
||||||
|
if (multilo != nullptr) {
|
||||||
|
free_multi();
|
||||||
|
memory->destroy(cutghostmulti);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
// delete any old user cutoffs if # of collections chanaged
|
||||||
|
if (cutusermulti && ncollections != ncollections_cutoff) {
|
||||||
|
if(me == 0) error->warning(FLERR, "cutoff/multi settings discarded, must be defined"
|
||||||
|
" after customizing collections in neigh_modify");
|
||||||
|
memory->destroy(cutusermulti);
|
||||||
|
cutusermulti = nullptr;
|
||||||
|
}
|
||||||
|
|
||||||
|
if (multilo == nullptr) {
|
||||||
|
allocate_multi(maxswap);
|
||||||
|
memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti");
|
||||||
|
}
|
||||||
}
|
}
|
||||||
if (mode == Comm::SINGLE && multilo) {
|
if ((mode == Comm::SINGLE || mode == Comm::MULTIOLD) && multilo) {
|
||||||
free_multi();
|
free_multi();
|
||||||
memory->destroy(cutghostmulti);
|
memory->destroy(cutghostmulti);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
// memory for multi/old-style communication
|
||||||
|
|
||||||
|
if (mode == Comm::MULTIOLD && multioldlo == nullptr) {
|
||||||
|
allocate_multiold(maxswap);
|
||||||
|
memory->create(cutghostmultiold,atom->ntypes+1,3,"comm:cutghostmultiold");
|
||||||
|
}
|
||||||
|
if ((mode == Comm::SINGLE || mode == Comm::MULTI) && multioldlo) {
|
||||||
|
free_multiold();
|
||||||
|
memory->destroy(cutghostmultiold);
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
setup spatial-decomposition communication patterns
|
setup spatial-decomposition communication patterns
|
||||||
function of neighbor cutoff(s) & cutghostuser & current box size
|
function of neighbor cutoff(s) & cutghostuser & current box size
|
||||||
single mode sets slab boundaries (slablo,slabhi) based on max cutoff
|
single mode sets slab boundaries (slablo,slabhi) based on max cutoff
|
||||||
multi mode sets type-dependent slab boundaries (multilo,multihi)
|
multi mode sets collection-dependent slab boundaries (multilo,multihi)
|
||||||
|
multi/old mode sets type-dependent slab boundaries (multioldlo,multioldhi)
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
void CommBrick::setup()
|
void CommBrick::setup()
|
||||||
@ -156,9 +196,11 @@ void CommBrick::setup()
|
|||||||
// neigh->cutghost = distance between tilted planes in box coords
|
// neigh->cutghost = distance between tilted planes in box coords
|
||||||
// cutghost is in lamda coords = distance between those planes
|
// cutghost is in lamda coords = distance between those planes
|
||||||
// for multi:
|
// for multi:
|
||||||
// cutghostmulti = same as cutghost, only for each atom type
|
// cutghostmulti = same as cutghost, only for each atom collection
|
||||||
|
// for multi/old:
|
||||||
|
// cutghostmultiold = same as cutghost, only for each atom type
|
||||||
|
|
||||||
int i;
|
int i,j;
|
||||||
int ntypes = atom->ntypes;
|
int ntypes = atom->ntypes;
|
||||||
double *prd,*sublo,*subhi;
|
double *prd,*sublo,*subhi;
|
||||||
|
|
||||||
@ -167,23 +209,51 @@ void CommBrick::setup()
|
|||||||
error->warning(FLERR,"Communication cutoff is 0.0. No ghost atoms "
|
error->warning(FLERR,"Communication cutoff is 0.0. No ghost atoms "
|
||||||
"will be generated. Atoms may get lost.");
|
"will be generated. Atoms may get lost.");
|
||||||
|
|
||||||
|
if (mode == Comm::MULTI) {
|
||||||
|
double **cutcollectionsq = neighbor->cutcollectionsq;
|
||||||
|
|
||||||
|
// build collection array for atom exchange
|
||||||
|
neighbor->build_collection(0);
|
||||||
|
|
||||||
|
// If using multi/reduce, communicate particles a distance equal
|
||||||
|
// to the max cutoff with equally sized or smaller collections
|
||||||
|
// If not, communicate the maximum cutoff of the entire collection
|
||||||
|
for (i = 0; i < ncollections; i++) {
|
||||||
|
if (cutusermulti) {
|
||||||
|
cutghostmulti[i][0] = cutusermulti[i];
|
||||||
|
cutghostmulti[i][1] = cutusermulti[i];
|
||||||
|
cutghostmulti[i][2] = cutusermulti[i];
|
||||||
|
} else {
|
||||||
|
cutghostmulti[i][0] = 0.0;
|
||||||
|
cutghostmulti[i][1] = 0.0;
|
||||||
|
cutghostmulti[i][2] = 0.0;
|
||||||
|
}
|
||||||
|
|
||||||
|
for (j = 0; j < ncollections; j++){
|
||||||
|
if (multi_reduce && (cutcollectionsq[j][j] > cutcollectionsq[i][i])) continue;
|
||||||
|
cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutcollectionsq[i][j]));
|
||||||
|
cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutcollectionsq[i][j]));
|
||||||
|
cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutcollectionsq[i][j]));
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if (mode == Comm::MULTIOLD) {
|
||||||
|
double *cuttype = neighbor->cuttype;
|
||||||
|
for (i = 1; i <= ntypes; i++) {
|
||||||
|
double tmp = 0.0;
|
||||||
|
if (cutusermultiold) tmp = cutusermultiold[i];
|
||||||
|
cutghostmultiold[i][0] = MAX(tmp,cuttype[i]);
|
||||||
|
cutghostmultiold[i][1] = MAX(tmp,cuttype[i]);
|
||||||
|
cutghostmultiold[i][2] = MAX(tmp,cuttype[i]);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
if (triclinic == 0) {
|
if (triclinic == 0) {
|
||||||
prd = domain->prd;
|
prd = domain->prd;
|
||||||
sublo = domain->sublo;
|
sublo = domain->sublo;
|
||||||
subhi = domain->subhi;
|
subhi = domain->subhi;
|
||||||
cutghost[0] = cutghost[1] = cutghost[2] = cut;
|
cutghost[0] = cutghost[1] = cutghost[2] = cut;
|
||||||
|
|
||||||
if (mode == Comm::MULTI) {
|
|
||||||
double *cuttype = neighbor->cuttype;
|
|
||||||
for (i = 1; i <= ntypes; i++) {
|
|
||||||
cut = 0.0;
|
|
||||||
if (cutusermulti) cut = cutusermulti[i];
|
|
||||||
cutghostmulti[i][0] = MAX(cut,cuttype[i]);
|
|
||||||
cutghostmulti[i][1] = MAX(cut,cuttype[i]);
|
|
||||||
cutghostmulti[i][2] = MAX(cut,cuttype[i]);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
} else {
|
} else {
|
||||||
prd = domain->prd_lamda;
|
prd = domain->prd_lamda;
|
||||||
sublo = domain->sublo_lamda;
|
sublo = domain->sublo_lamda;
|
||||||
@ -196,15 +266,19 @@ void CommBrick::setup()
|
|||||||
cutghost[1] = cut * length1;
|
cutghost[1] = cut * length1;
|
||||||
length2 = h_inv[2];
|
length2 = h_inv[2];
|
||||||
cutghost[2] = cut * length2;
|
cutghost[2] = cut * length2;
|
||||||
|
|
||||||
if (mode == Comm::MULTI) {
|
if (mode == Comm::MULTI) {
|
||||||
double *cuttype = neighbor->cuttype;
|
for (i = 0; i < ncollections; i++) {
|
||||||
|
cutghostmulti[i][0] *= length0;
|
||||||
|
cutghostmulti[i][1] *= length1;
|
||||||
|
cutghostmulti[i][2] *= length2;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if (mode == Comm::MULTIOLD) {
|
||||||
for (i = 1; i <= ntypes; i++) {
|
for (i = 1; i <= ntypes; i++) {
|
||||||
cut = 0.0;
|
cutghostmultiold[i][0] *= length0;
|
||||||
if (cutusermulti) cut = cutusermulti[i];
|
cutghostmultiold[i][1] *= length1;
|
||||||
cutghostmulti[i][0] = length0 * MAX(cut,cuttype[i]);
|
cutghostmultiold[i][2] *= length2;
|
||||||
cutghostmulti[i][1] = length1 * MAX(cut,cuttype[i]);
|
|
||||||
cutghostmulti[i][2] = length2 * MAX(cut,cuttype[i]);
|
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
@ -350,12 +424,18 @@ void CommBrick::setup()
|
|||||||
if (ineed < 2) slablo[iswap] = -BIG;
|
if (ineed < 2) slablo[iswap] = -BIG;
|
||||||
else slablo[iswap] = 0.5 * (sublo[dim] + subhi[dim]);
|
else slablo[iswap] = 0.5 * (sublo[dim] + subhi[dim]);
|
||||||
slabhi[iswap] = sublo[dim] + cutghost[dim];
|
slabhi[iswap] = sublo[dim] + cutghost[dim];
|
||||||
} else {
|
} else if (mode == Comm::MULTI) {
|
||||||
for (i = 1; i <= ntypes; i++) {
|
for (i = 0; i < ncollections; i++) {
|
||||||
if (ineed < 2) multilo[iswap][i] = -BIG;
|
if (ineed < 2) multilo[iswap][i] = -BIG;
|
||||||
else multilo[iswap][i] = 0.5 * (sublo[dim] + subhi[dim]);
|
else multilo[iswap][i] = 0.5 * (sublo[dim] + subhi[dim]);
|
||||||
multihi[iswap][i] = sublo[dim] + cutghostmulti[i][dim];
|
multihi[iswap][i] = sublo[dim] + cutghostmulti[i][dim];
|
||||||
}
|
}
|
||||||
|
} else {
|
||||||
|
for (i = 1; i <= ntypes; i++) {
|
||||||
|
if (ineed < 2) multioldlo[iswap][i] = -BIG;
|
||||||
|
else multioldlo[iswap][i] = 0.5 * (sublo[dim] + subhi[dim]);
|
||||||
|
multioldhi[iswap][i] = sublo[dim] + cutghostmultiold[i][dim];
|
||||||
|
}
|
||||||
}
|
}
|
||||||
if (myloc[dim] == 0) {
|
if (myloc[dim] == 0) {
|
||||||
pbc_flag[iswap] = 1;
|
pbc_flag[iswap] = 1;
|
||||||
@ -373,12 +453,18 @@ void CommBrick::setup()
|
|||||||
slablo[iswap] = subhi[dim] - cutghost[dim];
|
slablo[iswap] = subhi[dim] - cutghost[dim];
|
||||||
if (ineed < 2) slabhi[iswap] = BIG;
|
if (ineed < 2) slabhi[iswap] = BIG;
|
||||||
else slabhi[iswap] = 0.5 * (sublo[dim] + subhi[dim]);
|
else slabhi[iswap] = 0.5 * (sublo[dim] + subhi[dim]);
|
||||||
} else {
|
} else if (mode == Comm::MULTI) {
|
||||||
for (i = 1; i <= ntypes; i++) {
|
for (i = 0; i < ncollections; i++) {
|
||||||
multilo[iswap][i] = subhi[dim] - cutghostmulti[i][dim];
|
multilo[iswap][i] = subhi[dim] - cutghostmulti[i][dim];
|
||||||
if (ineed < 2) multihi[iswap][i] = BIG;
|
if (ineed < 2) multihi[iswap][i] = BIG;
|
||||||
else multihi[iswap][i] = 0.5 * (sublo[dim] + subhi[dim]);
|
else multihi[iswap][i] = 0.5 * (sublo[dim] + subhi[dim]);
|
||||||
}
|
}
|
||||||
|
} else {
|
||||||
|
for (i = 1; i <= ntypes; i++) {
|
||||||
|
multioldlo[iswap][i] = subhi[dim] - cutghostmultiold[i][dim];
|
||||||
|
if (ineed < 2) multioldhi[iswap][i] = BIG;
|
||||||
|
else multioldhi[iswap][i] = 0.5 * (sublo[dim] + subhi[dim]);
|
||||||
|
}
|
||||||
}
|
}
|
||||||
if (myloc[dim] == procgrid[dim]-1) {
|
if (myloc[dim] == procgrid[dim]-1) {
|
||||||
pbc_flag[iswap] = 1;
|
pbc_flag[iswap] = 1;
|
||||||
@ -699,15 +785,19 @@ void CommBrick::exchange()
|
|||||||
|
|
||||||
void CommBrick::borders()
|
void CommBrick::borders()
|
||||||
{
|
{
|
||||||
int i,n,itype,iswap,dim,ineed,twoneed;
|
int i,n,itype,icollection,iswap,dim,ineed,twoneed;
|
||||||
int nsend,nrecv,sendflag,nfirst,nlast,ngroup;
|
int nsend,nrecv,sendflag,nfirst,nlast,ngroup,nprior;
|
||||||
double lo,hi;
|
double lo,hi;
|
||||||
int *type;
|
int *type;
|
||||||
|
int *collection;
|
||||||
double **x;
|
double **x;
|
||||||
double *buf,*mlo,*mhi;
|
double *buf,*mlo,*mhi;
|
||||||
MPI_Request request;
|
MPI_Request request;
|
||||||
AtomVec *avec = atom->avec;
|
AtomVec *avec = atom->avec;
|
||||||
|
|
||||||
|
// After exchanging/sorting, need to reconstruct collection array for border communication
|
||||||
|
if (mode == Comm::MULTI) neighbor->build_collection(0);
|
||||||
|
|
||||||
// do swaps over all 3 dimensions
|
// do swaps over all 3 dimensions
|
||||||
|
|
||||||
iswap = 0;
|
iswap = 0;
|
||||||
@ -728,10 +818,14 @@ void CommBrick::borders()
|
|||||||
if (mode == Comm::SINGLE) {
|
if (mode == Comm::SINGLE) {
|
||||||
lo = slablo[iswap];
|
lo = slablo[iswap];
|
||||||
hi = slabhi[iswap];
|
hi = slabhi[iswap];
|
||||||
} else {
|
} else if (mode == Comm::MULTI) {
|
||||||
type = atom->type;
|
collection = neighbor->collection;
|
||||||
mlo = multilo[iswap];
|
mlo = multilo[iswap];
|
||||||
mhi = multihi[iswap];
|
mhi = multihi[iswap];
|
||||||
|
} else {
|
||||||
|
type = atom->type;
|
||||||
|
mlo = multioldlo[iswap];
|
||||||
|
mhi = multioldhi[iswap];
|
||||||
}
|
}
|
||||||
if (ineed % 2 == 0) {
|
if (ineed % 2 == 0) {
|
||||||
nfirst = nlast;
|
nfirst = nlast;
|
||||||
@ -760,6 +854,14 @@ void CommBrick::borders()
|
|||||||
if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
|
if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
|
||||||
sendlist[iswap][nsend++] = i;
|
sendlist[iswap][nsend++] = i;
|
||||||
}
|
}
|
||||||
|
} else if (mode == Comm::MULTI) {
|
||||||
|
for (i = nfirst; i < nlast; i++) {
|
||||||
|
icollection = collection[i];
|
||||||
|
if (x[i][dim] >= mlo[icollection] && x[i][dim] <= mhi[icollection]) {
|
||||||
|
if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
|
||||||
|
sendlist[iswap][nsend++] = i;
|
||||||
|
}
|
||||||
|
}
|
||||||
} else {
|
} else {
|
||||||
for (i = nfirst; i < nlast; i++) {
|
for (i = nfirst; i < nlast; i++) {
|
||||||
itype = type[i];
|
itype = type[i];
|
||||||
@ -783,6 +885,22 @@ void CommBrick::borders()
|
|||||||
if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
|
if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
|
||||||
sendlist[iswap][nsend++] = i;
|
sendlist[iswap][nsend++] = i;
|
||||||
}
|
}
|
||||||
|
} else if (mode == Comm::MULTI) {
|
||||||
|
ngroup = atom->nfirst;
|
||||||
|
for (i = 0; i < ngroup; i++) {
|
||||||
|
icollection = collection[i];
|
||||||
|
if (x[i][dim] >= mlo[icollection] && x[i][dim] <= mhi[icollection]) {
|
||||||
|
if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
|
||||||
|
sendlist[iswap][nsend++] = i;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
for (i = atom->nlocal; i < nlast; i++) {
|
||||||
|
icollection = collection[i];
|
||||||
|
if (x[i][dim] >= mlo[icollection] && x[i][dim] <= mhi[icollection]) {
|
||||||
|
if (nsend == maxsendlist[iswap]) grow_list(iswap,nsend);
|
||||||
|
sendlist[iswap][nsend++] = i;
|
||||||
|
}
|
||||||
|
}
|
||||||
} else {
|
} else {
|
||||||
ngroup = atom->nfirst;
|
ngroup = atom->nfirst;
|
||||||
for (i = 0; i < ngroup; i++) {
|
for (i = 0; i < ngroup; i++) {
|
||||||
@ -850,7 +968,10 @@ void CommBrick::borders()
|
|||||||
size_reverse_send[iswap] = nrecv*size_reverse;
|
size_reverse_send[iswap] = nrecv*size_reverse;
|
||||||
size_reverse_recv[iswap] = nsend*size_reverse;
|
size_reverse_recv[iswap] = nsend*size_reverse;
|
||||||
firstrecv[iswap] = atom->nlocal + atom->nghost;
|
firstrecv[iswap] = atom->nlocal + atom->nghost;
|
||||||
|
nprior = atom->nlocal + atom->nghost;
|
||||||
atom->nghost += nrecv;
|
atom->nghost += nrecv;
|
||||||
|
if (neighbor->style == Neighbor::MULTI) neighbor->build_collection(nprior);
|
||||||
|
|
||||||
iswap++;
|
iswap++;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
@ -1403,6 +1524,12 @@ void CommBrick::grow_swap(int n)
|
|||||||
allocate_multi(n);
|
allocate_multi(n);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
if (mode == Comm::MULTIOLD) {
|
||||||
|
free_multiold();
|
||||||
|
allocate_multiold(n);
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
sendlist = (int **)
|
sendlist = (int **)
|
||||||
memory->srealloc(sendlist,n*sizeof(int *),"comm:sendlist");
|
memory->srealloc(sendlist,n*sizeof(int *),"comm:sendlist");
|
||||||
memory->grow(maxsendlist,n,"comm:maxsendlist");
|
memory->grow(maxsendlist,n,"comm:maxsendlist");
|
||||||
@ -1434,15 +1561,26 @@ void CommBrick::allocate_swap(int n)
|
|||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
allocation of multi-type swap info
|
allocation of multi-collection swap info
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
void CommBrick::allocate_multi(int n)
|
void CommBrick::allocate_multi(int n)
|
||||||
{
|
{
|
||||||
multilo = memory->create(multilo,n,atom->ntypes+1,"comm:multilo");
|
multilo = memory->create(multilo,n,ncollections,"comm:multilo");
|
||||||
multihi = memory->create(multihi,n,atom->ntypes+1,"comm:multihi");
|
multihi = memory->create(multihi,n,ncollections,"comm:multihi");
|
||||||
}
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
allocation of multi/old-type swap info
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void CommBrick::allocate_multiold(int n)
|
||||||
|
{
|
||||||
|
multioldlo = memory->create(multioldlo,n,atom->ntypes+1,"comm:multioldlo");
|
||||||
|
multioldhi = memory->create(multioldhi,n,atom->ntypes+1,"comm:multioldhi");
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
free memory for swaps
|
free memory for swaps
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
@ -1464,7 +1602,7 @@ void CommBrick::free_swap()
|
|||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
free memory for multi-type swaps
|
free memory for multi-collection swaps
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
void CommBrick::free_multi()
|
void CommBrick::free_multi()
|
||||||
@ -1474,6 +1612,17 @@ void CommBrick::free_multi()
|
|||||||
multilo = multihi = nullptr;
|
multilo = multihi = nullptr;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
free memory for multi/old-type swaps
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void CommBrick::free_multiold()
|
||||||
|
{
|
||||||
|
memory->destroy(multioldlo);
|
||||||
|
memory->destroy(multioldhi);
|
||||||
|
multioldlo = multioldhi = nullptr;
|
||||||
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
extract data potentially useful to other classes
|
extract data potentially useful to other classes
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|||||||
@ -61,8 +61,10 @@ class CommBrick : public Comm {
|
|||||||
int *size_reverse_send; // # to send in each reverse comm
|
int *size_reverse_send; // # to send in each reverse comm
|
||||||
int *size_reverse_recv; // # to recv in each reverse comm
|
int *size_reverse_recv; // # to recv in each reverse comm
|
||||||
double *slablo,*slabhi; // bounds of slab to send at each swap
|
double *slablo,*slabhi; // bounds of slab to send at each swap
|
||||||
double **multilo,**multihi; // bounds of slabs for multi-type swap
|
double **multilo,**multihi; // bounds of slabs for multi-collection swap
|
||||||
double **cutghostmulti; // cutghost on a per-type basis
|
double **multioldlo,**multioldhi; // bounds of slabs for multi-type swap
|
||||||
|
double **cutghostmulti; // cutghost on a per-collection basis
|
||||||
|
double **cutghostmultiold; // cutghost on a per-type basis
|
||||||
int *pbc_flag; // general flag for sending atoms thru PBC
|
int *pbc_flag; // general flag for sending atoms thru PBC
|
||||||
int **pbc; // dimension flags for PBC adjustments
|
int **pbc; // dimension flags for PBC adjustments
|
||||||
|
|
||||||
@ -84,11 +86,13 @@ class CommBrick : public Comm {
|
|||||||
virtual void grow_send(int, int); // reallocate send buffer
|
virtual void grow_send(int, int); // reallocate send buffer
|
||||||
virtual void grow_recv(int); // free/allocate recv buffer
|
virtual void grow_recv(int); // free/allocate recv buffer
|
||||||
virtual void grow_list(int, int); // reallocate one sendlist
|
virtual void grow_list(int, int); // reallocate one sendlist
|
||||||
virtual void grow_swap(int); // grow swap and multi arrays
|
virtual void grow_swap(int); // grow swap, multi, and multi/old arrays
|
||||||
virtual void allocate_swap(int); // allocate swap arrays
|
virtual void allocate_swap(int); // allocate swap arrays
|
||||||
virtual void allocate_multi(int); // allocate multi arrays
|
virtual void allocate_multi(int); // allocate multi arrays
|
||||||
|
virtual void allocate_multiold(int); // allocate multi/old arrays
|
||||||
virtual void free_swap(); // free swap arrays
|
virtual void free_swap(); // free swap arrays
|
||||||
virtual void free_multi(); // free multi arrays
|
virtual void free_multi(); // free multi arrays
|
||||||
|
virtual void free_multiold(); // free multi/old arrays
|
||||||
};
|
};
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|||||||
@ -31,6 +31,7 @@
|
|||||||
|
|
||||||
#include <cmath>
|
#include <cmath>
|
||||||
#include <cstring>
|
#include <cstring>
|
||||||
|
#include <vector>
|
||||||
|
|
||||||
using namespace LAMMPS_NS;
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
@ -53,6 +54,7 @@ CommTiled::CommTiled(LAMMPS *lmp) : Comm(lmp)
|
|||||||
overlap = nullptr;
|
overlap = nullptr;
|
||||||
rcbinfo = nullptr;
|
rcbinfo = nullptr;
|
||||||
cutghostmulti = nullptr;
|
cutghostmulti = nullptr;
|
||||||
|
cutghostmultiold = nullptr;
|
||||||
init_buffers();
|
init_buffers();
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -81,6 +83,7 @@ CommTiled::~CommTiled()
|
|||||||
deallocate_swap(maxswap);
|
deallocate_swap(maxswap);
|
||||||
memory->sfree(rcbinfo);
|
memory->sfree(rcbinfo);
|
||||||
memory->destroy(cutghostmulti);
|
memory->destroy(cutghostmulti);
|
||||||
|
memory->destroy(cutghostmultiold);
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
@ -98,8 +101,11 @@ void CommTiled::init_buffers()
|
|||||||
overlap = nullptr;
|
overlap = nullptr;
|
||||||
rcbinfo = nullptr;
|
rcbinfo = nullptr;
|
||||||
cutghostmulti = nullptr;
|
cutghostmulti = nullptr;
|
||||||
|
cutghostmultiold = nullptr;
|
||||||
sendbox_multi = nullptr;
|
sendbox_multi = nullptr;
|
||||||
|
sendbox_multiold = nullptr;
|
||||||
|
|
||||||
|
// Note this may skip growing multi arrays, will call again in init()
|
||||||
maxswap = 6;
|
maxswap = 6;
|
||||||
allocate_swap(maxswap);
|
allocate_swap(maxswap);
|
||||||
}
|
}
|
||||||
@ -116,8 +122,30 @@ void CommTiled::init()
|
|||||||
nswap = 2*domain->dimension;
|
nswap = 2*domain->dimension;
|
||||||
|
|
||||||
memory->destroy(cutghostmulti);
|
memory->destroy(cutghostmulti);
|
||||||
if (mode == Comm::MULTI)
|
if (mode == Comm::MULTI) {
|
||||||
memory->create(cutghostmulti,atom->ntypes+1,3,"comm:cutghostmulti");
|
// If inconsitent # of collections, destroy any preexisting arrays (may be missized)
|
||||||
|
if (ncollections != neighbor->ncollections) {
|
||||||
|
ncollections = neighbor->ncollections;
|
||||||
|
}
|
||||||
|
|
||||||
|
// delete any old user cutoffs if # of collections chanaged
|
||||||
|
if (cutusermulti && ncollections != ncollections_cutoff) {
|
||||||
|
if(me == 0) error->warning(FLERR, "cutoff/multi settings discarded, must be defined"
|
||||||
|
" after customizing collections in neigh_modify");
|
||||||
|
memory->destroy(cutusermulti);
|
||||||
|
cutusermulti = nullptr;
|
||||||
|
}
|
||||||
|
|
||||||
|
// grow sendbox_multi now that ncollections is known
|
||||||
|
for (int i = 0; i < maxswap; i ++)
|
||||||
|
grow_swap_send_multi(i,DELTA_PROCS);
|
||||||
|
|
||||||
|
memory->create(cutghostmulti,ncollections,3,"comm:cutghostmulti");
|
||||||
|
}
|
||||||
|
|
||||||
|
memory->destroy(cutghostmultiold);
|
||||||
|
if (mode == Comm::MULTIOLD)
|
||||||
|
memory->create(cutghostmultiold,atom->ntypes+1,3,"comm:cutghostmultiold");
|
||||||
|
|
||||||
int bufextra_old = bufextra;
|
int bufextra_old = bufextra;
|
||||||
init_exchange();
|
init_exchange();
|
||||||
@ -175,14 +203,42 @@ void CommTiled::setup()
|
|||||||
// check that cutoff < any periodic box length
|
// check that cutoff < any periodic box length
|
||||||
|
|
||||||
if (mode == Comm::MULTI) {
|
if (mode == Comm::MULTI) {
|
||||||
|
double **cutcollectionsq = neighbor->cutcollectionsq;
|
||||||
|
|
||||||
|
// build collection array for atom exchange
|
||||||
|
neighbor->build_collection(0);
|
||||||
|
|
||||||
|
// If using multi/reduce, communicate particles a distance equal
|
||||||
|
// to the max cutoff with equally sized or smaller collections
|
||||||
|
// If not, communicate the maximum cutoff of the entire collection
|
||||||
|
for (i = 0; i < ncollections; i++) {
|
||||||
|
if (cutusermulti) {
|
||||||
|
cutghostmulti[i][0] = cutusermulti[i];
|
||||||
|
cutghostmulti[i][1] = cutusermulti[i];
|
||||||
|
cutghostmulti[i][2] = cutusermulti[i];
|
||||||
|
} else {
|
||||||
|
cutghostmulti[i][0] = 0.0;
|
||||||
|
cutghostmulti[i][1] = 0.0;
|
||||||
|
cutghostmulti[i][2] = 0.0;
|
||||||
|
}
|
||||||
|
|
||||||
|
for (j = 0; j < ncollections; j++){
|
||||||
|
if (multi_reduce && (cutcollectionsq[j][j] > cutcollectionsq[i][i])) continue;
|
||||||
|
cutghostmulti[i][0] = MAX(cutghostmulti[i][0],sqrt(cutcollectionsq[i][j]));
|
||||||
|
cutghostmulti[i][1] = MAX(cutghostmulti[i][1],sqrt(cutcollectionsq[i][j]));
|
||||||
|
cutghostmulti[i][2] = MAX(cutghostmulti[i][2],sqrt(cutcollectionsq[i][j]));
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if (mode == Comm::MULTIOLD) {
|
||||||
double *cuttype = neighbor->cuttype;
|
double *cuttype = neighbor->cuttype;
|
||||||
double cut;
|
|
||||||
for (i = 1; i <= ntypes; i++) {
|
for (i = 1; i <= ntypes; i++) {
|
||||||
cut = 0.0;
|
double tmp = 0.0;
|
||||||
if (cutusermulti) cut = cutusermulti[i];
|
if (cutusermultiold) tmp = cutusermultiold[i];
|
||||||
cutghostmulti[i][0] = MAX(cut,cuttype[i]);
|
cutghostmultiold[i][0] = MAX(tmp,cuttype[i]);
|
||||||
cutghostmulti[i][1] = MAX(cut,cuttype[i]);
|
cutghostmultiold[i][1] = MAX(tmp,cuttype[i]);
|
||||||
cutghostmulti[i][2] = MAX(cut,cuttype[i]);
|
cutghostmultiold[i][2] = MAX(tmp,cuttype[i]);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -202,12 +258,20 @@ void CommTiled::setup()
|
|||||||
length2 = h_inv[2];
|
length2 = h_inv[2];
|
||||||
cutghost[2] = cut * length2;
|
cutghost[2] = cut * length2;
|
||||||
if (mode == Comm::MULTI) {
|
if (mode == Comm::MULTI) {
|
||||||
for (i = 1; i <= ntypes; i++) {
|
for (i = 0; i < ncollections; i++) {
|
||||||
cutghostmulti[i][0] *= length0;
|
cutghostmulti[i][0] *= length0;
|
||||||
cutghostmulti[i][1] *= length1;
|
cutghostmulti[i][1] *= length1;
|
||||||
cutghostmulti[i][2] *= length2;
|
cutghostmulti[i][2] *= length2;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
if (mode == Comm::MULTIOLD) {
|
||||||
|
for (i = 1; i <= ntypes; i++) {
|
||||||
|
cutghostmultiold[i][0] *= length0;
|
||||||
|
cutghostmultiold[i][1] *= length1;
|
||||||
|
cutghostmultiold[i][2] *= length2;
|
||||||
|
}
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
if ((periodicity[0] && cutghost[0] > prd[0]) ||
|
if ((periodicity[0] && cutghost[0] > prd[0]) ||
|
||||||
@ -345,7 +409,7 @@ void CommTiled::setup()
|
|||||||
// extend sbox in those lower dims to include ghost atoms
|
// extend sbox in those lower dims to include ghost atoms
|
||||||
// single mode and multi mode
|
// single mode and multi mode
|
||||||
|
|
||||||
double oboxlo[3],oboxhi[3],sbox[6],sbox_multi[6];
|
double oboxlo[3],oboxhi[3],sbox[6],sbox_multi[6],sbox_multiold[6];
|
||||||
|
|
||||||
if (mode == Comm::SINGLE) {
|
if (mode == Comm::SINGLE) {
|
||||||
for (i = 0; i < noverlap; i++) {
|
for (i = 0; i < noverlap; i++) {
|
||||||
@ -434,7 +498,7 @@ void CommTiled::setup()
|
|||||||
sbox[5] = MIN(oboxhi[2],hi2[2]);
|
sbox[5] = MIN(oboxhi[2],hi2[2]);
|
||||||
}
|
}
|
||||||
|
|
||||||
for (int itype = 1; itype <= atom->ntypes; itype++) {
|
for (int icollection = 0; icollection < ncollections; icollection++) {
|
||||||
sbox_multi[0] = sbox[0];
|
sbox_multi[0] = sbox[0];
|
||||||
sbox_multi[1] = sbox[1];
|
sbox_multi[1] = sbox[1];
|
||||||
sbox_multi[2] = sbox[2];
|
sbox_multi[2] = sbox[2];
|
||||||
@ -445,36 +509,112 @@ void CommTiled::setup()
|
|||||||
sbox_multi[idim] = sublo[idim];
|
sbox_multi[idim] = sublo[idim];
|
||||||
if (i < noverlap1)
|
if (i < noverlap1)
|
||||||
sbox_multi[3+idim] =
|
sbox_multi[3+idim] =
|
||||||
MIN(sbox_multi[3+idim]+cutghostmulti[itype][idim],subhi[idim]);
|
MIN(sbox_multi[3+idim]+cutghostmulti[icollection][idim],subhi[idim]);
|
||||||
else
|
else
|
||||||
sbox_multi[3+idim] =
|
sbox_multi[3+idim] =
|
||||||
MIN(sbox_multi[3+idim]-prd[idim]+cutghostmulti[itype][idim],
|
MIN(sbox_multi[3+idim]-prd[idim]+cutghostmulti[icollection][idim],
|
||||||
subhi[idim]);
|
subhi[idim]);
|
||||||
} else {
|
} else {
|
||||||
if (i < noverlap1)
|
if (i < noverlap1)
|
||||||
sbox_multi[idim] =
|
sbox_multi[idim] =
|
||||||
MAX(sbox_multi[idim]-cutghostmulti[itype][idim],sublo[idim]);
|
MAX(sbox_multi[idim]-cutghostmulti[icollection][idim],sublo[idim]);
|
||||||
else
|
else
|
||||||
sbox_multi[idim] =
|
sbox_multi[idim] =
|
||||||
MAX(sbox_multi[idim]+prd[idim]-cutghostmulti[itype][idim],
|
MAX(sbox_multi[idim]+prd[idim]-cutghostmulti[icollection][idim],
|
||||||
sublo[idim]);
|
sublo[idim]);
|
||||||
sbox_multi[3+idim] = subhi[idim];
|
sbox_multi[3+idim] = subhi[idim];
|
||||||
}
|
}
|
||||||
|
|
||||||
if (idim >= 1) {
|
if (idim >= 1) {
|
||||||
if (sbox_multi[0] == oboxlo[0])
|
if (sbox_multi[0] == oboxlo[0])
|
||||||
sbox_multi[0] -= cutghostmulti[itype][idim];
|
sbox_multi[0] -= cutghostmulti[icollection][idim];
|
||||||
if (sbox_multi[3] == oboxhi[0])
|
if (sbox_multi[3] == oboxhi[0])
|
||||||
sbox_multi[3] += cutghostmulti[itype][idim];
|
sbox_multi[3] += cutghostmulti[icollection][idim];
|
||||||
}
|
}
|
||||||
if (idim == 2) {
|
if (idim == 2) {
|
||||||
if (sbox_multi[1] == oboxlo[1])
|
if (sbox_multi[1] == oboxlo[1])
|
||||||
sbox_multi[1] -= cutghostmulti[itype][idim];
|
sbox_multi[1] -= cutghostmulti[icollection][idim];
|
||||||
if (sbox_multi[4] == oboxhi[1])
|
if (sbox_multi[4] == oboxhi[1])
|
||||||
sbox_multi[4] += cutghostmulti[itype][idim];
|
sbox_multi[4] += cutghostmulti[icollection][idim];
|
||||||
}
|
}
|
||||||
|
|
||||||
memcpy(sendbox_multi[iswap][i][itype],sbox_multi,6*sizeof(double));
|
memcpy(sendbox_multi[iswap][i][icollection],sbox_multi,6*sizeof(double));
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if (mode == Comm::MULTIOLD) {
|
||||||
|
for (i = 0; i < noverlap; i++) {
|
||||||
|
pbc_flag[iswap][i] = 0;
|
||||||
|
pbc[iswap][i][0] = pbc[iswap][i][1] = pbc[iswap][i][2] =
|
||||||
|
pbc[iswap][i][3] = pbc[iswap][i][4] = pbc[iswap][i][5] = 0;
|
||||||
|
|
||||||
|
(this->*box_other)(idim,idir,overlap[i],oboxlo,oboxhi);
|
||||||
|
|
||||||
|
if (i < noverlap1) {
|
||||||
|
sbox[0] = MAX(oboxlo[0],lo1[0]);
|
||||||
|
sbox[1] = MAX(oboxlo[1],lo1[1]);
|
||||||
|
sbox[2] = MAX(oboxlo[2],lo1[2]);
|
||||||
|
sbox[3] = MIN(oboxhi[0],hi1[0]);
|
||||||
|
sbox[4] = MIN(oboxhi[1],hi1[1]);
|
||||||
|
sbox[5] = MIN(oboxhi[2],hi1[2]);
|
||||||
|
} else {
|
||||||
|
pbc_flag[iswap][i] = 1;
|
||||||
|
if (idir == 0) pbc[iswap][i][idim] = 1;
|
||||||
|
else pbc[iswap][i][idim] = -1;
|
||||||
|
if (triclinic) {
|
||||||
|
if (idim == 1) pbc[iswap][i][5] = pbc[iswap][i][idim];
|
||||||
|
if (idim == 2) pbc[iswap][i][4] = pbc[iswap][i][3] = pbc[iswap][i][idim];
|
||||||
|
}
|
||||||
|
sbox[0] = MAX(oboxlo[0],lo2[0]);
|
||||||
|
sbox[1] = MAX(oboxlo[1],lo2[1]);
|
||||||
|
sbox[2] = MAX(oboxlo[2],lo2[2]);
|
||||||
|
sbox[3] = MIN(oboxhi[0],hi2[0]);
|
||||||
|
sbox[4] = MIN(oboxhi[1],hi2[1]);
|
||||||
|
sbox[5] = MIN(oboxhi[2],hi2[2]);
|
||||||
|
}
|
||||||
|
|
||||||
|
for (int itype = 1; itype <= atom->ntypes; itype++) {
|
||||||
|
sbox_multiold[0] = sbox[0];
|
||||||
|
sbox_multiold[1] = sbox[1];
|
||||||
|
sbox_multiold[2] = sbox[2];
|
||||||
|
sbox_multiold[3] = sbox[3];
|
||||||
|
sbox_multiold[4] = sbox[4];
|
||||||
|
sbox_multiold[5] = sbox[5];
|
||||||
|
if (idir == 0) {
|
||||||
|
sbox_multiold[idim] = sublo[idim];
|
||||||
|
if (i < noverlap1)
|
||||||
|
sbox_multiold[3+idim] =
|
||||||
|
MIN(sbox_multiold[3+idim]+cutghostmultiold[itype][idim],subhi[idim]);
|
||||||
|
else
|
||||||
|
sbox_multiold[3+idim] =
|
||||||
|
MIN(sbox_multiold[3+idim]-prd[idim]+cutghostmultiold[itype][idim],
|
||||||
|
subhi[idim]);
|
||||||
|
} else {
|
||||||
|
if (i < noverlap1)
|
||||||
|
sbox_multiold[idim] =
|
||||||
|
MAX(sbox_multiold[idim]-cutghostmultiold[itype][idim],sublo[idim]);
|
||||||
|
else
|
||||||
|
sbox_multiold[idim] =
|
||||||
|
MAX(sbox_multiold[idim]+prd[idim]-cutghostmultiold[itype][idim],
|
||||||
|
sublo[idim]);
|
||||||
|
sbox_multiold[3+idim] = subhi[idim];
|
||||||
|
}
|
||||||
|
|
||||||
|
if (idim >= 1) {
|
||||||
|
if (sbox_multiold[0] == oboxlo[0])
|
||||||
|
sbox_multiold[0] -= cutghostmultiold[itype][idim];
|
||||||
|
if (sbox_multiold[3] == oboxhi[0])
|
||||||
|
sbox_multiold[3] += cutghostmultiold[itype][idim];
|
||||||
|
}
|
||||||
|
if (idim == 2) {
|
||||||
|
if (sbox_multiold[1] == oboxlo[1])
|
||||||
|
sbox_multiold[1] -= cutghostmultiold[itype][idim];
|
||||||
|
if (sbox_multiold[4] == oboxhi[1])
|
||||||
|
sbox_multiold[4] += cutghostmultiold[itype][idim];
|
||||||
|
}
|
||||||
|
|
||||||
|
memcpy(sendbox_multiold[iswap][i][itype],sbox_multiold,6*sizeof(double));
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
@ -906,12 +1046,15 @@ void CommTiled::exchange()
|
|||||||
|
|
||||||
void CommTiled::borders()
|
void CommTiled::borders()
|
||||||
{
|
{
|
||||||
int i,m,n,nlast,nsend,nrecv,ngroup,ncount,ncountall;
|
int i,m,n,nlast,nsend,nrecv,ngroup,nprior,ncount,ncountall;
|
||||||
double xlo,xhi,ylo,yhi,zlo,zhi;
|
double xlo,xhi,ylo,yhi,zlo,zhi;
|
||||||
double *bbox;
|
double *bbox;
|
||||||
double **x;
|
double **x;
|
||||||
AtomVec *avec = atom->avec;
|
AtomVec *avec = atom->avec;
|
||||||
|
|
||||||
|
// After exchanging, need to reconstruct collection array for border communication
|
||||||
|
if (mode == Comm::MULTI) neighbor->build_collection(0);
|
||||||
|
|
||||||
// send/recv max one = max # of atoms in single send/recv for any swap
|
// send/recv max one = max # of atoms in single send/recv for any swap
|
||||||
// send/recv max all = max # of atoms in all sends/recvs within any swap
|
// send/recv max all = max # of atoms in all sends/recvs within any swap
|
||||||
|
|
||||||
@ -977,6 +1120,56 @@ void CommTiled::borders()
|
|||||||
smaxone = MAX(smaxone,ncount);
|
smaxone = MAX(smaxone,ncount);
|
||||||
ncountall += ncount;
|
ncountall += ncount;
|
||||||
|
|
||||||
|
} else if (mode == Comm::MULTI) {
|
||||||
|
|
||||||
|
int* collection=neighbor->collection;
|
||||||
|
int icollection;
|
||||||
|
ncount = 0;
|
||||||
|
|
||||||
|
if (!bordergroup) {
|
||||||
|
for (i = 0; i < nlast; i++) {
|
||||||
|
icollection=collection[i];
|
||||||
|
bbox = sendbox_multi[iswap][m][icollection];
|
||||||
|
xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2];
|
||||||
|
xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5];
|
||||||
|
if (x[i][0] >= xlo && x[i][0] < xhi &&
|
||||||
|
x[i][1] >= ylo && x[i][1] < yhi &&
|
||||||
|
x[i][2] >= zlo && x[i][2] < zhi) {
|
||||||
|
if (ncount == maxsendlist[iswap][m]) grow_list(iswap,m,ncount);
|
||||||
|
sendlist[iswap][m][ncount++] = i;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
ngroup = atom->nfirst;
|
||||||
|
for (i = 0; i < ngroup; i++) {
|
||||||
|
icollection=collection[i];
|
||||||
|
bbox = sendbox_multi[iswap][m][icollection];
|
||||||
|
xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2];
|
||||||
|
xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5];
|
||||||
|
if (x[i][0] >= xlo && x[i][0] < xhi &&
|
||||||
|
x[i][1] >= ylo && x[i][1] < yhi &&
|
||||||
|
x[i][2] >= zlo && x[i][2] < zhi) {
|
||||||
|
if (ncount == maxsendlist[iswap][m]) grow_list(iswap,m,ncount);
|
||||||
|
sendlist[iswap][m][ncount++] = i;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
for (i = atom->nlocal; i < nlast; i++) {
|
||||||
|
icollection=collection[i];
|
||||||
|
bbox = sendbox_multi[iswap][m][icollection];
|
||||||
|
xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2];
|
||||||
|
xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5];
|
||||||
|
if (x[i][0] >= xlo && x[i][0] < xhi &&
|
||||||
|
x[i][1] >= ylo && x[i][1] < yhi &&
|
||||||
|
x[i][2] >= zlo && x[i][2] < zhi) {
|
||||||
|
if (ncount == maxsendlist[iswap][m]) grow_list(iswap,m,ncount);
|
||||||
|
sendlist[iswap][m][ncount++] = i;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
sendnum[iswap][m] = ncount;
|
||||||
|
smaxone = MAX(smaxone,ncount);
|
||||||
|
ncountall += ncount;
|
||||||
} else {
|
} else {
|
||||||
|
|
||||||
int* type=atom->type;
|
int* type=atom->type;
|
||||||
@ -986,7 +1179,7 @@ void CommTiled::borders()
|
|||||||
if (!bordergroup) {
|
if (!bordergroup) {
|
||||||
for (i = 0; i < nlast; i++) {
|
for (i = 0; i < nlast; i++) {
|
||||||
itype=type[i];
|
itype=type[i];
|
||||||
bbox = sendbox_multi[iswap][m][itype];
|
bbox = sendbox_multiold[iswap][m][itype];
|
||||||
xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2];
|
xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2];
|
||||||
xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5];
|
xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5];
|
||||||
if (x[i][0] >= xlo && x[i][0] < xhi &&
|
if (x[i][0] >= xlo && x[i][0] < xhi &&
|
||||||
@ -1000,7 +1193,7 @@ void CommTiled::borders()
|
|||||||
ngroup = atom->nfirst;
|
ngroup = atom->nfirst;
|
||||||
for (i = 0; i < ngroup; i++) {
|
for (i = 0; i < ngroup; i++) {
|
||||||
itype=type[i];
|
itype=type[i];
|
||||||
bbox = sendbox_multi[iswap][m][itype];
|
bbox = sendbox_multiold[iswap][m][itype];
|
||||||
xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2];
|
xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2];
|
||||||
xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5];
|
xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5];
|
||||||
if (x[i][0] >= xlo && x[i][0] < xhi &&
|
if (x[i][0] >= xlo && x[i][0] < xhi &&
|
||||||
@ -1012,7 +1205,7 @@ void CommTiled::borders()
|
|||||||
}
|
}
|
||||||
for (i = atom->nlocal; i < nlast; i++) {
|
for (i = atom->nlocal; i < nlast; i++) {
|
||||||
itype=type[i];
|
itype=type[i];
|
||||||
bbox = sendbox_multi[iswap][m][itype];
|
bbox = sendbox_multiold[iswap][m][itype];
|
||||||
xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2];
|
xlo = bbox[0]; ylo = bbox[1]; zlo = bbox[2];
|
||||||
xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5];
|
xhi = bbox[3]; yhi = bbox[4]; zhi = bbox[5];
|
||||||
if (x[i][0] >= xlo && x[i][0] < xhi &&
|
if (x[i][0] >= xlo && x[i][0] < xhi &&
|
||||||
@ -1148,8 +1341,11 @@ void CommTiled::borders()
|
|||||||
// increment ghost atoms
|
// increment ghost atoms
|
||||||
|
|
||||||
n = nrecvproc[iswap];
|
n = nrecvproc[iswap];
|
||||||
if (n)
|
if (n) {
|
||||||
|
nprior = atom->nghost + atom->nlocal;
|
||||||
atom->nghost += forward_recv_offset[iswap][n-1] + recvnum[iswap][n-1];
|
atom->nghost += forward_recv_offset[iswap][n-1] + recvnum[iswap][n-1];
|
||||||
|
if (neighbor->style == Neighbor::MULTI) neighbor->build_collection(nprior);
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
// For molecular systems we lose some bits for local atom indices due
|
// For molecular systems we lose some bits for local atom indices due
|
||||||
@ -2089,6 +2285,7 @@ void CommTiled::allocate_swap(int n)
|
|||||||
pbc = new int**[n];
|
pbc = new int**[n];
|
||||||
sendbox = new double**[n];
|
sendbox = new double**[n];
|
||||||
sendbox_multi = new double***[n];
|
sendbox_multi = new double***[n];
|
||||||
|
sendbox_multiold = new double***[n];
|
||||||
maxsendlist = new int*[n];
|
maxsendlist = new int*[n];
|
||||||
sendlist = new int**[n];
|
sendlist = new int**[n];
|
||||||
|
|
||||||
@ -2103,6 +2300,7 @@ void CommTiled::allocate_swap(int n)
|
|||||||
pbc[i] = nullptr;
|
pbc[i] = nullptr;
|
||||||
sendbox[i] = nullptr;
|
sendbox[i] = nullptr;
|
||||||
sendbox_multi[i] = nullptr;
|
sendbox_multi[i] = nullptr;
|
||||||
|
sendbox_multiold[i] = nullptr;
|
||||||
maxsendlist[i] = nullptr;
|
maxsendlist[i] = nullptr;
|
||||||
sendlist[i] = nullptr;
|
sendlist[i] = nullptr;
|
||||||
}
|
}
|
||||||
@ -2151,8 +2349,9 @@ void CommTiled::grow_swap_send(int i, int n, int nold)
|
|||||||
memory->create(pbc[i],n,6,"comm:pbc_flag");
|
memory->create(pbc[i],n,6,"comm:pbc_flag");
|
||||||
memory->destroy(sendbox[i]);
|
memory->destroy(sendbox[i]);
|
||||||
memory->create(sendbox[i],n,6,"comm:sendbox");
|
memory->create(sendbox[i],n,6,"comm:sendbox");
|
||||||
memory->destroy(sendbox_multi[i]);
|
grow_swap_send_multi(i,n);
|
||||||
memory->create(sendbox_multi[i],n,atom->ntypes+1,6,"comm:sendbox_multi");
|
memory->destroy(sendbox_multiold[i]);
|
||||||
|
memory->create(sendbox_multiold[i],n,atom->ntypes+1,6,"comm:sendbox_multiold");
|
||||||
|
|
||||||
delete [] maxsendlist[i];
|
delete [] maxsendlist[i];
|
||||||
maxsendlist[i] = new int[n];
|
maxsendlist[i] = new int[n];
|
||||||
@ -2184,6 +2383,19 @@ void CommTiled::grow_swap_recv(int i, int n)
|
|||||||
size_reverse_send[i] = new int[n];
|
size_reverse_send[i] = new int[n];
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
grow info for swap I for multi as ncollections can change
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void CommTiled::grow_swap_send_multi(int i, int n)
|
||||||
|
{
|
||||||
|
memory->destroy(sendbox_multi[i]);
|
||||||
|
|
||||||
|
if (ncollections > 0)
|
||||||
|
memory->create(sendbox_multi[i],n,ncollections,6,"comm:sendbox_multi");
|
||||||
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
deallocate swap info
|
deallocate swap info
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
@ -2212,6 +2424,7 @@ void CommTiled::deallocate_swap(int n)
|
|||||||
memory->destroy(pbc[i]);
|
memory->destroy(pbc[i]);
|
||||||
memory->destroy(sendbox[i]);
|
memory->destroy(sendbox[i]);
|
||||||
memory->destroy(sendbox_multi[i]);
|
memory->destroy(sendbox_multi[i]);
|
||||||
|
memory->destroy(sendbox_multiold[i]);
|
||||||
|
|
||||||
delete [] maxsendlist[i];
|
delete [] maxsendlist[i];
|
||||||
|
|
||||||
@ -2234,6 +2447,7 @@ void CommTiled::deallocate_swap(int n)
|
|||||||
delete [] pbc;
|
delete [] pbc;
|
||||||
delete [] sendbox;
|
delete [] sendbox;
|
||||||
delete [] sendbox_multi;
|
delete [] sendbox_multi;
|
||||||
|
delete [] sendbox_multiold;
|
||||||
delete [] maxsendlist;
|
delete [] maxsendlist;
|
||||||
delete [] sendlist;
|
delete [] sendlist;
|
||||||
|
|
||||||
|
|||||||
@ -77,9 +77,12 @@ class CommTiled : public Comm {
|
|||||||
|
|
||||||
double ***sendbox; // bounding box of atoms to send per swap/proc
|
double ***sendbox; // bounding box of atoms to send per swap/proc
|
||||||
|
|
||||||
double **cutghostmulti; // cutghost on a per-type basis
|
double **cutghostmulti; // cutghost on a per-collection basis
|
||||||
|
double **cutghostmultiold; // cutghost on a per-type basis
|
||||||
double ****sendbox_multi; // bounding box of atoms to send
|
double ****sendbox_multi; // bounding box of atoms to send
|
||||||
// per swap/proc for multi comm
|
// per swap/proc for multi comm
|
||||||
|
double ****sendbox_multiold; // bounding box of atoms to send
|
||||||
|
// per swap/proc for multi/old comm
|
||||||
|
|
||||||
// exchange comm info, proc lists do not include self
|
// exchange comm info, proc lists do not include self
|
||||||
|
|
||||||
@ -148,6 +151,7 @@ class CommTiled : public Comm {
|
|||||||
void grow_list(int, int, int); // reallocate sendlist for one swap/proc
|
void grow_list(int, int, int); // reallocate sendlist for one swap/proc
|
||||||
void allocate_swap(int); // allocate swap arrays
|
void allocate_swap(int); // allocate swap arrays
|
||||||
void grow_swap_send(int, int, int); // grow swap arrays for send and recv
|
void grow_swap_send(int, int, int); // grow swap arrays for send and recv
|
||||||
|
void grow_swap_send_multi(int, int); // grow multi swap arrays for send and recv
|
||||||
void grow_swap_recv(int, int);
|
void grow_swap_recv(int, int);
|
||||||
void deallocate_swap(int); // deallocate swap arrays
|
void deallocate_swap(int); // deallocate swap arrays
|
||||||
|
|
||||||
@ -163,10 +167,6 @@ E: Cannot yet use comm_style tiled with triclinic box
|
|||||||
|
|
||||||
Self-explanatory.
|
Self-explanatory.
|
||||||
|
|
||||||
E: Cannot yet use comm_style tiled with multi-mode comm
|
|
||||||
|
|
||||||
Self-explanatory.
|
|
||||||
|
|
||||||
E: Communication cutoff for comm_style tiled cannot exceed periodic box length
|
E: Communication cutoff for comm_style tiled cannot exceed periodic box length
|
||||||
|
|
||||||
Self-explanatory.
|
Self-explanatory.
|
||||||
|
|||||||
@ -35,7 +35,7 @@ enum{TYPE,RADIUS};
|
|||||||
|
|
||||||
ComputePropertyLocal::ComputePropertyLocal(LAMMPS *lmp, int narg, char **arg) :
|
ComputePropertyLocal::ComputePropertyLocal(LAMMPS *lmp, int narg, char **arg) :
|
||||||
Compute(lmp, narg, arg),
|
Compute(lmp, narg, arg),
|
||||||
vlocal(nullptr), alocal(nullptr), indices(nullptr), pack_choice(nullptr)
|
vlocal(NULL), alocal(NULL), indices(NULL), pack_choice(NULL)
|
||||||
{
|
{
|
||||||
if (narg < 4) error->all(FLERR,"Illegal compute property/local command");
|
if (narg < 4) error->all(FLERR,"Illegal compute property/local command");
|
||||||
|
|
||||||
@ -233,7 +233,7 @@ ComputePropertyLocal::ComputePropertyLocal(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
|
|
||||||
// error check
|
// error check
|
||||||
|
|
||||||
if (atom->molecular == Atom::TEMPLATE && (kindflag == BOND || kindflag == ANGLE ||
|
if (atom->molecular == 2 && (kindflag == BOND || kindflag == ANGLE ||
|
||||||
kindflag == DIHEDRAL || kindflag == IMPROPER))
|
kindflag == DIHEDRAL || kindflag == IMPROPER))
|
||||||
error->all(FLERR,"Compute property/local does not (yet) work "
|
error->all(FLERR,"Compute property/local does not (yet) work "
|
||||||
"with atom_style template");
|
"with atom_style template");
|
||||||
@ -254,8 +254,8 @@ ComputePropertyLocal::ComputePropertyLocal(LAMMPS *lmp, int narg, char **arg) :
|
|||||||
error->all(FLERR,"Compute property/local requires atom attribute radius");
|
error->all(FLERR,"Compute property/local requires atom attribute radius");
|
||||||
|
|
||||||
nmax = 0;
|
nmax = 0;
|
||||||
vlocal = nullptr;
|
vlocal = NULL;
|
||||||
alocal = nullptr;
|
alocal = NULL;
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
@ -273,7 +273,7 @@ ComputePropertyLocal::~ComputePropertyLocal()
|
|||||||
void ComputePropertyLocal::init()
|
void ComputePropertyLocal::init()
|
||||||
{
|
{
|
||||||
if (kindflag == NEIGH || kindflag == PAIR) {
|
if (kindflag == NEIGH || kindflag == PAIR) {
|
||||||
if (force->pair == nullptr)
|
if (force->pair == NULL)
|
||||||
error->all(FLERR,"No pair style is defined for compute property/local");
|
error->all(FLERR,"No pair style is defined for compute property/local");
|
||||||
if (force->pair->single_enable == 0)
|
if (force->pair->single_enable == 0)
|
||||||
error->all(FLERR,"Pair style does not support compute property/local");
|
error->all(FLERR,"Pair style does not support compute property/local");
|
||||||
|
|||||||
17
src/info.cpp
17
src/info.cpp
@ -367,9 +367,24 @@ void Info::command(int narg, char **arg)
|
|||||||
if (comm->mode == 1) {
|
if (comm->mode == 1) {
|
||||||
fputs("Communication mode = multi\n",out);
|
fputs("Communication mode = multi\n",out);
|
||||||
double cut;
|
double cut;
|
||||||
|
for (int i=0; i < neighbor->ncollections; ++i) {
|
||||||
|
if (comm->cutusermulti) cut = comm->cutusermulti[i];
|
||||||
|
else cut = 0.0;
|
||||||
|
for (int j=0; j < neighbor->ncollections; ++j) {
|
||||||
|
cut = MAX(cut,sqrt(neighbor->cutcollectionsq[i][j]));
|
||||||
|
}
|
||||||
|
|
||||||
|
if (comm->cutusermulti) cut = MAX(cut,comm->cutusermulti[i]);
|
||||||
|
fmt::print(out,"Communication cutoff for collection {} = {:.8}\n", i, cut);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if (comm->mode == 2) {
|
||||||
|
fputs("Communication mode = multi/old\n",out);
|
||||||
|
double cut;
|
||||||
for (int i=1; i <= atom->ntypes && neighbor->cuttype; ++i) {
|
for (int i=1; i <= atom->ntypes && neighbor->cuttype; ++i) {
|
||||||
cut = neighbor->cuttype[i];
|
cut = neighbor->cuttype[i];
|
||||||
if (comm->cutusermulti) cut = MAX(cut,comm->cutusermulti[i]);
|
if (comm->cutusermultiold) cut = MAX(cut,comm->cutusermultiold[i]);
|
||||||
fmt::print(out,"Communication cutoff for type {} = {:.8}\n", i, cut);
|
fmt::print(out,"Communication cutoff for type {} = {:.8}\n", i, cut);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|||||||
115
src/nbin.cpp
115
src/nbin.cpp
@ -31,6 +31,19 @@ NBin::NBin(LAMMPS *lmp) : Pointers(lmp)
|
|||||||
bins = nullptr;
|
bins = nullptr;
|
||||||
atom2bin = nullptr;
|
atom2bin = nullptr;
|
||||||
|
|
||||||
|
nbinx_multi = nullptr; nbiny_multi = nullptr; nbinz_multi = nullptr;
|
||||||
|
mbins_multi = nullptr;
|
||||||
|
mbinx_multi = nullptr; mbiny_multi = nullptr, mbinz_multi = nullptr;
|
||||||
|
mbinxlo_multi = nullptr;
|
||||||
|
mbinylo_multi = nullptr;
|
||||||
|
mbinzlo_multi = nullptr;
|
||||||
|
binsizex_multi = nullptr; binsizey_multi = nullptr; binsizez_multi = nullptr;
|
||||||
|
bininvx_multi = nullptr; bininvy_multi = nullptr; bininvz_multi = nullptr;
|
||||||
|
binhead_multi = nullptr;
|
||||||
|
maxbins_multi = nullptr;
|
||||||
|
|
||||||
|
maxcollections = 0;
|
||||||
|
|
||||||
neighbor->last_setup_bins = -1;
|
neighbor->last_setup_bins = -1;
|
||||||
|
|
||||||
// geometry settings
|
// geometry settings
|
||||||
@ -48,6 +61,33 @@ NBin::~NBin()
|
|||||||
memory->destroy(binhead);
|
memory->destroy(binhead);
|
||||||
memory->destroy(bins);
|
memory->destroy(bins);
|
||||||
memory->destroy(atom2bin);
|
memory->destroy(atom2bin);
|
||||||
|
|
||||||
|
if (!binhead_multi) return;
|
||||||
|
|
||||||
|
memory->destroy(nbinx_multi);
|
||||||
|
memory->destroy(nbiny_multi);
|
||||||
|
memory->destroy(nbinz_multi);
|
||||||
|
memory->destroy(mbins_multi);
|
||||||
|
memory->destroy(mbinx_multi);
|
||||||
|
memory->destroy(mbiny_multi);
|
||||||
|
memory->destroy(mbinz_multi);
|
||||||
|
memory->destroy(mbinxlo_multi);
|
||||||
|
memory->destroy(mbinylo_multi);
|
||||||
|
memory->destroy(mbinzlo_multi);
|
||||||
|
|
||||||
|
memory->destroy(binsizex_multi);
|
||||||
|
memory->destroy(binsizey_multi);
|
||||||
|
memory->destroy(binsizez_multi);
|
||||||
|
memory->destroy(bininvx_multi);
|
||||||
|
memory->destroy(bininvy_multi);
|
||||||
|
memory->destroy(bininvz_multi);
|
||||||
|
|
||||||
|
for (int n = 0; n < maxcollections; n++) {
|
||||||
|
memory->destroy(binhead_multi[n]);
|
||||||
|
}
|
||||||
|
delete [] binhead_multi;
|
||||||
|
|
||||||
|
memory->destroy(maxbins_multi);
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
@ -72,38 +112,16 @@ void NBin::copy_neighbor_info()
|
|||||||
bboxlo = neighbor->bboxlo;
|
bboxlo = neighbor->bboxlo;
|
||||||
bboxhi = neighbor->bboxhi;
|
bboxhi = neighbor->bboxhi;
|
||||||
|
|
||||||
|
ncollections = neighbor->ncollections;
|
||||||
|
cutcollectionsq = neighbor->cutcollectionsq;
|
||||||
|
|
||||||
// overwrite Neighbor cutoff with custom value set by requestor
|
// overwrite Neighbor cutoff with custom value set by requestor
|
||||||
// only works for style = BIN (checked by Neighbor class)
|
// only works for style = BIN (checked by Neighbor class)
|
||||||
|
|
||||||
if (cutoff_custom > 0.0) cutneighmax = cutoff_custom;
|
if (cutoff_custom > 0.0) cutneighmax = cutoff_custom;
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
|
||||||
setup for bin_atoms()
|
|
||||||
------------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
void NBin::bin_atoms_setup(int nall)
|
|
||||||
{
|
|
||||||
// binhead = per-bin vector, mbins in length
|
|
||||||
// add 1 bin for USER-INTEL package
|
|
||||||
|
|
||||||
if (mbins > maxbin) {
|
|
||||||
maxbin = mbins;
|
|
||||||
memory->destroy(binhead);
|
|
||||||
memory->create(binhead,maxbin,"neigh:binhead");
|
|
||||||
}
|
|
||||||
|
|
||||||
// bins and atom2bin = per-atom vectors
|
|
||||||
// for both local and ghost atoms
|
|
||||||
|
|
||||||
if (nall > maxatom) {
|
|
||||||
maxatom = nall;
|
|
||||||
memory->destroy(bins);
|
|
||||||
memory->create(bins,maxatom,"neigh:bins");
|
|
||||||
memory->destroy(atom2bin);
|
|
||||||
memory->create(atom2bin,maxatom,"neigh:atom2bin");
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
convert atom coords into local bin #
|
convert atom coords into local bin #
|
||||||
@ -151,12 +169,47 @@ int NBin::coord2bin(double *x)
|
|||||||
return (iz-mbinzlo)*mbiny*mbinx + (iy-mbinylo)*mbinx + (ix-mbinxlo);
|
return (iz-mbinzlo)*mbiny*mbinx + (iy-mbinylo)*mbinx + (ix-mbinxlo);
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
|
||||||
|
|
||||||
double NBin::memory_usage()
|
/* ----------------------------------------------------------------------
|
||||||
|
convert atom coords into local bin # for a particular collection
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
int NBin::coord2bin_multi(double *x, int ic)
|
||||||
{
|
{
|
||||||
double bytes = 0;
|
int ix,iy,iz;
|
||||||
bytes += (double)maxbin*sizeof(int);
|
int ibin;
|
||||||
bytes += (double)2*maxatom*sizeof(int);
|
|
||||||
return bytes;
|
if (!std::isfinite(x[0]) || !std::isfinite(x[1]) || !std::isfinite(x[2]))
|
||||||
|
error->one(FLERR,"Non-numeric positions - simulation unstable");
|
||||||
|
|
||||||
|
if (x[0] >= bboxhi[0])
|
||||||
|
ix = static_cast<int> ((x[0]-bboxhi[0])*bininvx_multi[ic]) + nbinx_multi[ic];
|
||||||
|
else if (x[0] >= bboxlo[0]) {
|
||||||
|
ix = static_cast<int> ((x[0]-bboxlo[0])*bininvx_multi[ic]);
|
||||||
|
ix = MIN(ix,nbinx_multi[ic]-1);
|
||||||
|
} else
|
||||||
|
ix = static_cast<int> ((x[0]-bboxlo[0])*bininvx_multi[ic]) - 1;
|
||||||
|
|
||||||
|
if (x[1] >= bboxhi[1])
|
||||||
|
iy = static_cast<int> ((x[1]-bboxhi[1])*bininvy_multi[ic]) + nbiny_multi[ic];
|
||||||
|
else if (x[1] >= bboxlo[1]) {
|
||||||
|
iy = static_cast<int> ((x[1]-bboxlo[1])*bininvy_multi[ic]);
|
||||||
|
iy = MIN(iy,nbiny_multi[ic]-1);
|
||||||
|
} else
|
||||||
|
iy = static_cast<int> ((x[1]-bboxlo[1])*bininvy_multi[ic]) - 1;
|
||||||
|
|
||||||
|
if (x[2] >= bboxhi[2])
|
||||||
|
iz = static_cast<int> ((x[2]-bboxhi[2])*bininvz_multi[ic]) + nbinz_multi[ic];
|
||||||
|
else if (x[2] >= bboxlo[2]) {
|
||||||
|
iz = static_cast<int> ((x[2]-bboxlo[2])*bininvz_multi[ic]);
|
||||||
|
iz = MIN(iz,nbinz_multi[ic]-1);
|
||||||
|
} else
|
||||||
|
iz = static_cast<int> ((x[2]-bboxlo[2])*bininvz_multi[ic]) - 1;
|
||||||
|
|
||||||
|
|
||||||
|
ibin = (iz-mbinzlo_multi[ic])*mbiny_multi[ic]*mbinx_multi[ic]
|
||||||
|
+ (iy-mbinylo_multi[ic])*mbinx_multi[ic]
|
||||||
|
+ (ix-mbinxlo_multi[ic]);
|
||||||
|
return ibin;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|||||||
30
src/nbin.h
30
src/nbin.h
@ -22,6 +22,9 @@ class NBin : protected Pointers {
|
|||||||
public:
|
public:
|
||||||
int istyle; // 1-N index into binnames
|
int istyle; // 1-N index into binnames
|
||||||
bigint last_bin; // last timestep atoms were binned
|
bigint last_bin; // last timestep atoms were binned
|
||||||
|
double cutoff_custom; // cutoff set by requestor
|
||||||
|
|
||||||
|
// Variables for NBinStandard
|
||||||
|
|
||||||
int nbinx,nbiny,nbinz; // # of global bins
|
int nbinx,nbiny,nbinz; // # of global bins
|
||||||
int mbins; // # of local bins and offset on this proc
|
int mbins; // # of local bins and offset on this proc
|
||||||
@ -35,17 +38,26 @@ class NBin : protected Pointers {
|
|||||||
int *bins; // index of next atom in same bin
|
int *bins; // index of next atom in same bin
|
||||||
int *atom2bin; // bin assignment for each atom (local+ghost)
|
int *atom2bin; // bin assignment for each atom (local+ghost)
|
||||||
|
|
||||||
double cutoff_custom; // cutoff set by requestor
|
// Analogues for NBinMultimulti
|
||||||
|
|
||||||
|
int *nbinx_multi, *nbiny_multi, *nbinz_multi;
|
||||||
|
int *mbins_multi;
|
||||||
|
int *mbinx_multi, *mbiny_multi, *mbinz_multi;
|
||||||
|
int *mbinxlo_multi, *mbinylo_multi, *mbinzlo_multi;
|
||||||
|
double *binsizex_multi, *binsizey_multi, *binsizez_multi;
|
||||||
|
double *bininvx_multi, *bininvy_multi, *bininvz_multi;
|
||||||
|
|
||||||
|
int **binhead_multi;
|
||||||
|
|
||||||
NBin(class LAMMPS *);
|
NBin(class LAMMPS *);
|
||||||
~NBin();
|
~NBin();
|
||||||
void post_constructor(class NeighRequest *);
|
void post_constructor(class NeighRequest *);
|
||||||
virtual void copy_neighbor_info();
|
virtual void copy_neighbor_info();
|
||||||
virtual void bin_atoms_setup(int);
|
|
||||||
double memory_usage();
|
|
||||||
|
|
||||||
|
virtual void bin_atoms_setup(int) = 0;
|
||||||
virtual void setup_bins(int) = 0;
|
virtual void setup_bins(int) = 0;
|
||||||
virtual void bin_atoms() = 0;
|
virtual void bin_atoms() = 0;
|
||||||
|
virtual double memory_usage() {return 0.0;}
|
||||||
|
|
||||||
// Kokkos package
|
// Kokkos package
|
||||||
|
|
||||||
@ -61,18 +73,28 @@ class NBin : protected Pointers {
|
|||||||
int binsizeflag;
|
int binsizeflag;
|
||||||
double binsize_user;
|
double binsize_user;
|
||||||
double *bboxlo,*bboxhi;
|
double *bboxlo,*bboxhi;
|
||||||
|
int ncollections;
|
||||||
|
double **cutcollectionsq;
|
||||||
|
|
||||||
// data common to all NBin variants
|
// data common to all NBin variants
|
||||||
|
|
||||||
int dimension;
|
int dimension;
|
||||||
int triclinic;
|
int triclinic;
|
||||||
|
|
||||||
int maxbin; // size of binhead array
|
// data for standard NBin
|
||||||
|
|
||||||
int maxatom; // size of bins array
|
int maxatom; // size of bins array
|
||||||
|
int maxbin; // size of binhead array
|
||||||
|
|
||||||
|
// data for multi NBin
|
||||||
|
|
||||||
|
int maxcollections; // size of multi arrays
|
||||||
|
int * maxbins_multi; // size of 2nd dimension of binhead_multi array
|
||||||
|
|
||||||
// methods
|
// methods
|
||||||
|
|
||||||
int coord2bin(double *);
|
int coord2bin(double *);
|
||||||
|
int coord2bin_multi(double *, int);
|
||||||
};
|
};
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|||||||
349
src/nbin_multi.cpp
Normal file
349
src/nbin_multi.cpp
Normal file
@ -0,0 +1,349 @@
|
|||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
https://lammps.sandia.gov/, 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 "nbin_multi.h"
|
||||||
|
#include "neighbor.h"
|
||||||
|
#include "atom.h"
|
||||||
|
#include "group.h"
|
||||||
|
#include "domain.h"
|
||||||
|
#include "comm.h"
|
||||||
|
#include "update.h"
|
||||||
|
#include "error.h"
|
||||||
|
#include "memory.h"
|
||||||
|
|
||||||
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
|
#define SMALL 1.0e-6
|
||||||
|
#define CUT2BIN_RATIO 100
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
NBinMulti::NBinMulti(LAMMPS *lmp) : NBin(lmp) {}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
setup for bin_atoms()
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void NBinMulti::bin_atoms_setup(int nall)
|
||||||
|
{
|
||||||
|
// binhead_multi[n] = per-bin vector mbins in length mbins_multi[n]
|
||||||
|
|
||||||
|
for (int n = 0; n < maxcollections; n++) {
|
||||||
|
if (mbins_multi[n] > maxbins_multi[n]) {
|
||||||
|
maxbins_multi[n] = mbins_multi[n];
|
||||||
|
memory->destroy(binhead_multi[n]);
|
||||||
|
memory->create(binhead_multi[n], mbins_multi[n], "neigh:mbins_multi");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
// bins and atom2bin = per-atom vectors
|
||||||
|
// for both local and ghost atoms
|
||||||
|
// for multi, bins and atom2bin correspond to different binlists
|
||||||
|
|
||||||
|
if (nall > maxatom) {
|
||||||
|
maxatom = nall;
|
||||||
|
memory->destroy(bins);
|
||||||
|
memory->create(bins,maxatom,"neigh:bins");
|
||||||
|
memory->destroy(atom2bin);
|
||||||
|
memory->create(atom2bin,maxatom,"neigh:atom2bin");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
setup neighbor binning geometry
|
||||||
|
bin numbering in each dimension is global:
|
||||||
|
0 = 0.0 to binsize, 1 = binsize to 2*binsize, etc
|
||||||
|
nbin-1,nbin,etc = bbox-binsize to bbox, bbox to bbox+binsize, etc
|
||||||
|
-1,-2,etc = -binsize to 0.0, -2*binsize to -binsize, etc
|
||||||
|
code will work for any binsize
|
||||||
|
since next(xyz) and stencil extend as far as necessary
|
||||||
|
binsize = 1/2 of cutoff is roughly optimal
|
||||||
|
for orthogonal boxes:
|
||||||
|
a dim must be filled exactly by integer # of bins
|
||||||
|
in periodic, procs on both sides of PBC must see same bin boundary
|
||||||
|
in non-periodic, coord2bin() still assumes this by use of nbin xyz
|
||||||
|
for triclinic boxes:
|
||||||
|
tilted simulation box cannot contain integer # of bins
|
||||||
|
stencil & neigh list built differently to account for this
|
||||||
|
mbinlo_multi = lowest global bin any of my ghost atoms could fall into for each collection
|
||||||
|
mbinhi_multi = highest global bin any of my ghost atoms could fall into for each collection
|
||||||
|
mbin_multi = number of bins I need in a dimension for each collection
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void NBinMulti::setup_bins(int /*style*/)
|
||||||
|
{
|
||||||
|
int n;
|
||||||
|
|
||||||
|
// Initialize arrays
|
||||||
|
if (ncollections > maxcollections) {
|
||||||
|
|
||||||
|
// Clear any/all memory for existing groupings
|
||||||
|
for (n = 0; n < maxcollections; n++)
|
||||||
|
memory->destroy(binhead_multi[n]);
|
||||||
|
|
||||||
|
delete [] binhead_multi;
|
||||||
|
|
||||||
|
maxcollections = ncollections;
|
||||||
|
|
||||||
|
binhead_multi = new int*[maxcollections]();
|
||||||
|
|
||||||
|
memory->destroy(nbinx_multi);
|
||||||
|
memory->destroy(nbiny_multi);
|
||||||
|
memory->destroy(nbinz_multi);
|
||||||
|
memory->create(nbinx_multi, maxcollections, "neigh:nbinx_multi");
|
||||||
|
memory->create(nbiny_multi, maxcollections, "neigh:nbiny_multi");
|
||||||
|
memory->create(nbinz_multi, maxcollections, "neigh:nbinz_multi");
|
||||||
|
|
||||||
|
memory->destroy(mbins_multi);
|
||||||
|
memory->destroy(mbinx_multi);
|
||||||
|
memory->destroy(mbiny_multi);
|
||||||
|
memory->destroy(mbinz_multi);
|
||||||
|
memory->create(mbins_multi, maxcollections, "neigh:mbins_multi");
|
||||||
|
memory->create(mbinx_multi, maxcollections, "neigh:mbinx_multi");
|
||||||
|
memory->create(mbiny_multi, maxcollections, "neigh:mbiny_multi");
|
||||||
|
memory->create(mbinz_multi, maxcollections, "neigh:mbinz_multi");
|
||||||
|
|
||||||
|
memory->destroy(mbinxlo_multi);
|
||||||
|
memory->destroy(mbinylo_multi);
|
||||||
|
memory->destroy(mbinzlo_multi);
|
||||||
|
memory->create(mbinxlo_multi, maxcollections, "neigh:mbinxlo_multi");
|
||||||
|
memory->create(mbinylo_multi, maxcollections, "neigh:mbinylo_multi");
|
||||||
|
memory->create(mbinzlo_multi, maxcollections, "neigh:mbinzlo_multi");
|
||||||
|
|
||||||
|
memory->destroy(binsizex_multi);
|
||||||
|
memory->destroy(binsizey_multi);
|
||||||
|
memory->destroy(binsizez_multi);
|
||||||
|
memory->create(binsizex_multi, maxcollections, "neigh:binsizex_multi");
|
||||||
|
memory->create(binsizey_multi, maxcollections, "neigh:binsizey_multi");
|
||||||
|
memory->create(binsizez_multi, maxcollections, "neigh:binsizez_multi");
|
||||||
|
|
||||||
|
memory->destroy(bininvx_multi);
|
||||||
|
memory->destroy(bininvy_multi);
|
||||||
|
memory->destroy(bininvz_multi);
|
||||||
|
memory->create(bininvx_multi, maxcollections, "neigh:bininvx_multi");
|
||||||
|
memory->create(bininvy_multi, maxcollections, "neigh:bininvy_multi");
|
||||||
|
memory->create(bininvz_multi, maxcollections, "neigh:bininvz_multi");
|
||||||
|
|
||||||
|
memory->destroy(maxbins_multi);
|
||||||
|
memory->create(maxbins_multi, maxcollections, "neigh:maxbins_multi");
|
||||||
|
|
||||||
|
// ensure reallocation occurs in bin_atoms_setup()
|
||||||
|
for (n = 0; n < maxcollections; n++) {
|
||||||
|
maxbins_multi[n] = 0;
|
||||||
|
}
|
||||||
|
maxatom = 0;
|
||||||
|
}
|
||||||
|
|
||||||
|
// Identify smallest collection
|
||||||
|
int icollectionmin = 0;
|
||||||
|
for (n = 0; n < ncollections; n++)
|
||||||
|
if (cutcollectionsq[n][n] < cutcollectionsq[icollectionmin][icollectionmin])
|
||||||
|
icollectionmin = n;
|
||||||
|
|
||||||
|
// bbox = size of bbox of entire domain
|
||||||
|
// bsubbox lo/hi = bounding box of my subdomain extended by comm->cutghost
|
||||||
|
// for triclinic:
|
||||||
|
// bbox bounds all 8 corners of tilted box
|
||||||
|
// subdomain is in lamda coords
|
||||||
|
// include dimension-dependent extension via comm->cutghost
|
||||||
|
// domain->bbox() converts lamda extent to box coords and computes bbox
|
||||||
|
|
||||||
|
double bbox[3],bsubboxlo[3],bsubboxhi[3];
|
||||||
|
double *cutghost = comm->cutghost;
|
||||||
|
|
||||||
|
if (triclinic == 0) {
|
||||||
|
bsubboxlo[0] = domain->sublo[0] - cutghost[0];
|
||||||
|
bsubboxlo[1] = domain->sublo[1] - cutghost[1];
|
||||||
|
bsubboxlo[2] = domain->sublo[2] - cutghost[2];
|
||||||
|
bsubboxhi[0] = domain->subhi[0] + cutghost[0];
|
||||||
|
bsubboxhi[1] = domain->subhi[1] + cutghost[1];
|
||||||
|
bsubboxhi[2] = domain->subhi[2] + cutghost[2];
|
||||||
|
} else {
|
||||||
|
double lo[3],hi[3];
|
||||||
|
lo[0] = domain->sublo_lamda[0] - cutghost[0];
|
||||||
|
lo[1] = domain->sublo_lamda[1] - cutghost[1];
|
||||||
|
lo[2] = domain->sublo_lamda[2] - cutghost[2];
|
||||||
|
hi[0] = domain->subhi_lamda[0] + cutghost[0];
|
||||||
|
hi[1] = domain->subhi_lamda[1] + cutghost[1];
|
||||||
|
hi[2] = domain->subhi_lamda[2] + cutghost[2];
|
||||||
|
domain->bbox(lo,hi,bsubboxlo,bsubboxhi);
|
||||||
|
}
|
||||||
|
|
||||||
|
bbox[0] = bboxhi[0] - bboxlo[0];
|
||||||
|
bbox[1] = bboxhi[1] - bboxlo[1];
|
||||||
|
bbox[2] = bboxhi[2] - bboxlo[2];
|
||||||
|
|
||||||
|
// For each grouping...
|
||||||
|
|
||||||
|
double binsize_optimal, binsizeinv, coord;
|
||||||
|
int mbinxhi,mbinyhi,mbinzhi;
|
||||||
|
|
||||||
|
for (n = 0; n < ncollections; n++) {
|
||||||
|
// binsize_user only relates to smallest collection
|
||||||
|
// optimal bin size is roughly 1/2 the collection-collection cutoff
|
||||||
|
// special case of all cutoffs = 0.0, binsize = box size
|
||||||
|
|
||||||
|
if (n == icollectionmin && binsizeflag) binsize_optimal = binsize_user;
|
||||||
|
else binsize_optimal = 0.5*sqrt(cutcollectionsq[n][n]);
|
||||||
|
if (binsize_optimal == 0.0) binsize_optimal = bbox[0];
|
||||||
|
binsizeinv = 1.0/binsize_optimal;
|
||||||
|
|
||||||
|
// test for too many global bins in any dimension due to huge global domain
|
||||||
|
|
||||||
|
if (bbox[0]*binsizeinv > MAXSMALLINT || bbox[1]*binsizeinv > MAXSMALLINT ||
|
||||||
|
bbox[2]*binsizeinv > MAXSMALLINT)
|
||||||
|
error->all(FLERR,"Domain too large for neighbor bins");
|
||||||
|
|
||||||
|
// create actual bins
|
||||||
|
// always have one bin even if cutoff > bbox
|
||||||
|
// for 2d, nbinz_multi[n] = 1
|
||||||
|
|
||||||
|
nbinx_multi[n] = static_cast<int> (bbox[0]*binsizeinv);
|
||||||
|
nbiny_multi[n] = static_cast<int> (bbox[1]*binsizeinv);
|
||||||
|
if (dimension == 3) nbinz_multi[n] = static_cast<int> (bbox[2]*binsizeinv);
|
||||||
|
else nbinz_multi[n] = 1;
|
||||||
|
|
||||||
|
if (nbinx_multi[n] == 0) nbinx_multi[n] = 1;
|
||||||
|
if (nbiny_multi[n] == 0) nbiny_multi[n] = 1;
|
||||||
|
if (nbinz_multi[n] == 0) nbinz_multi[n] = 1;
|
||||||
|
|
||||||
|
// compute actual bin size for nbins to fit into box exactly
|
||||||
|
// error if actual bin size << cutoff, since will create a zillion bins
|
||||||
|
// this happens when nbin = 1 and box size << cutoff
|
||||||
|
// typically due to non-periodic, flat system in a particular dim
|
||||||
|
// in that extreme case, cannot use multi, should use NSQ not BIN neighbor style
|
||||||
|
|
||||||
|
binsizex_multi[n] = bbox[0]/nbinx_multi[n];
|
||||||
|
binsizey_multi[n] = bbox[1]/nbiny_multi[n];
|
||||||
|
binsizez_multi[n] = bbox[2]/nbinz_multi[n];
|
||||||
|
|
||||||
|
bininvx_multi[n] = 1.0 / binsizex_multi[n];
|
||||||
|
bininvy_multi[n] = 1.0 / binsizey_multi[n];
|
||||||
|
bininvz_multi[n] = 1.0 / binsizez_multi[n];
|
||||||
|
|
||||||
|
if (binsize_optimal*bininvx_multi[n] > CUT2BIN_RATIO ||
|
||||||
|
binsize_optimal*bininvy_multi[n] > CUT2BIN_RATIO)
|
||||||
|
error->all(FLERR,"Cannot use neighbor bins - box size << cutoff");
|
||||||
|
if ((dimension == 3) && (binsize_optimal*bininvz_multi[n] > CUT2BIN_RATIO))
|
||||||
|
error->all(FLERR,"Cannot use neighbor bins - box size << cutoff");
|
||||||
|
|
||||||
|
// mbinlo/hi = lowest and highest global bins my ghost atoms could be in
|
||||||
|
// coord = lowest and highest values of coords for my ghost atoms
|
||||||
|
// static_cast(-1.5) = -1, so subract additional -1
|
||||||
|
// add in SMALL for round-off safety
|
||||||
|
|
||||||
|
coord = bsubboxlo[0] - SMALL*bbox[0];
|
||||||
|
mbinxlo_multi[n] = static_cast<int> ((coord-bboxlo[0])*bininvx_multi[n]);
|
||||||
|
if (coord < bboxlo[0]) mbinxlo_multi[n] = mbinxlo_multi[n] - 1;
|
||||||
|
coord = bsubboxhi[0] + SMALL*bbox[0];
|
||||||
|
mbinxhi = static_cast<int> ((coord-bboxlo[0])*bininvx_multi[n]);
|
||||||
|
|
||||||
|
coord = bsubboxlo[1] - SMALL*bbox[1];
|
||||||
|
mbinylo_multi[n] = static_cast<int> ((coord-bboxlo[1])*bininvy_multi[n]);
|
||||||
|
if (coord < bboxlo[1]) mbinylo_multi[n] = mbinylo_multi[n] - 1;
|
||||||
|
coord = bsubboxhi[1] + SMALL*bbox[1];
|
||||||
|
mbinyhi = static_cast<int> ((coord-bboxlo[1])*bininvy_multi[n]);
|
||||||
|
|
||||||
|
if (dimension == 3) {
|
||||||
|
coord = bsubboxlo[2] - SMALL*bbox[2];
|
||||||
|
mbinzlo_multi[n] = static_cast<int> ((coord-bboxlo[2])*bininvz_multi[n]);
|
||||||
|
if (coord < bboxlo[2]) mbinzlo_multi[n] = mbinzlo_multi[n] - 1;
|
||||||
|
coord = bsubboxhi[2] + SMALL*bbox[2];
|
||||||
|
mbinzhi = static_cast<int> ((coord-bboxlo[2])*bininvz_multi[n]);
|
||||||
|
}
|
||||||
|
|
||||||
|
// extend bins by 1 to insure stencil extent is included
|
||||||
|
// for 2d, only 1 bin in z
|
||||||
|
|
||||||
|
mbinxlo_multi[n] = mbinxlo_multi[n] - 1;
|
||||||
|
mbinxhi = mbinxhi + 1;
|
||||||
|
mbinx_multi[n] = mbinxhi - mbinxlo_multi[n] + 1;
|
||||||
|
|
||||||
|
mbinylo_multi[n] = mbinylo_multi[n] - 1;
|
||||||
|
mbinyhi = mbinyhi + 1;
|
||||||
|
mbiny_multi[n] = mbinyhi - mbinylo_multi[n] + 1;
|
||||||
|
|
||||||
|
if (dimension == 3) {
|
||||||
|
mbinzlo_multi[n] = mbinzlo_multi[n] - 1;
|
||||||
|
mbinzhi = mbinzhi + 1;
|
||||||
|
} else mbinzlo_multi[n] = mbinzhi = 0;
|
||||||
|
mbinz_multi[n] = mbinzhi - mbinzlo_multi[n] + 1;
|
||||||
|
|
||||||
|
bigint bbin = ((bigint) mbinx_multi[n])
|
||||||
|
* ((bigint) mbiny_multi[n]) * ((bigint) mbinz_multi[n]) + 1;
|
||||||
|
if (bbin > MAXSMALLINT) error->one(FLERR,"Too many neighbor bins");
|
||||||
|
mbins_multi[n] = bbin;
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
bin owned and ghost atoms by type
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void NBinMulti::bin_atoms()
|
||||||
|
{
|
||||||
|
int i,ibin,n;
|
||||||
|
|
||||||
|
last_bin = update->ntimestep;
|
||||||
|
for (n = 0; n < ncollections; n++) {
|
||||||
|
for (i = 0; i < mbins_multi[n]; i++) binhead_multi[n][i] = -1;
|
||||||
|
}
|
||||||
|
// bin in reverse order so linked list will be in forward order
|
||||||
|
// also puts ghost atoms at end of list, which is necessary
|
||||||
|
|
||||||
|
int *collection = neighbor->collection;
|
||||||
|
double **x = atom->x;
|
||||||
|
int *mask = atom->mask;
|
||||||
|
int nlocal = atom->nlocal;
|
||||||
|
int nall = nlocal + atom->nghost;
|
||||||
|
|
||||||
|
if (includegroup) {
|
||||||
|
int bitmask = group->bitmask[includegroup];
|
||||||
|
for (i = nall-1; i >= nlocal; i--) {
|
||||||
|
if (mask[i] & bitmask) {
|
||||||
|
n = collection[i];
|
||||||
|
ibin = coord2bin_multi(x[i], n);
|
||||||
|
atom2bin[i] = ibin;
|
||||||
|
bins[i] = binhead_multi[n][ibin];
|
||||||
|
binhead_multi[n][ibin] = i;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
for (i = atom->nfirst-1; i >= 0; i--) {
|
||||||
|
n = collection[i];
|
||||||
|
ibin = coord2bin_multi(x[i], n);
|
||||||
|
atom2bin[i] = ibin;
|
||||||
|
bins[i] = binhead_multi[n][ibin];
|
||||||
|
binhead_multi[n][ibin] = i;
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
for (i = nall-1; i >= 0; i--) {
|
||||||
|
n = collection[i];
|
||||||
|
ibin = coord2bin_multi(x[i], n);
|
||||||
|
atom2bin[i] = ibin;
|
||||||
|
bins[i] = binhead_multi[n][ibin];
|
||||||
|
binhead_multi[n][ibin] = i;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
double NBinMulti::memory_usage()
|
||||||
|
{
|
||||||
|
double bytes = 0;
|
||||||
|
for (int m = 0; m < maxcollections; m++)
|
||||||
|
bytes += (double)maxbins_multi[m]*sizeof(int);
|
||||||
|
bytes += (double)2*maxatom*sizeof(int);
|
||||||
|
return bytes;
|
||||||
|
}
|
||||||
63
src/nbin_multi.h
Normal file
63
src/nbin_multi.h
Normal file
@ -0,0 +1,63 @@
|
|||||||
|
/* -*- c++ -*- ----------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
https://lammps.sandia.gov/, 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.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#ifdef NBIN_CLASS
|
||||||
|
|
||||||
|
NBinStyle(multi,
|
||||||
|
NBinMulti,
|
||||||
|
NB_MULTI)
|
||||||
|
|
||||||
|
#else
|
||||||
|
|
||||||
|
#ifndef LMP_NBIN_MULTI_H
|
||||||
|
#define LMP_NBIN_MULTI_H
|
||||||
|
|
||||||
|
#include "nbin.h"
|
||||||
|
|
||||||
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
|
class NBinMulti : public NBin {
|
||||||
|
public:
|
||||||
|
|
||||||
|
NBinMulti(class LAMMPS *);
|
||||||
|
~NBinMulti() {}
|
||||||
|
void bin_atoms_setup(int);
|
||||||
|
void setup_bins(int);
|
||||||
|
void bin_atoms();
|
||||||
|
double memory_usage();
|
||||||
|
};
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
#endif
|
||||||
|
#endif
|
||||||
|
|
||||||
|
/* ERROR/WARNING messages:
|
||||||
|
|
||||||
|
E: Domain too large for neighbor bins
|
||||||
|
|
||||||
|
UNDOCUMENTED
|
||||||
|
|
||||||
|
E: Cannot use neighbor bins - box size << cutoff
|
||||||
|
|
||||||
|
UNDOCUMENTED
|
||||||
|
|
||||||
|
E: Too many neighbor bins
|
||||||
|
|
||||||
|
UNDOCUMENTED
|
||||||
|
|
||||||
|
E Non-numeric positions - simulation unstable
|
||||||
|
|
||||||
|
UNDOCUMENTED
|
||||||
|
|
||||||
|
*/
|
||||||
@ -19,6 +19,7 @@
|
|||||||
#include "comm.h"
|
#include "comm.h"
|
||||||
#include "update.h"
|
#include "update.h"
|
||||||
#include "error.h"
|
#include "error.h"
|
||||||
|
#include "memory.h"
|
||||||
|
|
||||||
using namespace LAMMPS_NS;
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
@ -29,6 +30,33 @@ using namespace LAMMPS_NS;
|
|||||||
|
|
||||||
NBinStandard::NBinStandard(LAMMPS *lmp) : NBin(lmp) {}
|
NBinStandard::NBinStandard(LAMMPS *lmp) : NBin(lmp) {}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
setup for bin_atoms()
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void NBinStandard::bin_atoms_setup(int nall)
|
||||||
|
{
|
||||||
|
// binhead = per-bin vector, mbins in length
|
||||||
|
// add 1 bin for USER-INTEL package
|
||||||
|
|
||||||
|
if (mbins > maxbin) {
|
||||||
|
maxbin = mbins;
|
||||||
|
memory->destroy(binhead);
|
||||||
|
memory->create(binhead,maxbin,"neigh:binhead");
|
||||||
|
}
|
||||||
|
|
||||||
|
// bins and atom2bin = per-atom vectors
|
||||||
|
// for both local and ghost atoms
|
||||||
|
|
||||||
|
if (nall > maxatom) {
|
||||||
|
maxatom = nall;
|
||||||
|
memory->destroy(bins);
|
||||||
|
memory->create(bins,maxatom,"neigh:bins");
|
||||||
|
memory->destroy(atom2bin);
|
||||||
|
memory->create(atom2bin,maxatom,"neigh:atom2bin");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
setup neighbor binning geometry
|
setup neighbor binning geometry
|
||||||
bin numbering in each dimension is global:
|
bin numbering in each dimension is global:
|
||||||
@ -87,7 +115,7 @@ void NBinStandard::setup_bins(int style)
|
|||||||
|
|
||||||
// optimal bin size is roughly 1/2 the cutoff
|
// optimal bin size is roughly 1/2 the cutoff
|
||||||
// for BIN style, binsize = 1/2 of max neighbor cutoff
|
// for BIN style, binsize = 1/2 of max neighbor cutoff
|
||||||
// for MULTI style, binsize = 1/2 of min neighbor cutoff
|
// for MULTI_OLD style, binsize = 1/2 of min neighbor cutoff
|
||||||
// special case of all cutoffs = 0.0, binsize = box size
|
// special case of all cutoffs = 0.0, binsize = box size
|
||||||
|
|
||||||
double binsize_optimal;
|
double binsize_optimal;
|
||||||
@ -230,3 +258,13 @@ void NBinStandard::bin_atoms()
|
|||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
double NBinStandard::memory_usage()
|
||||||
|
{
|
||||||
|
double bytes = 0;
|
||||||
|
bytes += (double)maxbin*sizeof(int);
|
||||||
|
bytes += (double)2*maxatom*sizeof(int);
|
||||||
|
return bytes;
|
||||||
|
}
|
||||||
|
|||||||
@ -15,7 +15,7 @@
|
|||||||
|
|
||||||
NBinStyle(standard,
|
NBinStyle(standard,
|
||||||
NBinStandard,
|
NBinStandard,
|
||||||
0)
|
NB_STANDARD)
|
||||||
|
|
||||||
#else
|
#else
|
||||||
|
|
||||||
@ -30,8 +30,10 @@ class NBinStandard : public NBin {
|
|||||||
public:
|
public:
|
||||||
NBinStandard(class LAMMPS *);
|
NBinStandard(class LAMMPS *);
|
||||||
~NBinStandard() {}
|
~NBinStandard() {}
|
||||||
|
void bin_atoms_setup(int);
|
||||||
void setup_bins(int);
|
void setup_bins(int);
|
||||||
void bin_atoms();
|
void bin_atoms();
|
||||||
|
double memory_usage();
|
||||||
};
|
};
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|||||||
336
src/neighbor.cpp
336
src/neighbor.cpp
@ -13,6 +13,7 @@
|
|||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
Contributing author (triclinic and multi-neigh) : Pieter in 't Veld (SNL)
|
Contributing author (triclinic and multi-neigh) : Pieter in 't Veld (SNL)
|
||||||
|
Contributing author (improved multi-neigh) : Joel Clemmer (SNL)
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
#include "neighbor.h"
|
#include "neighbor.h"
|
||||||
@ -43,6 +44,7 @@
|
|||||||
#include "style_npair.h"
|
#include "style_npair.h"
|
||||||
#include "style_nstencil.h"
|
#include "style_nstencil.h"
|
||||||
#include "style_ntopo.h"
|
#include "style_ntopo.h"
|
||||||
|
#include "tokenizer.h"
|
||||||
#include "update.h"
|
#include "update.h"
|
||||||
|
|
||||||
#include <cmath>
|
#include <cmath>
|
||||||
@ -53,13 +55,14 @@ using namespace NeighConst;
|
|||||||
|
|
||||||
#define RQDELTA 1
|
#define RQDELTA 1
|
||||||
#define EXDELTA 1
|
#define EXDELTA 1
|
||||||
|
#define DELTA_PERATOM 64
|
||||||
|
|
||||||
#define BIG 1.0e20
|
#define BIG 1.0e20
|
||||||
|
|
||||||
enum{NONE,ALL,PARTIAL,TEMPLATE};
|
enum{NONE,ALL,PARTIAL,TEMPLATE};
|
||||||
|
|
||||||
static const char cite_neigh_multi[] =
|
static const char cite_neigh_multi_old[] =
|
||||||
"neighbor multi command:\n\n"
|
"neighbor multi/old command: doi:10.1016/j.cpc.2008.03.005\n\n"
|
||||||
"@Article{Intveld08,\n"
|
"@Article{Intveld08,\n"
|
||||||
" author = {P.{\\,}J.~in{\\,}'t~Veld and S.{\\,}J.~Plimpton"
|
" author = {P.{\\,}J.~in{\\,}'t~Veld and S.{\\,}J.~Plimpton"
|
||||||
" and G.{\\,}S.~Grest},\n"
|
" and G.{\\,}S.~Grest},\n"
|
||||||
@ -71,6 +74,31 @@ static const char cite_neigh_multi[] =
|
|||||||
" pages = {320--329}\n"
|
" pages = {320--329}\n"
|
||||||
"}\n\n";
|
"}\n\n";
|
||||||
|
|
||||||
|
static const char cite_neigh_multi[] =
|
||||||
|
"neighbor multi command: doi:10.1016/j.cpc.2008.03.005, doi:10.1007/s40571-020-00361-2\n\n"
|
||||||
|
"@Article{Intveld08,\n"
|
||||||
|
" author = {P.{\\,}J.~in{\\,}'t~Veld and S.{\\,}J.~Plimpton"
|
||||||
|
" and G.{\\,}S.~Grest},\n"
|
||||||
|
" title = {Accurate and Efficient Methods for Modeling Colloidal\n"
|
||||||
|
" Mixtures in an Explicit Solvent using Molecular Dynamics},\n"
|
||||||
|
" journal = {Comp.~Phys.~Comm.},\n"
|
||||||
|
" year = 2008,\n"
|
||||||
|
" volume = 179,\n"
|
||||||
|
" pages = {320--329}\n"
|
||||||
|
"}\n\n"
|
||||||
|
"@article{Stratford2018,\n"
|
||||||
|
" author = {Stratford, Kevin and Shire, Tom and Hanley, Kevin},\n"
|
||||||
|
" title = {Implementation of multi-level contact detection in LAMMPS},\n"
|
||||||
|
" year = {2018}\n"
|
||||||
|
"}\n\n"
|
||||||
|
"@article{Shire2020,\n"
|
||||||
|
" author = {Shire, Tom and Hanley, Kevin J. and Stratford, Kevin},\n"
|
||||||
|
" title = {DEM simulations of polydisperse media: efficient contact\n"
|
||||||
|
" detection applied to investigate the quasi-static limit},\n"
|
||||||
|
" journal = {Computational Particle Mechanics},\n"
|
||||||
|
" year = {2020}\n"
|
||||||
|
"}\n\n";
|
||||||
|
|
||||||
//#define NEIGH_LIST_DEBUG 1
|
//#define NEIGH_LIST_DEBUG 1
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
@ -168,6 +196,16 @@ pairclass(nullptr), pairnames(nullptr), pairmasks(nullptr)
|
|||||||
nex_mol = maxex_mol = 0;
|
nex_mol = maxex_mol = 0;
|
||||||
ex_mol_group = ex_mol_bit = ex_mol_intra = nullptr;
|
ex_mol_group = ex_mol_bit = ex_mol_intra = nullptr;
|
||||||
|
|
||||||
|
// Multi data
|
||||||
|
|
||||||
|
type2collection = nullptr;
|
||||||
|
collection2cut = nullptr;
|
||||||
|
collection = nullptr;
|
||||||
|
cutcollectionsq = nullptr;
|
||||||
|
custom_collection_flag = 0;
|
||||||
|
interval_collection_flag = 0;
|
||||||
|
nmax_collection = 0;
|
||||||
|
|
||||||
// Kokkos setting
|
// Kokkos setting
|
||||||
|
|
||||||
copymode = 0;
|
copymode = 0;
|
||||||
@ -233,6 +271,11 @@ Neighbor::~Neighbor()
|
|||||||
memory->destroy(ex_mol_group);
|
memory->destroy(ex_mol_group);
|
||||||
delete [] ex_mol_bit;
|
delete [] ex_mol_bit;
|
||||||
memory->destroy(ex_mol_intra);
|
memory->destroy(ex_mol_intra);
|
||||||
|
|
||||||
|
memory->destroy(type2collection);
|
||||||
|
memory->destroy(collection2cut);
|
||||||
|
memory->destroy(collection);
|
||||||
|
memory->destroy(cutcollectionsq);
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ---------------------------------------------------------------------- */
|
/* ---------------------------------------------------------------------- */
|
||||||
@ -316,6 +359,101 @@ void Neighbor::init()
|
|||||||
}
|
}
|
||||||
cutneighmaxsq = cutneighmax * cutneighmax;
|
cutneighmaxsq = cutneighmax * cutneighmax;
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||||||
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|
||||||
|
// Define cutoffs for multi
|
||||||
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if (style == Neighbor::MULTI) {
|
||||||
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int icollection, jcollection;
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||||||
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|
||||||
|
// If collections not yet defined, create default map using types
|
||||||
|
if (not custom_collection_flag) {
|
||||||
|
ncollections = n;
|
||||||
|
interval_collection_flag = 0;
|
||||||
|
if (not type2collection)
|
||||||
|
memory->create(type2collection,n+1,"neigh:type2collection");
|
||||||
|
for (i = 1; i <= n; i++)
|
||||||
|
type2collection[i] = i-1;
|
||||||
|
}
|
||||||
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|
||||||
|
memory->grow(cutcollectionsq, ncollections, ncollections, "neigh:cutcollectionsq");
|
||||||
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|
||||||
|
// 3 possible ways of defining collections
|
||||||
|
// 1) Types are used to define collections
|
||||||
|
// Each collection loops through its owned types, and uses cutneighsq to calculate its cutoff
|
||||||
|
// 2) Collections are defined by intervals, point particles
|
||||||
|
// Types are first sorted into collections based on cutneighsq[i][i]
|
||||||
|
// Each collection loops through its owned types, and uses cutneighsq to calculate its cutoff
|
||||||
|
// 3) Collections are defined by intervals, finite particles
|
||||||
|
//
|
||||||
|
|
||||||
|
// Define collection cutoffs
|
||||||
|
for (i = 0; i < ncollections; i++)
|
||||||
|
for (j = 0; j < ncollections; j++)
|
||||||
|
cutcollectionsq[i][j] = 0.0;
|
||||||
|
|
||||||
|
if (not interval_collection_flag) {
|
||||||
|
finite_cut_flag = 0;
|
||||||
|
for (i = 1; i <= n; i++){
|
||||||
|
icollection = type2collection[i];
|
||||||
|
for (j = 1; j <= n; j++){
|
||||||
|
jcollection = type2collection[j];
|
||||||
|
if (cutneighsq[i][j] > cutcollectionsq[icollection][jcollection]) {
|
||||||
|
cutcollectionsq[icollection][jcollection] = cutneighsq[i][j];
|
||||||
|
cutcollectionsq[jcollection][icollection] = cutneighsq[i][j];
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
if (force->pair->finitecutflag) {
|
||||||
|
finite_cut_flag = 1;
|
||||||
|
// If cutoffs depend on finite atom sizes, use radii of intervals to find cutoffs
|
||||||
|
double ri, rj, tmp;
|
||||||
|
for (i = 0; i < ncollections; i++){
|
||||||
|
ri = collection2cut[i]*0.5;
|
||||||
|
for (j = 0; j < ncollections; j++){
|
||||||
|
rj = collection2cut[j]*0.5;
|
||||||
|
tmp = force->pair->radii2cut(ri, rj) + skin;
|
||||||
|
cutcollectionsq[i][j] = tmp*tmp;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
finite_cut_flag = 0;
|
||||||
|
|
||||||
|
// Map types to collections
|
||||||
|
if (not type2collection)
|
||||||
|
memory->create(type2collection,n+1,"neigh:type2collection");
|
||||||
|
|
||||||
|
for (i = 1; i <= n; i++)
|
||||||
|
type2collection[i] = -1;
|
||||||
|
|
||||||
|
double cuttmp;
|
||||||
|
for (i = 1; i <= n; i++){
|
||||||
|
// Remove skin added to cutneighsq
|
||||||
|
cuttmp = sqrt(cutneighsq[i][i]) - skin;
|
||||||
|
for (icollection = 0; icollection < ncollections; icollection ++){
|
||||||
|
if (collection2cut[icollection] >= cuttmp) {
|
||||||
|
type2collection[i] = icollection;
|
||||||
|
break;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if (type2collection[i] == -1)
|
||||||
|
error->all(FLERR, "Pair cutoff exceeds interval cutoffs for multi");
|
||||||
|
}
|
||||||
|
|
||||||
|
// Define cutoffs
|
||||||
|
for (i = 1; i <= n; i++){
|
||||||
|
icollection = type2collection[i];
|
||||||
|
for (j = 1; j <= n; j++){
|
||||||
|
jcollection = type2collection[j];
|
||||||
|
if (cutneighsq[i][j] > cutcollectionsq[icollection][jcollection]) {
|
||||||
|
cutcollectionsq[icollection][jcollection] = cutneighsq[i][j];
|
||||||
|
cutcollectionsq[jcollection][icollection] = cutneighsq[i][j];
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
// rRESPA cutoffs
|
// rRESPA cutoffs
|
||||||
|
|
||||||
int respa = 0;
|
int respa = 0;
|
||||||
@ -1621,6 +1759,13 @@ int Neighbor::choose_bin(NeighRequest *rq)
|
|||||||
if (!rq->kokkos_device != !(mask & NB_KOKKOS_DEVICE)) continue;
|
if (!rq->kokkos_device != !(mask & NB_KOKKOS_DEVICE)) continue;
|
||||||
if (!rq->kokkos_host != !(mask & NB_KOKKOS_HOST)) continue;
|
if (!rq->kokkos_host != !(mask & NB_KOKKOS_HOST)) continue;
|
||||||
|
|
||||||
|
// multi neighbor style require multi bin style
|
||||||
|
if (style == Neighbor::MULTI) {
|
||||||
|
if (!(mask & NB_MULTI)) continue;
|
||||||
|
} else {
|
||||||
|
if (!(mask & NB_STANDARD)) continue;
|
||||||
|
}
|
||||||
|
|
||||||
return i+1;
|
return i+1;
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -1653,9 +1798,14 @@ int Neighbor::choose_stencil(NeighRequest *rq)
|
|||||||
else if (rq->newton == 1) newtflag = 1;
|
else if (rq->newton == 1) newtflag = 1;
|
||||||
else if (rq->newton == 2) newtflag = 0;
|
else if (rq->newton == 2) newtflag = 0;
|
||||||
|
|
||||||
//printf("STENCIL RQ FLAGS: hff %d %d n %d g %d s %d newtflag %d\n",
|
// request a full stencil if building full neighbor list or newton is off
|
||||||
|
int fullflag = 0;
|
||||||
|
if (rq->full) fullflag = 1;
|
||||||
|
if (!newtflag) fullflag = 1;
|
||||||
|
|
||||||
|
//printf("STENCIL RQ FLAGS: hff %d %d n %d g %d s %d newtflag %d fullflag %d\n",
|
||||||
// rq->half,rq->full,rq->newton,rq->ghost,rq->ssa,
|
// rq->half,rq->full,rq->newton,rq->ghost,rq->ssa,
|
||||||
// newtflag);
|
// newtflag, fullflag);
|
||||||
|
|
||||||
// use request and system settings to match exactly one NStencil class mask
|
// use request and system settings to match exactly one NStencil class mask
|
||||||
// checks are bitwise using NeighConst bit masks
|
// checks are bitwise using NeighConst bit masks
|
||||||
@ -1665,24 +1815,15 @@ int Neighbor::choose_stencil(NeighRequest *rq)
|
|||||||
for (int i = 0; i < nsclass; i++) {
|
for (int i = 0; i < nsclass; i++) {
|
||||||
mask = stencilmasks[i];
|
mask = stencilmasks[i];
|
||||||
|
|
||||||
//printf("III %d: half %d full %d newton %d newtoff %d ghost %d ssa %d\n",
|
//printf("III %d: half %d full %d ghost %d ssa %d\n",
|
||||||
// i,mask & NS_HALF,mask & NS_FULL,mask & NS_NEWTON,
|
// i,mask & NS_HALF,mask & NS_FULL,mask & NS_GHOST,mask & NS_SSA);
|
||||||
// mask & NS_NEWTOFF,mask & NS_GHOST,mask & NS_SSA);
|
|
||||||
|
|
||||||
// exactly one of half or full is set and must match
|
// exactly one of half or full is set and must match
|
||||||
|
|
||||||
if (rq->half) {
|
if (fullflag) {
|
||||||
if (!(mask & NS_HALF)) continue;
|
|
||||||
} else if (rq->full) {
|
|
||||||
if (!(mask & NS_FULL)) continue;
|
if (!(mask & NS_FULL)) continue;
|
||||||
}
|
} else {
|
||||||
|
if (!(mask & NS_HALF)) continue;
|
||||||
// newtflag is on or off and must match
|
|
||||||
|
|
||||||
if (newtflag) {
|
|
||||||
if (!(mask & NS_NEWTON)) continue;
|
|
||||||
} else if (!newtflag) {
|
|
||||||
if (!(mask & NS_NEWTOFF)) continue;
|
|
||||||
}
|
}
|
||||||
|
|
||||||
// require match of these request flags and mask bits
|
// require match of these request flags and mask bits
|
||||||
@ -1691,10 +1832,12 @@ int Neighbor::choose_stencil(NeighRequest *rq)
|
|||||||
if (!rq->ghost != !(mask & NS_GHOST)) continue;
|
if (!rq->ghost != !(mask & NS_GHOST)) continue;
|
||||||
if (!rq->ssa != !(mask & NS_SSA)) continue;
|
if (!rq->ssa != !(mask & NS_SSA)) continue;
|
||||||
|
|
||||||
// neighbor style is BIN or MULTI and must match
|
// neighbor style is one of BIN, MULTI_OLD, or MULTI and must match
|
||||||
|
|
||||||
if (style == Neighbor::BIN) {
|
if (style == Neighbor::BIN) {
|
||||||
if (!(mask & NS_BIN)) continue;
|
if (!(mask & NS_BIN)) continue;
|
||||||
|
} else if (style == Neighbor::MULTI_OLD) {
|
||||||
|
if (!(mask & NS_MULTI_OLD)) continue;
|
||||||
} else if (style == Neighbor::MULTI) {
|
} else if (style == Neighbor::MULTI) {
|
||||||
if (!(mask & NS_MULTI)) continue;
|
if (!(mask & NS_MULTI)) continue;
|
||||||
}
|
}
|
||||||
@ -1826,12 +1969,14 @@ int Neighbor::choose_pair(NeighRequest *rq)
|
|||||||
if (!rq->halffull != !(mask & NP_HALF_FULL)) continue;
|
if (!rq->halffull != !(mask & NP_HALF_FULL)) continue;
|
||||||
if (!rq->off2on != !(mask & NP_OFF2ON)) continue;
|
if (!rq->off2on != !(mask & NP_OFF2ON)) continue;
|
||||||
|
|
||||||
// neighbor style is one of NSQ,BIN,MULTI and must match
|
// neighbor style is one of NSQ, BIN, MULTI_OLD, or MULTI and must match
|
||||||
|
|
||||||
if (style == Neighbor::NSQ) {
|
if (style == Neighbor::NSQ) {
|
||||||
if (!(mask & NP_NSQ)) continue;
|
if (!(mask & NP_NSQ)) continue;
|
||||||
} else if (style == Neighbor::BIN) {
|
} else if (style == Neighbor::BIN) {
|
||||||
if (!(mask & NP_BIN)) continue;
|
if (!(mask & NP_BIN)) continue;
|
||||||
|
} else if (style == Neighbor::MULTI_OLD) {
|
||||||
|
if (!(mask & NP_MULTI_OLD)) continue;
|
||||||
} else if (style == Neighbor::MULTI) {
|
} else if (style == Neighbor::MULTI) {
|
||||||
if (!(mask & NP_MULTI)) continue;
|
if (!(mask & NP_MULTI)) continue;
|
||||||
}
|
}
|
||||||
@ -2030,6 +2175,8 @@ void Neighbor::build(int topoflag)
|
|||||||
|
|
||||||
int nlocal = atom->nlocal;
|
int nlocal = atom->nlocal;
|
||||||
int nall = nlocal + atom->nghost;
|
int nall = nlocal + atom->nghost;
|
||||||
|
// rebuild collection array from scratch
|
||||||
|
if (style == Neighbor::MULTI) build_collection(0);
|
||||||
|
|
||||||
// check that using special bond flags will not overflow neigh lists
|
// check that using special bond flags will not overflow neigh lists
|
||||||
|
|
||||||
@ -2202,9 +2349,13 @@ void Neighbor::set(int narg, char **arg)
|
|||||||
|
|
||||||
if (strcmp(arg[1],"nsq") == 0) style = Neighbor::NSQ;
|
if (strcmp(arg[1],"nsq") == 0) style = Neighbor::NSQ;
|
||||||
else if (strcmp(arg[1],"bin") == 0) style = Neighbor::BIN;
|
else if (strcmp(arg[1],"bin") == 0) style = Neighbor::BIN;
|
||||||
else if (strcmp(arg[1],"multi") == 0) style = Neighbor::MULTI;
|
else if (strcmp(arg[1],"multi") == 0) {
|
||||||
|
style = Neighbor::MULTI;
|
||||||
|
ncollections = atom->ntypes;
|
||||||
|
} else if (strcmp(arg[1],"multi/old") == 0) style = Neighbor::MULTI_OLD;
|
||||||
else error->all(FLERR,"Illegal neighbor command");
|
else error->all(FLERR,"Illegal neighbor command");
|
||||||
|
|
||||||
|
if (style == Neighbor::MULTI_OLD && lmp->citeme) lmp->citeme->add(cite_neigh_multi_old);
|
||||||
if (style == Neighbor::MULTI && lmp->citeme) lmp->citeme->add(cite_neigh_multi);
|
if (style == Neighbor::MULTI && lmp->citeme) lmp->citeme->add(cite_neigh_multi);
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -2351,7 +2502,97 @@ void Neighbor::modify_params(int narg, char **arg)
|
|||||||
iarg += 2;
|
iarg += 2;
|
||||||
|
|
||||||
} else error->all(FLERR,"Illegal neigh_modify command");
|
} else error->all(FLERR,"Illegal neigh_modify command");
|
||||||
|
} else if (strcmp(arg[iarg],"collection/interval") == 0) {
|
||||||
|
if (style != Neighbor::MULTI)
|
||||||
|
error->all(FLERR,"Cannot use collection/interval command without multi setting");
|
||||||
|
|
||||||
|
if (iarg+2 > narg)
|
||||||
|
error->all(FLERR,"Invalid collection/interval command");
|
||||||
|
ncollections = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
|
||||||
|
if (ncollections < 1)
|
||||||
|
error->all(FLERR,"Invalid collection/interval command");
|
||||||
|
if (iarg+1+ncollections > narg)
|
||||||
|
error->all(FLERR,"Invalid collection/interval command");
|
||||||
|
|
||||||
|
int i;
|
||||||
|
|
||||||
|
// Invalidate old user cutoffs
|
||||||
|
comm->ncollections_cutoff = 0;
|
||||||
|
interval_collection_flag = 1;
|
||||||
|
custom_collection_flag = 1;
|
||||||
|
memory->grow(collection2cut,ncollections,"neigh:collection2cut");
|
||||||
|
|
||||||
|
// Set upper cutoff for each collection
|
||||||
|
|
||||||
|
double cut_interval;
|
||||||
|
for (i = 0; i < ncollections; i++){
|
||||||
|
cut_interval = utils::numeric(FLERR,arg[iarg+2+i],false,lmp);
|
||||||
|
collection2cut[i] = cut_interval;
|
||||||
|
|
||||||
|
if (i != 0)
|
||||||
|
if (collection2cut[i-1] >= collection2cut[i])
|
||||||
|
error->all(FLERR,"Nonsequential interval cutoffs in collection/interval setting");
|
||||||
|
}
|
||||||
|
|
||||||
|
iarg += 2 + ncollections;
|
||||||
|
} else if (strcmp(arg[iarg],"collection/type") == 0) {
|
||||||
|
if (style != Neighbor::MULTI)
|
||||||
|
error->all(FLERR,"Cannot use collection/type command without multi setting");
|
||||||
|
|
||||||
|
if (iarg+2 > narg)
|
||||||
|
error->all(FLERR,"Invalid collection/type command");
|
||||||
|
ncollections = utils::inumeric(FLERR,arg[iarg+1],false,lmp);
|
||||||
|
if (ncollections < 1)
|
||||||
|
error->all(FLERR,"Invalid collection/interval command");
|
||||||
|
if (iarg+1+ncollections > narg)
|
||||||
|
error->all(FLERR,"Invalid collection/type command");
|
||||||
|
|
||||||
|
int ntypes = atom->ntypes;
|
||||||
|
int n, nlo, nhi, i, j, k;
|
||||||
|
|
||||||
|
// Invalidate old user cutoffs
|
||||||
|
comm->ncollections_cutoff = 0;
|
||||||
|
interval_collection_flag = 0;
|
||||||
|
custom_collection_flag = 1;
|
||||||
|
if (not type2collection)
|
||||||
|
memory->create(type2collection,ntypes+1,"neigh:type2collection");
|
||||||
|
|
||||||
|
// Erase previous mapping
|
||||||
|
for (i = 1; i <= ntypes; i++)
|
||||||
|
type2collection[i] = -1;
|
||||||
|
|
||||||
|
// For each custom range, define mapping for types in interval
|
||||||
|
int nfield;
|
||||||
|
char *str;
|
||||||
|
for (i = 0; i < ncollections; i++){
|
||||||
|
n = strlen(arg[iarg+2+i]) + 1;
|
||||||
|
str = new char[n];
|
||||||
|
strcpy(str,arg[iarg+2+i]);
|
||||||
|
std::vector<std::string> words = Tokenizer(str, ",").as_vector();
|
||||||
|
nfield = words.size();
|
||||||
|
|
||||||
|
for (j = 0; j < nfield; j++) {
|
||||||
|
const char * field = words[j].c_str();
|
||||||
|
utils::bounds(FLERR,field,1,ntypes,nlo,nhi,error);
|
||||||
|
|
||||||
|
for (k = nlo; k <= nhi; k++) {
|
||||||
|
if (type2collection[k] != -1)
|
||||||
|
error->all(FLERR,"Type specified more than once in collection/type commnd");
|
||||||
|
type2collection[k] = i;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
delete [] str;
|
||||||
|
}
|
||||||
|
|
||||||
|
// Check for undefined atom type
|
||||||
|
for (i = 1; i <= ntypes; i++){
|
||||||
|
if (type2collection[i] == -1) {
|
||||||
|
error->all(FLERR,"Type missing in collection/type commnd");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
iarg += 2 + ncollections;
|
||||||
} else error->all(FLERR,"Illegal neigh_modify command");
|
} else error->all(FLERR,"Illegal neigh_modify command");
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
@ -2406,6 +2647,59 @@ int Neighbor::exclude_setting()
|
|||||||
return exclude;
|
return exclude;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
check if any of the old requested neighbor lists are full
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
int Neighbor::any_full()
|
||||||
|
{
|
||||||
|
int any_full = 0;
|
||||||
|
for (int i = 0; i < old_nrequest; i++) {
|
||||||
|
if (old_requests[i]->full) any_full = 1;
|
||||||
|
}
|
||||||
|
return any_full;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
populate collection array for multi starting at the index istart
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void Neighbor::build_collection(int istart)
|
||||||
|
{
|
||||||
|
if (style != Neighbor::MULTI)
|
||||||
|
error->all(FLERR, "Cannot define atom collections without neighbor style multi");
|
||||||
|
|
||||||
|
int nmax = atom->nlocal+atom->nghost;
|
||||||
|
if (nmax > nmax_collection) {
|
||||||
|
nmax_collection = nmax+DELTA_PERATOM;
|
||||||
|
memory->grow(collection, nmax_collection, "neigh:collection");
|
||||||
|
}
|
||||||
|
|
||||||
|
if (finite_cut_flag) {
|
||||||
|
double cut;
|
||||||
|
int icollection;
|
||||||
|
for (int i = istart; i < nmax; i++){
|
||||||
|
cut = force->pair->atom2cut(i);
|
||||||
|
collection[i] = -1;
|
||||||
|
|
||||||
|
for (icollection = 0; icollection < ncollections; icollection++){
|
||||||
|
if (collection2cut[icollection] >= cut) {
|
||||||
|
collection[i] = icollection;
|
||||||
|
break;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if (collection[i] == -1)
|
||||||
|
error->one(FLERR, "Atom cutoff exceeds interval cutoffs for multi");
|
||||||
|
}
|
||||||
|
} else {
|
||||||
|
int *type = atom->type;
|
||||||
|
for (int i = istart; i < nmax; i++){
|
||||||
|
collection[i] = type2collection[type[i]];
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
return # of bytes of allocated memory
|
return # of bytes of allocated memory
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|||||||
@ -20,8 +20,8 @@ namespace LAMMPS_NS {
|
|||||||
|
|
||||||
class Neighbor : protected Pointers {
|
class Neighbor : protected Pointers {
|
||||||
public:
|
public:
|
||||||
enum{NSQ,BIN,MULTI};
|
enum{NSQ,BIN,MULTI_OLD,MULTI};
|
||||||
int style; // 0,1,2 = nsq, bin, multi
|
int style; // 0,1,2,3 = nsq, bin, multi/old, multi
|
||||||
int every; // build every this many steps
|
int every; // build every this many steps
|
||||||
int delay; // delay build for this many steps
|
int delay; // delay build for this many steps
|
||||||
int dist_check; // 0 = always build, 1 = only if 1/2 dist
|
int dist_check; // 0 = always build, 1 = only if 1/2 dist
|
||||||
@ -102,6 +102,18 @@ class Neighbor : protected Pointers {
|
|||||||
int nimproperlist; // list of impropers to compute
|
int nimproperlist; // list of impropers to compute
|
||||||
int **improperlist;
|
int **improperlist;
|
||||||
|
|
||||||
|
// optional type grouping for multi
|
||||||
|
|
||||||
|
int custom_collection_flag; // 1 if custom collections are defined for multi
|
||||||
|
int interval_collection_flag; // 1 if custom collections use intervals
|
||||||
|
int finite_cut_flag; // 1 if multi considers finite atom size
|
||||||
|
int ncollections; // # of custom collections
|
||||||
|
int nmax_collection; // maximum atoms stored in collection array
|
||||||
|
int *type2collection; // ntype array mapping types to custom collections
|
||||||
|
double *collection2cut; // ncollection array with upper bounds on cutoff intervals
|
||||||
|
double **cutcollectionsq; // cutoffs for each combination of collections
|
||||||
|
int *collection; // local per-atom array to store collection id
|
||||||
|
|
||||||
// public methods
|
// public methods
|
||||||
|
|
||||||
Neighbor(class LAMMPS *);
|
Neighbor(class LAMMPS *);
|
||||||
@ -123,6 +135,8 @@ class Neighbor : protected Pointers {
|
|||||||
void exclusion_group_group_delete(int, int); // rm a group-group exclusion
|
void exclusion_group_group_delete(int, int); // rm a group-group exclusion
|
||||||
int exclude_setting(); // return exclude value to accelerator pkg
|
int exclude_setting(); // return exclude value to accelerator pkg
|
||||||
class NeighRequest *find_request(void *); // find a neighbor request
|
class NeighRequest *find_request(void *); // find a neighbor request
|
||||||
|
int any_full(); // Check if any old requests had full neighbor lists
|
||||||
|
void build_collection(int); // build peratom collection array starting at the given index
|
||||||
|
|
||||||
double memory_usage();
|
double memory_usage();
|
||||||
|
|
||||||
@ -240,7 +254,9 @@ namespace NeighConst {
|
|||||||
NB_INTEL = 1<<0,
|
NB_INTEL = 1<<0,
|
||||||
NB_KOKKOS_DEVICE = 1<<1,
|
NB_KOKKOS_DEVICE = 1<<1,
|
||||||
NB_KOKKOS_HOST = 1<<2,
|
NB_KOKKOS_HOST = 1<<2,
|
||||||
NB_SSA = 1<<3
|
NB_SSA = 1<<3,
|
||||||
|
NB_STANDARD = 1<<4,
|
||||||
|
NB_MULTI = 1<<5
|
||||||
};
|
};
|
||||||
|
|
||||||
enum {
|
enum {
|
||||||
@ -250,12 +266,11 @@ namespace NeighConst {
|
|||||||
NS_FULL = 1<<3,
|
NS_FULL = 1<<3,
|
||||||
NS_2D = 1<<4,
|
NS_2D = 1<<4,
|
||||||
NS_3D = 1<<5,
|
NS_3D = 1<<5,
|
||||||
NS_NEWTON = 1<<6,
|
NS_ORTHO = 1<<6,
|
||||||
NS_NEWTOFF = 1<<7,
|
NS_TRI = 1<<7,
|
||||||
NS_ORTHO = 1<<8,
|
NS_GHOST = 1<<8,
|
||||||
NS_TRI = 1<<9,
|
NS_SSA = 1<<9,
|
||||||
NS_GHOST = 1<<10,
|
NS_MULTI_OLD = 1<<10
|
||||||
NS_SSA = 1<<11
|
|
||||||
};
|
};
|
||||||
|
|
||||||
enum {
|
enum {
|
||||||
@ -283,7 +298,8 @@ namespace NeighConst {
|
|||||||
NP_COPY = 1<<21,
|
NP_COPY = 1<<21,
|
||||||
NP_SKIP = 1<<22,
|
NP_SKIP = 1<<22,
|
||||||
NP_HALF_FULL = 1<<23,
|
NP_HALF_FULL = 1<<23,
|
||||||
NP_OFF2ON = 1<<24
|
NP_OFF2ON = 1<<24,
|
||||||
|
NP_MULTI_OLD = 1<<25
|
||||||
};
|
};
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|||||||
@ -95,6 +95,11 @@ void NPair::copy_neighbor_info()
|
|||||||
|
|
||||||
special_flag = neighbor->special_flag;
|
special_flag = neighbor->special_flag;
|
||||||
|
|
||||||
|
// multi info
|
||||||
|
|
||||||
|
ncollections = neighbor->ncollections;
|
||||||
|
cutcollectionsq = neighbor->cutcollectionsq;
|
||||||
|
|
||||||
// overwrite per-type Neighbor cutoffs with custom value set by requestor
|
// overwrite per-type Neighbor cutoffs with custom value set by requestor
|
||||||
// only works for style = BIN (checked by Neighbor class)
|
// only works for style = BIN (checked by Neighbor class)
|
||||||
|
|
||||||
@ -134,6 +139,23 @@ void NPair::copy_bin_info()
|
|||||||
atom2bin = nb->atom2bin;
|
atom2bin = nb->atom2bin;
|
||||||
bins = nb->bins;
|
bins = nb->bins;
|
||||||
binhead = nb->binhead;
|
binhead = nb->binhead;
|
||||||
|
|
||||||
|
nbinx_multi = nb->nbinx_multi;
|
||||||
|
nbiny_multi = nb->nbiny_multi;
|
||||||
|
nbinz_multi = nb->nbinz_multi;
|
||||||
|
mbins_multi = nb->mbins_multi;
|
||||||
|
mbinx_multi = nb->mbinx_multi;
|
||||||
|
mbiny_multi = nb->mbiny_multi;
|
||||||
|
mbinz_multi = nb->mbinz_multi;
|
||||||
|
mbinxlo_multi = nb->mbinxlo_multi;
|
||||||
|
mbinylo_multi = nb->mbinylo_multi;
|
||||||
|
mbinzlo_multi = nb->mbinzlo_multi;
|
||||||
|
|
||||||
|
bininvx_multi = nb->bininvx_multi;
|
||||||
|
bininvy_multi = nb->bininvy_multi;
|
||||||
|
bininvz_multi = nb->bininvz_multi;
|
||||||
|
|
||||||
|
binhead_multi = nb->binhead_multi;
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
@ -145,9 +167,12 @@ void NPair::copy_stencil_info()
|
|||||||
nstencil = ns->nstencil;
|
nstencil = ns->nstencil;
|
||||||
stencil = ns->stencil;
|
stencil = ns->stencil;
|
||||||
stencilxyz = ns->stencilxyz;
|
stencilxyz = ns->stencilxyz;
|
||||||
|
nstencil_multi_old = ns->nstencil_multi_old;
|
||||||
|
stencil_multi_old = ns->stencil_multi_old;
|
||||||
|
distsq_multi_old = ns->distsq_multi_old;
|
||||||
|
|
||||||
nstencil_multi = ns->nstencil_multi;
|
nstencil_multi = ns->nstencil_multi;
|
||||||
stencil_multi = ns->stencil_multi;
|
stencil_multi = ns->stencil_multi;
|
||||||
distsq_multi = ns->distsq_multi;
|
|
||||||
}
|
}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
@ -160,7 +185,6 @@ void NPair::build_setup()
|
|||||||
if (ns) copy_stencil_info();
|
if (ns) copy_stencil_info();
|
||||||
|
|
||||||
// set here, since build_setup() always called before build()
|
// set here, since build_setup() always called before build()
|
||||||
|
|
||||||
last_build = update->ntimestep;
|
last_build = update->ntimestep;
|
||||||
}
|
}
|
||||||
|
|
||||||
@ -241,3 +265,46 @@ int NPair::coord2bin(double *x, int &ix, int &iy, int &iz)
|
|||||||
return iz*mbiny*mbinx + iy*mbinx + ix;
|
return iz*mbiny*mbinx + iy*mbinx + ix;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
multi version of coord2bin for a given collection
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
int NPair::coord2bin(double *x, int ic)
|
||||||
|
{
|
||||||
|
int ix,iy,iz;
|
||||||
|
int ibin;
|
||||||
|
|
||||||
|
if (!std::isfinite(x[0]) || !std::isfinite(x[1]) || !std::isfinite(x[2]))
|
||||||
|
error->one(FLERR,"Non-numeric positions - simulation unstable");
|
||||||
|
|
||||||
|
if (x[0] >= bboxhi[0])
|
||||||
|
ix = static_cast<int> ((x[0]-bboxhi[0])*bininvx_multi[ic]) + nbinx_multi[ic];
|
||||||
|
else if (x[0] >= bboxlo[0]) {
|
||||||
|
ix = static_cast<int> ((x[0]-bboxlo[0])*bininvx_multi[ic]);
|
||||||
|
ix = MIN(ix,nbinx_multi[ic]-1);
|
||||||
|
} else
|
||||||
|
ix = static_cast<int> ((x[0]-bboxlo[0])*bininvx_multi[ic]) - 1;
|
||||||
|
|
||||||
|
if (x[1] >= bboxhi[1])
|
||||||
|
iy = static_cast<int> ((x[1]-bboxhi[1])*bininvy_multi[ic]) + nbiny_multi[ic];
|
||||||
|
else if (x[1] >= bboxlo[1]) {
|
||||||
|
iy = static_cast<int> ((x[1]-bboxlo[1])*bininvy_multi[ic]);
|
||||||
|
iy = MIN(iy,nbiny_multi[ic]-1);
|
||||||
|
} else
|
||||||
|
iy = static_cast<int> ((x[1]-bboxlo[1])*bininvy_multi[ic]) - 1;
|
||||||
|
|
||||||
|
if (x[2] >= bboxhi[2])
|
||||||
|
iz = static_cast<int> ((x[2]-bboxhi[2])*bininvz_multi[ic]) + nbinz_multi[ic];
|
||||||
|
else if (x[2] >= bboxlo[2]) {
|
||||||
|
iz = static_cast<int> ((x[2]-bboxlo[2])*bininvz_multi[ic]);
|
||||||
|
iz = MIN(iz,nbinz_multi[ic]-1);
|
||||||
|
} else
|
||||||
|
iz = static_cast<int> ((x[2]-bboxlo[2])*bininvz_multi[ic]) - 1;
|
||||||
|
|
||||||
|
ix -= mbinxlo_multi[ic];
|
||||||
|
iy -= mbinylo_multi[ic];
|
||||||
|
iz -= mbinzlo_multi[ic];
|
||||||
|
ibin = iz*mbiny_multi[ic]*mbinx_multi[ic] + iy*mbinx_multi[ic] + ix;
|
||||||
|
return ibin;
|
||||||
|
}
|
||||||
|
|||||||
21
src/npair.h
21
src/npair.h
@ -48,6 +48,8 @@ class NPair : protected Pointers {
|
|||||||
double cut_middle_sq;
|
double cut_middle_sq;
|
||||||
double cut_middle_inside_sq;
|
double cut_middle_inside_sq;
|
||||||
double *bboxlo,*bboxhi;
|
double *bboxlo,*bboxhi;
|
||||||
|
int ncollections;
|
||||||
|
double **cutcollectionsq;
|
||||||
|
|
||||||
// exclusion data from Neighbor class
|
// exclusion data from Neighbor class
|
||||||
|
|
||||||
@ -79,14 +81,24 @@ class NPair : protected Pointers {
|
|||||||
int *atom2bin,*bins;
|
int *atom2bin,*bins;
|
||||||
int *binhead;
|
int *binhead;
|
||||||
|
|
||||||
|
int *nbinx_multi, *nbiny_multi, *nbinz_multi;
|
||||||
|
int *mbins_multi;
|
||||||
|
int *mbinx_multi, *mbiny_multi, *mbinz_multi;
|
||||||
|
int *mbinxlo_multi, *mbinylo_multi, *mbinzlo_multi;
|
||||||
|
double *bininvx_multi, *bininvy_multi, *bininvz_multi;
|
||||||
|
int **binhead_multi;
|
||||||
|
|
||||||
// data from NStencil class
|
// data from NStencil class
|
||||||
|
|
||||||
int nstencil;
|
int nstencil;
|
||||||
int *stencil;
|
int *stencil;
|
||||||
int **stencilxyz;
|
int **stencilxyz;
|
||||||
int *nstencil_multi;
|
int *nstencil_multi_old;
|
||||||
int **stencil_multi;
|
int **stencil_multi_old;
|
||||||
double **distsq_multi;
|
double **distsq_multi_old;
|
||||||
|
|
||||||
|
int ** nstencil_multi;
|
||||||
|
int *** stencil_multi;
|
||||||
|
|
||||||
// data common to all NPair variants
|
// data common to all NPair variants
|
||||||
|
|
||||||
@ -102,6 +114,9 @@ class NPair : protected Pointers {
|
|||||||
int coord2bin(double *); // mapping atom coord to a bin
|
int coord2bin(double *); // mapping atom coord to a bin
|
||||||
int coord2bin(double *, int &, int &, int&); // ditto
|
int coord2bin(double *, int &, int &, int&); // ditto
|
||||||
|
|
||||||
|
int coord2bin(double *, int); // mapping atom coord to group bin
|
||||||
|
|
||||||
|
|
||||||
// find_special: determine if atom j is in special list of atom i
|
// find_special: determine if atom j is in special list of atom i
|
||||||
// if it is not, return 0
|
// if it is not, return 0
|
||||||
// if it is and special flag is 0 (both coeffs are 0.0), return -1
|
// if it is and special flag is 0 (both coeffs are 0.0), return -1
|
||||||
|
|||||||
@ -12,13 +12,15 @@
|
|||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
#include "npair_full_multi.h"
|
#include "npair_full_multi.h"
|
||||||
#include "neigh_list.h"
|
|
||||||
#include "atom.h"
|
#include "atom.h"
|
||||||
#include "atom_vec.h"
|
#include "atom_vec.h"
|
||||||
#include "molecule.h"
|
|
||||||
#include "domain.h"
|
#include "domain.h"
|
||||||
#include "my_page.h"
|
|
||||||
#include "error.h"
|
#include "error.h"
|
||||||
|
#include "molecule.h"
|
||||||
|
#include "my_page.h"
|
||||||
|
#include "neighbor.h"
|
||||||
|
#include "neigh_list.h"
|
||||||
|
|
||||||
using namespace LAMMPS_NS;
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
@ -28,18 +30,19 @@ NPairFullMulti::NPairFullMulti(LAMMPS *lmp) : NPair(lmp) {}
|
|||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
binned neighbor list construction for all neighbors
|
binned neighbor list construction for all neighbors
|
||||||
multi-type stencil is itype dependent and is distance checked
|
multi stencil is icollection-jcollection dependent
|
||||||
every neighbor pair appears in list of both atoms i and j
|
every neighbor pair appears in list of both atoms i and j
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
void NPairFullMulti::build(NeighList *list)
|
void NPairFullMulti::build(NeighList *list)
|
||||||
{
|
{
|
||||||
int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate;
|
int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,which,ns,imol,iatom,moltemplate;
|
||||||
tagint tagprev;
|
tagint tagprev;
|
||||||
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
||||||
int *neighptr,*s;
|
int *neighptr,*s;
|
||||||
double *cutsq,*distsq;
|
int js;
|
||||||
|
|
||||||
|
int *collection = neighbor->collection;
|
||||||
double **x = atom->x;
|
double **x = atom->x;
|
||||||
int *type = atom->type;
|
int *type = atom->type;
|
||||||
int *mask = atom->mask;
|
int *mask = atom->mask;
|
||||||
@ -67,8 +70,8 @@ void NPairFullMulti::build(NeighList *list)
|
|||||||
for (i = 0; i < nlocal; i++) {
|
for (i = 0; i < nlocal; i++) {
|
||||||
n = 0;
|
n = 0;
|
||||||
neighptr = ipage->vget();
|
neighptr = ipage->vget();
|
||||||
|
|
||||||
itype = type[i];
|
itype = type[i];
|
||||||
|
icollection = collection[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];
|
||||||
@ -78,43 +81,51 @@ void NPairFullMulti::build(NeighList *list)
|
|||||||
tagprev = tag[i] - iatom - 1;
|
tagprev = tag[i] - iatom - 1;
|
||||||
}
|
}
|
||||||
|
|
||||||
// loop over all atoms in other bins in stencil, including self
|
|
||||||
// skip if i,j neighbor cutoff is less than bin distance
|
|
||||||
// skip i = j
|
|
||||||
|
|
||||||
ibin = atom2bin[i];
|
ibin = atom2bin[i];
|
||||||
s = stencil_multi[itype];
|
|
||||||
distsq = distsq_multi[itype];
|
|
||||||
cutsq = cutneighsq[itype];
|
|
||||||
ns = nstencil_multi[itype];
|
|
||||||
for (k = 0; k < ns; k++) {
|
|
||||||
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
|
|
||||||
jtype = type[j];
|
|
||||||
if (cutsq[jtype] < distsq[k]) continue;
|
|
||||||
if (i == j) continue;
|
|
||||||
|
|
||||||
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
// loop through stencils for all collections
|
||||||
|
for (jcollection = 0; jcollection < ncollections; jcollection++) {
|
||||||
|
|
||||||
delx = xtmp - x[j][0];
|
// if same collection use own bin
|
||||||
dely = ytmp - x[j][1];
|
if(icollection == jcollection) jbin = ibin;
|
||||||
delz = ztmp - x[j][2];
|
else jbin = coord2bin(x[i], jcollection);
|
||||||
rsq = delx*delx + dely*dely + delz*delz;
|
|
||||||
|
|
||||||
if (rsq <= cutneighsq[itype][jtype]) {
|
// loop over all atoms in surrounding bins in stencil including self
|
||||||
if (molecular != Atom::ATOMIC) {
|
// skip i = j
|
||||||
if (!moltemplate)
|
// use full stencil for all collection combinations
|
||||||
which = find_special(special[i],nspecial[i],tag[j]);
|
|
||||||
else if (imol >= 0)
|
s = stencil_multi[icollection][jcollection];
|
||||||
which = find_special(onemols[imol]->special[iatom],
|
ns = nstencil_multi[icollection][jcollection];
|
||||||
onemols[imol]->nspecial[iatom],
|
|
||||||
tag[j]-tagprev);
|
for (k = 0; k < ns; k++) {
|
||||||
else which = 0;
|
js = binhead_multi[jcollection][jbin + s[k]];
|
||||||
if (which == 0) neighptr[n++] = j;
|
for (j = js; j >= 0; j = bins[j]) {
|
||||||
else if (domain->minimum_image_check(delx,dely,delz))
|
if (i == j) continue;
|
||||||
neighptr[n++] = j;
|
|
||||||
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
|
jtype = type[j];
|
||||||
} else neighptr[n++] = j;
|
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
||||||
}
|
|
||||||
|
delx = xtmp - x[j][0];
|
||||||
|
dely = ytmp - x[j][1];
|
||||||
|
delz = ztmp - x[j][2];
|
||||||
|
rsq = delx*delx + dely*dely + delz*delz;
|
||||||
|
|
||||||
|
if (rsq <= cutneighsq[itype][jtype]) {
|
||||||
|
if (molecular != Atom::ATOMIC) {
|
||||||
|
if (!moltemplate)
|
||||||
|
which = find_special(special[i],nspecial[i],tag[j]);
|
||||||
|
else if (imol >= 0)
|
||||||
|
which = find_special(onemols[imol]->special[iatom],
|
||||||
|
onemols[imol]->nspecial[iatom],
|
||||||
|
tag[j]-tagprev);
|
||||||
|
else which = 0;
|
||||||
|
if (which == 0) neighptr[n++] = j;
|
||||||
|
else if (domain->minimum_image_check(delx,dely,delz))
|
||||||
|
neighptr[n++] = j;
|
||||||
|
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
|
||||||
|
} else neighptr[n++] = j;
|
||||||
|
}
|
||||||
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|||||||
132
src/npair_full_multi_old.cpp
Normal file
132
src/npair_full_multi_old.cpp
Normal file
@ -0,0 +1,132 @@
|
|||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
https://lammps.sandia.gov/, 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 "npair_full_multi_old.h"
|
||||||
|
|
||||||
|
#include "atom.h"
|
||||||
|
#include "atom_vec.h"
|
||||||
|
#include "domain.h"
|
||||||
|
#include "error.h"
|
||||||
|
#include "molecule.h"
|
||||||
|
#include "my_page.h"
|
||||||
|
#include "neigh_list.h"
|
||||||
|
|
||||||
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
NPairFullMultiOld::NPairFullMultiOld(LAMMPS *lmp) : NPair(lmp) {}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
binned neighbor list construction for all neighbors
|
||||||
|
multi-type stencil is itype dependent and is distance checked
|
||||||
|
every neighbor pair appears in list of both atoms i and j
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void NPairFullMultiOld::build(NeighList *list)
|
||||||
|
{
|
||||||
|
int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate;
|
||||||
|
tagint tagprev;
|
||||||
|
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
||||||
|
int *neighptr,*s;
|
||||||
|
double *cutsq,*distsq;
|
||||||
|
|
||||||
|
double **x = atom->x;
|
||||||
|
int *type = atom->type;
|
||||||
|
int *mask = atom->mask;
|
||||||
|
tagint *tag = atom->tag;
|
||||||
|
tagint *molecule = atom->molecule;
|
||||||
|
tagint **special = atom->special;
|
||||||
|
int **nspecial = atom->nspecial;
|
||||||
|
int nlocal = atom->nlocal;
|
||||||
|
if (includegroup) nlocal = atom->nfirst;
|
||||||
|
|
||||||
|
int *molindex = atom->molindex;
|
||||||
|
int *molatom = atom->molatom;
|
||||||
|
Molecule **onemols = atom->avec->onemols;
|
||||||
|
if (molecular == Atom::TEMPLATE) moltemplate = 1;
|
||||||
|
else moltemplate = 0;
|
||||||
|
|
||||||
|
int *ilist = list->ilist;
|
||||||
|
int *numneigh = list->numneigh;
|
||||||
|
int **firstneigh = list->firstneigh;
|
||||||
|
MyPage<int> *ipage = list->ipage;
|
||||||
|
|
||||||
|
int inum = 0;
|
||||||
|
ipage->reset();
|
||||||
|
|
||||||
|
for (i = 0; i < nlocal; i++) {
|
||||||
|
n = 0;
|
||||||
|
neighptr = ipage->vget();
|
||||||
|
|
||||||
|
itype = type[i];
|
||||||
|
xtmp = x[i][0];
|
||||||
|
ytmp = x[i][1];
|
||||||
|
ztmp = x[i][2];
|
||||||
|
if (moltemplate) {
|
||||||
|
imol = molindex[i];
|
||||||
|
iatom = molatom[i];
|
||||||
|
tagprev = tag[i] - iatom - 1;
|
||||||
|
}
|
||||||
|
|
||||||
|
// loop over all atoms in other bins in stencil, including self
|
||||||
|
// skip if i,j neighbor cutoff is less than bin distance
|
||||||
|
// skip i = j
|
||||||
|
|
||||||
|
ibin = atom2bin[i];
|
||||||
|
s = stencil_multi_old[itype];
|
||||||
|
distsq = distsq_multi_old[itype];
|
||||||
|
cutsq = cutneighsq[itype];
|
||||||
|
ns = nstencil_multi_old[itype];
|
||||||
|
for (k = 0; k < ns; k++) {
|
||||||
|
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
|
||||||
|
jtype = type[j];
|
||||||
|
if (cutsq[jtype] < distsq[k]) continue;
|
||||||
|
if (i == j) continue;
|
||||||
|
|
||||||
|
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
||||||
|
|
||||||
|
delx = xtmp - x[j][0];
|
||||||
|
dely = ytmp - x[j][1];
|
||||||
|
delz = ztmp - x[j][2];
|
||||||
|
rsq = delx*delx + dely*dely + delz*delz;
|
||||||
|
|
||||||
|
if (rsq <= cutneighsq[itype][jtype]) {
|
||||||
|
if (molecular != Atom::ATOMIC) {
|
||||||
|
if (!moltemplate)
|
||||||
|
which = find_special(special[i],nspecial[i],tag[j]);
|
||||||
|
else if (imol >= 0)
|
||||||
|
which = find_special(onemols[imol]->special[iatom],
|
||||||
|
onemols[imol]->nspecial[iatom],
|
||||||
|
tag[j]-tagprev);
|
||||||
|
else which = 0;
|
||||||
|
if (which == 0) neighptr[n++] = j;
|
||||||
|
else if (domain->minimum_image_check(delx,dely,delz))
|
||||||
|
neighptr[n++] = j;
|
||||||
|
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
|
||||||
|
} else neighptr[n++] = j;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
ilist[inum++] = i;
|
||||||
|
firstneigh[i] = neighptr;
|
||||||
|
numneigh[i] = n;
|
||||||
|
ipage->vgot(n);
|
||||||
|
if (ipage->status())
|
||||||
|
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
|
||||||
|
}
|
||||||
|
|
||||||
|
list->inum = inum;
|
||||||
|
list->gnum = 0;
|
||||||
|
}
|
||||||
@ -11,26 +11,26 @@
|
|||||||
See the README file in the top-level LAMMPS directory.
|
See the README file in the top-level LAMMPS directory.
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
#ifdef NSTENCIL_CLASS
|
#ifdef NPAIR_CLASS
|
||||||
|
|
||||||
NStencilStyle(half/bin/3d/newtoff,
|
NPairStyle(full/multi/old,
|
||||||
NStencilHalfBin3dNewtoff,
|
NPairFullMultiOld,
|
||||||
NS_HALF | NS_BIN | NS_3D | NS_NEWTOFF | NS_ORTHO | NS_TRI)
|
NP_FULL | NP_MULTI_OLD | NP_NEWTON | NP_NEWTOFF | NP_ORTHO | NP_TRI)
|
||||||
|
|
||||||
#else
|
#else
|
||||||
|
|
||||||
#ifndef LMP_NSTENCIL_HALF_BIN_3D_NEWTOFF_H
|
#ifndef LMP_NPAIR_FULL_MULTI_OLD_H
|
||||||
#define LMP_NSTENCIL_HALF_BIN_3D_NEWTOFF_H
|
#define LMP_NPAIR_FULL_MULTI_OLD_H
|
||||||
|
|
||||||
#include "nstencil.h"
|
#include "npair.h"
|
||||||
|
|
||||||
namespace LAMMPS_NS {
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
class NStencilHalfBin3dNewtoff : public NStencil {
|
class NPairFullMultiOld : public NPair {
|
||||||
public:
|
public:
|
||||||
NStencilHalfBin3dNewtoff(class LAMMPS *);
|
NPairFullMultiOld(class LAMMPS *);
|
||||||
~NStencilHalfBin3dNewtoff() {}
|
~NPairFullMultiOld() {}
|
||||||
void create();
|
void build(class NeighList *);
|
||||||
};
|
};
|
||||||
|
|
||||||
}
|
}
|
||||||
@ -40,4 +40,8 @@ class NStencilHalfBin3dNewtoff : public NStencil {
|
|||||||
|
|
||||||
/* ERROR/WARNING messages:
|
/* ERROR/WARNING messages:
|
||||||
|
|
||||||
|
E: Neighbor list overflow, boost neigh_modify one
|
||||||
|
|
||||||
|
UNDOCUMENTED
|
||||||
|
|
||||||
*/
|
*/
|
||||||
@ -12,13 +12,15 @@
|
|||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
#include "npair_half_multi_newtoff.h"
|
#include "npair_half_multi_newtoff.h"
|
||||||
#include "neigh_list.h"
|
|
||||||
#include "atom.h"
|
#include "atom.h"
|
||||||
#include "atom_vec.h"
|
#include "atom_vec.h"
|
||||||
#include "molecule.h"
|
|
||||||
#include "domain.h"
|
#include "domain.h"
|
||||||
#include "my_page.h"
|
|
||||||
#include "error.h"
|
#include "error.h"
|
||||||
|
#include "molecule.h"
|
||||||
|
#include "my_page.h"
|
||||||
|
#include "neighbor.h"
|
||||||
|
#include "neigh_list.h"
|
||||||
|
|
||||||
using namespace LAMMPS_NS;
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
@ -28,20 +30,21 @@ NPairHalfMultiNewtoff::NPairHalfMultiNewtoff(LAMMPS *lmp) : NPair(lmp) {}
|
|||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
binned neighbor list construction with partial Newton's 3rd law
|
binned neighbor list construction with partial Newton's 3rd law
|
||||||
|
multi stencil is icollection-jcollection dependent
|
||||||
each owned atom i checks own bin and other bins in stencil
|
each owned atom i checks own bin and other bins in stencil
|
||||||
multi-type stencil is itype dependent and is distance checked
|
|
||||||
pair stored once if i,j are both owned and i < j
|
pair stored once if i,j are both owned and i < j
|
||||||
pair stored by me if j is ghost (also stored by proc owning j)
|
pair stored by me if j is ghost (also stored by proc owning j)
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
void NPairHalfMultiNewtoff::build(NeighList *list)
|
void NPairHalfMultiNewtoff::build(NeighList *list)
|
||||||
{
|
{
|
||||||
int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate;
|
int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,which,ns,imol,iatom,moltemplate;
|
||||||
tagint tagprev;
|
tagint tagprev;
|
||||||
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
||||||
int *neighptr,*s;
|
int *neighptr,*s;
|
||||||
double *cutsq,*distsq;
|
int js;
|
||||||
|
|
||||||
|
int *collection = neighbor->collection;
|
||||||
double **x = atom->x;
|
double **x = atom->x;
|
||||||
int *type = atom->type;
|
int *type = atom->type;
|
||||||
int *mask = atom->mask;
|
int *mask = atom->mask;
|
||||||
@ -69,8 +72,8 @@ void NPairHalfMultiNewtoff::build(NeighList *list)
|
|||||||
for (i = 0; i < nlocal; i++) {
|
for (i = 0; i < nlocal; i++) {
|
||||||
n = 0;
|
n = 0;
|
||||||
neighptr = ipage->vget();
|
neighptr = ipage->vget();
|
||||||
|
|
||||||
itype = type[i];
|
itype = type[i];
|
||||||
|
icollection = collection[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];
|
||||||
@ -80,44 +83,52 @@ void NPairHalfMultiNewtoff::build(NeighList *list)
|
|||||||
tagprev = tag[i] - iatom - 1;
|
tagprev = tag[i] - iatom - 1;
|
||||||
}
|
}
|
||||||
|
|
||||||
// loop over all atoms in other bins in stencil including self
|
|
||||||
// only store pair if i < j
|
|
||||||
// skip if i,j neighbor cutoff is less than bin distance
|
|
||||||
// stores own/own pairs only once
|
|
||||||
// stores own/ghost pairs on both procs
|
|
||||||
|
|
||||||
ibin = atom2bin[i];
|
ibin = atom2bin[i];
|
||||||
s = stencil_multi[itype];
|
|
||||||
distsq = distsq_multi[itype];
|
|
||||||
cutsq = cutneighsq[itype];
|
|
||||||
ns = nstencil_multi[itype];
|
|
||||||
for (k = 0; k < ns; k++) {
|
|
||||||
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
|
|
||||||
if (j <= i) continue;
|
|
||||||
jtype = type[j];
|
|
||||||
if (cutsq[jtype] < distsq[k]) continue;
|
|
||||||
|
|
||||||
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
// loop through stencils for all collections
|
||||||
|
for (jcollection = 0; jcollection < ncollections; jcollection++) {
|
||||||
|
|
||||||
delx = xtmp - x[j][0];
|
// if same collection use own bin
|
||||||
dely = ytmp - x[j][1];
|
if (icollection == jcollection) jbin = ibin;
|
||||||
delz = ztmp - x[j][2];
|
else jbin = coord2bin(x[i], jcollection);
|
||||||
rsq = delx*delx + dely*dely + delz*delz;
|
|
||||||
|
|
||||||
if (rsq <= cutneighsq[itype][jtype]) {
|
// loop over all atoms in other bins in stencil including self
|
||||||
if (molecular != Atom::ATOMIC) {
|
// only store pair if i < j
|
||||||
if (!moltemplate)
|
// stores own/own pairs only once
|
||||||
which = find_special(special[i],nspecial[i],tag[j]);
|
// stores own/ghost pairs on both procs
|
||||||
else if (imol >= 0)
|
// use full stencil for all collection combinations
|
||||||
which = find_special(onemols[imol]->special[iatom],
|
|
||||||
onemols[imol]->nspecial[iatom],
|
s = stencil_multi[icollection][jcollection];
|
||||||
tag[j]-tagprev);
|
ns = nstencil_multi[icollection][jcollection];
|
||||||
else which = 0;
|
|
||||||
if (which == 0) neighptr[n++] = j;
|
for (k = 0; k < ns; k++) {
|
||||||
else if (domain->minimum_image_check(delx,dely,delz))
|
js = binhead_multi[jcollection][jbin + s[k]];
|
||||||
neighptr[n++] = j;
|
for (j = js; j >= 0; j = bins[j]) {
|
||||||
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
|
if (j <= i) continue;
|
||||||
} else neighptr[n++] = j;
|
|
||||||
|
jtype = type[j];
|
||||||
|
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
||||||
|
|
||||||
|
delx = xtmp - x[j][0];
|
||||||
|
dely = ytmp - x[j][1];
|
||||||
|
delz = ztmp - x[j][2];
|
||||||
|
rsq = delx*delx + dely*dely + delz*delz;
|
||||||
|
|
||||||
|
if (rsq <= cutneighsq[itype][jtype]) {
|
||||||
|
if (molecular != Atom::ATOMIC) {
|
||||||
|
if (!moltemplate)
|
||||||
|
which = find_special(special[i],nspecial[i],tag[j]);
|
||||||
|
else if (imol >= 0)
|
||||||
|
which = find_special(onemols[imol]->special[iatom],
|
||||||
|
onemols[imol]->nspecial[iatom],
|
||||||
|
tag[j]-tagprev);
|
||||||
|
else which = 0;
|
||||||
|
if (which == 0) neighptr[n++] = j;
|
||||||
|
else if (domain->minimum_image_check(delx,dely,delz))
|
||||||
|
neighptr[n++] = j;
|
||||||
|
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
|
||||||
|
} else neighptr[n++] = j;
|
||||||
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|||||||
@ -12,13 +12,15 @@
|
|||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
#include "npair_half_multi_newton.h"
|
#include "npair_half_multi_newton.h"
|
||||||
#include "neigh_list.h"
|
|
||||||
#include "atom.h"
|
#include "atom.h"
|
||||||
#include "atom_vec.h"
|
#include "atom_vec.h"
|
||||||
#include "molecule.h"
|
|
||||||
#include "domain.h"
|
#include "domain.h"
|
||||||
#include "my_page.h"
|
|
||||||
#include "error.h"
|
#include "error.h"
|
||||||
|
#include "molecule.h"
|
||||||
|
#include "my_page.h"
|
||||||
|
#include "neighbor.h"
|
||||||
|
#include "neigh_list.h"
|
||||||
|
|
||||||
using namespace LAMMPS_NS;
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
@ -28,19 +30,20 @@ NPairHalfMultiNewton::NPairHalfMultiNewton(LAMMPS *lmp) : NPair(lmp) {}
|
|||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
binned neighbor list construction with full Newton's 3rd law
|
binned neighbor list construction with full Newton's 3rd law
|
||||||
|
multi stencil is icollection-jcollection dependent
|
||||||
each owned atom i checks its own bin and other bins in Newton stencil
|
each owned atom i checks its own bin and other bins in Newton stencil
|
||||||
multi-type stencil is itype dependent and is distance checked
|
|
||||||
every pair stored exactly once by some processor
|
every pair stored exactly once by some processor
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
void NPairHalfMultiNewton::build(NeighList *list)
|
void NPairHalfMultiNewton::build(NeighList *list)
|
||||||
{
|
{
|
||||||
int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate;
|
int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,which,ns,imol,iatom,moltemplate;
|
||||||
tagint tagprev;
|
tagint tagprev;
|
||||||
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
||||||
int *neighptr,*s;
|
int *neighptr,*s;
|
||||||
double *cutsq,*distsq;
|
int js;
|
||||||
|
|
||||||
|
int *collection = neighbor->collection;
|
||||||
double **x = atom->x;
|
double **x = atom->x;
|
||||||
int *type = atom->type;
|
int *type = atom->type;
|
||||||
int *mask = atom->mask;
|
int *mask = atom->mask;
|
||||||
@ -54,7 +57,7 @@ void NPairHalfMultiNewton::build(NeighList *list)
|
|||||||
int *molindex = atom->molindex;
|
int *molindex = atom->molindex;
|
||||||
int *molatom = atom->molatom;
|
int *molatom = atom->molatom;
|
||||||
Molecule **onemols = atom->avec->onemols;
|
Molecule **onemols = atom->avec->onemols;
|
||||||
if (molecular == Atom::TEMPLATE) moltemplate = 1;
|
if (molecular == 2) moltemplate = 1;
|
||||||
else moltemplate = 0;
|
else moltemplate = 0;
|
||||||
|
|
||||||
int *ilist = list->ilist;
|
int *ilist = list->ilist;
|
||||||
@ -68,8 +71,8 @@ void NPairHalfMultiNewton::build(NeighList *list)
|
|||||||
for (i = 0; i < nlocal; i++) {
|
for (i = 0; i < nlocal; i++) {
|
||||||
n = 0;
|
n = 0;
|
||||||
neighptr = ipage->vget();
|
neighptr = ipage->vget();
|
||||||
|
|
||||||
itype = type[i];
|
itype = type[i];
|
||||||
|
icollection = collection[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];
|
||||||
@ -79,80 +82,103 @@ void NPairHalfMultiNewton::build(NeighList *list)
|
|||||||
tagprev = tag[i] - iatom - 1;
|
tagprev = tag[i] - iatom - 1;
|
||||||
}
|
}
|
||||||
|
|
||||||
// loop over rest of atoms in i's bin, ghosts are at end of linked list
|
|
||||||
// if j is owned atom, store it, since j is beyond i in linked list
|
|
||||||
// if j is ghost, only store if j coords are "above and to the right" of i
|
|
||||||
|
|
||||||
for (j = bins[i]; j >= 0; j = bins[j]) {
|
|
||||||
if (j >= nlocal) {
|
|
||||||
if (x[j][2] < ztmp) continue;
|
|
||||||
if (x[j][2] == ztmp) {
|
|
||||||
if (x[j][1] < ytmp) continue;
|
|
||||||
if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
jtype = type[j];
|
|
||||||
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
|
||||||
|
|
||||||
delx = xtmp - x[j][0];
|
|
||||||
dely = ytmp - x[j][1];
|
|
||||||
delz = ztmp - x[j][2];
|
|
||||||
rsq = delx*delx + dely*dely + delz*delz;
|
|
||||||
|
|
||||||
if (rsq <= cutneighsq[itype][jtype]) {
|
|
||||||
if (molecular != Atom::ATOMIC) {
|
|
||||||
if (!moltemplate)
|
|
||||||
which = find_special(special[i],nspecial[i],tag[j]);
|
|
||||||
else if (imol >= 0)
|
|
||||||
which = find_special(onemols[imol]->special[iatom],
|
|
||||||
onemols[imol]->nspecial[iatom],
|
|
||||||
tag[j]-tagprev);
|
|
||||||
else which = 0;
|
|
||||||
if (which == 0) neighptr[n++] = j;
|
|
||||||
else if (domain->minimum_image_check(delx,dely,delz))
|
|
||||||
neighptr[n++] = j;
|
|
||||||
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
|
|
||||||
} else neighptr[n++] = j;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
// loop over all atoms in other bins in stencil, store every pair
|
|
||||||
// skip if i,j neighbor cutoff is less than bin distance
|
|
||||||
|
|
||||||
ibin = atom2bin[i];
|
ibin = atom2bin[i];
|
||||||
s = stencil_multi[itype];
|
|
||||||
distsq = distsq_multi[itype];
|
|
||||||
cutsq = cutneighsq[itype];
|
|
||||||
ns = nstencil_multi[itype];
|
|
||||||
for (k = 0; k < ns; k++) {
|
|
||||||
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
|
|
||||||
jtype = type[j];
|
|
||||||
if (cutsq[jtype] < distsq[k]) continue;
|
|
||||||
|
|
||||||
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
// loop through stencils for all collections
|
||||||
|
for (jcollection = 0; jcollection < ncollections; jcollection++) {
|
||||||
|
|
||||||
delx = xtmp - x[j][0];
|
// if same collection use own bin
|
||||||
dely = ytmp - x[j][1];
|
if(icollection == jcollection) jbin = ibin;
|
||||||
delz = ztmp - x[j][2];
|
else jbin = coord2bin(x[i], jcollection);
|
||||||
rsq = delx*delx + dely*dely + delz*delz;
|
|
||||||
|
|
||||||
if (rsq <= cutneighsq[itype][jtype]) {
|
// if same size: uses half stencil so check central bin
|
||||||
if (molecular != Atom::ATOMIC) {
|
if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){
|
||||||
if (!moltemplate)
|
|
||||||
which = find_special(special[i],nspecial[i],tag[j]);
|
if (icollection == jcollection) js = bins[i];
|
||||||
else if (imol >= 0)
|
else js = binhead_multi[jcollection][jbin];
|
||||||
which = find_special(onemols[imol]->special[iatom],
|
|
||||||
onemols[imol]->nspecial[iatom],
|
// if same collection,
|
||||||
tag[j]-tagprev);
|
// if j is owned atom, store it, since j is beyond i in linked list
|
||||||
else which = 0;
|
// if j is ghost, only store if j coords are "above and to the right" of i
|
||||||
if (which == 0) neighptr[n++] = j;
|
|
||||||
else if (domain->minimum_image_check(delx,dely,delz))
|
// if different collections,
|
||||||
neighptr[n++] = j;
|
// if j is owned atom, store it if j > i
|
||||||
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
|
// if j is ghost, only store if j coords are "above and to the right" of i
|
||||||
} else neighptr[n++] = j;
|
|
||||||
}
|
for (j = js; j >= 0; j = bins[j]) {
|
||||||
|
if((icollection != jcollection) && (j < i)) continue;
|
||||||
|
|
||||||
|
if (j >= nlocal) {
|
||||||
|
if (x[j][2] < ztmp) continue;
|
||||||
|
if (x[j][2] == ztmp) {
|
||||||
|
if (x[j][1] < ytmp) continue;
|
||||||
|
if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
jtype = type[j];
|
||||||
|
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
||||||
|
|
||||||
|
delx = xtmp - x[j][0];
|
||||||
|
dely = ytmp - x[j][1];
|
||||||
|
delz = ztmp - x[j][2];
|
||||||
|
rsq = delx*delx + dely*dely + delz*delz;
|
||||||
|
|
||||||
|
if (rsq <= cutneighsq[itype][jtype]) {
|
||||||
|
if (molecular) {
|
||||||
|
if (!moltemplate)
|
||||||
|
which = find_special(special[i],nspecial[i],tag[j]);
|
||||||
|
else if (imol >= 0)
|
||||||
|
which = find_special(onemols[imol]->special[iatom],
|
||||||
|
onemols[imol]->nspecial[iatom],
|
||||||
|
tag[j]-tagprev);
|
||||||
|
else which = 0;
|
||||||
|
if (which == 0) neighptr[n++] = j;
|
||||||
|
else if (domain->minimum_image_check(delx,dely,delz))
|
||||||
|
neighptr[n++] = j;
|
||||||
|
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
|
||||||
|
} else neighptr[n++] = j;
|
||||||
|
}
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
// for all collections, loop over all atoms in other bins in stencil, store every pair
|
||||||
|
// stencil is empty if i larger than j
|
||||||
|
// stencil is half if i same size as j
|
||||||
|
// stencil is full if i smaller than j
|
||||||
|
|
||||||
|
s = stencil_multi[icollection][jcollection];
|
||||||
|
ns = nstencil_multi[icollection][jcollection];
|
||||||
|
|
||||||
|
for (k = 0; k < ns; k++) {
|
||||||
|
js = binhead_multi[jcollection][jbin + s[k]];
|
||||||
|
for (j = js; j >= 0; j = bins[j]) {
|
||||||
|
|
||||||
|
jtype = type[j];
|
||||||
|
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
||||||
|
|
||||||
|
delx = xtmp - x[j][0];
|
||||||
|
dely = ytmp - x[j][1];
|
||||||
|
delz = ztmp - x[j][2];
|
||||||
|
rsq = delx*delx + dely*dely + delz*delz;
|
||||||
|
|
||||||
|
if (rsq <= cutneighsq[itype][jtype]) {
|
||||||
|
if (molecular != Atom::ATOMIC) {
|
||||||
|
if (!moltemplate)
|
||||||
|
which = find_special(special[i],nspecial[i],tag[j]);
|
||||||
|
else if (imol >= 0)
|
||||||
|
which = find_special(onemols[imol]->special[iatom],
|
||||||
|
onemols[imol]->nspecial[iatom],
|
||||||
|
tag[j]-tagprev);
|
||||||
|
else which = 0;
|
||||||
|
if (which == 0) neighptr[n++] = j;
|
||||||
|
else if (domain->minimum_image_check(delx,dely,delz))
|
||||||
|
neighptr[n++] = j;
|
||||||
|
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
|
||||||
|
} else neighptr[n++] = j;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
ilist[inum++] = i;
|
ilist[inum++] = i;
|
||||||
|
|||||||
@ -40,8 +40,4 @@ class NPairHalfMultiNewton : public NPair {
|
|||||||
|
|
||||||
/* ERROR/WARNING messages:
|
/* ERROR/WARNING messages:
|
||||||
|
|
||||||
E: Neighbor list overflow, boost neigh_modify one
|
|
||||||
|
|
||||||
UNDOCUMENTED
|
|
||||||
|
|
||||||
*/
|
*/
|
||||||
|
|||||||
@ -12,13 +12,15 @@
|
|||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
#include "npair_half_multi_newton_tri.h"
|
#include "npair_half_multi_newton_tri.h"
|
||||||
#include "neigh_list.h"
|
|
||||||
#include "atom.h"
|
#include "atom.h"
|
||||||
#include "atom_vec.h"
|
#include "atom_vec.h"
|
||||||
#include "molecule.h"
|
|
||||||
#include "domain.h"
|
#include "domain.h"
|
||||||
#include "my_page.h"
|
|
||||||
#include "error.h"
|
#include "error.h"
|
||||||
|
#include "molecule.h"
|
||||||
|
#include "my_page.h"
|
||||||
|
#include "neighbor.h"
|
||||||
|
#include "neigh_list.h"
|
||||||
|
|
||||||
using namespace LAMMPS_NS;
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
@ -28,19 +30,20 @@ NPairHalfMultiNewtonTri::NPairHalfMultiNewtonTri(LAMMPS *lmp) : NPair(lmp) {}
|
|||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
binned neighbor list construction with Newton's 3rd law for triclinic
|
binned neighbor list construction with Newton's 3rd law for triclinic
|
||||||
|
multi stencil is icollection-jcollection dependent
|
||||||
each owned atom i checks its own bin and other bins in triclinic stencil
|
each owned atom i checks its own bin and other bins in triclinic stencil
|
||||||
multi-type stencil is itype dependent and is distance checked
|
|
||||||
every pair stored exactly once by some processor
|
every pair stored exactly once by some processor
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
void NPairHalfMultiNewtonTri::build(NeighList *list)
|
void NPairHalfMultiNewtonTri::build(NeighList *list)
|
||||||
{
|
{
|
||||||
int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate;
|
int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,which,ns,imol,iatom,moltemplate;
|
||||||
tagint tagprev;
|
tagint tagprev;
|
||||||
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
||||||
int *neighptr,*s;
|
int *neighptr,*s;
|
||||||
double *cutsq,*distsq;
|
int js;
|
||||||
|
|
||||||
|
int *collection = neighbor->collection;
|
||||||
double **x = atom->x;
|
double **x = atom->x;
|
||||||
int *type = atom->type;
|
int *type = atom->type;
|
||||||
int *mask = atom->mask;
|
int *mask = atom->mask;
|
||||||
@ -54,7 +57,7 @@ void NPairHalfMultiNewtonTri::build(NeighList *list)
|
|||||||
int *molindex = atom->molindex;
|
int *molindex = atom->molindex;
|
||||||
int *molatom = atom->molatom;
|
int *molatom = atom->molatom;
|
||||||
Molecule **onemols = atom->avec->onemols;
|
Molecule **onemols = atom->avec->onemols;
|
||||||
if (molecular == Atom::TEMPLATE) moltemplate = 1;
|
if (molecular == 2) moltemplate = 1;
|
||||||
else moltemplate = 0;
|
else moltemplate = 0;
|
||||||
|
|
||||||
int *ilist = list->ilist;
|
int *ilist = list->ilist;
|
||||||
@ -68,8 +71,8 @@ void NPairHalfMultiNewtonTri::build(NeighList *list)
|
|||||||
for (i = 0; i < nlocal; i++) {
|
for (i = 0; i < nlocal; i++) {
|
||||||
n = 0;
|
n = 0;
|
||||||
neighptr = ipage->vget();
|
neighptr = ipage->vget();
|
||||||
|
|
||||||
itype = type[i];
|
itype = type[i];
|
||||||
|
icollection = collection[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];
|
||||||
@ -79,55 +82,68 @@ void NPairHalfMultiNewtonTri::build(NeighList *list)
|
|||||||
tagprev = tag[i] - iatom - 1;
|
tagprev = tag[i] - iatom - 1;
|
||||||
}
|
}
|
||||||
|
|
||||||
// loop over all atoms in bins, including self, in stencil
|
|
||||||
// skip if i,j neighbor cutoff is less than bin distance
|
|
||||||
// bins below self are excluded from stencil
|
|
||||||
// pairs for atoms j "below" i are excluded
|
|
||||||
// below = lower z or (equal z and lower y) or (equal zy and lower x)
|
|
||||||
// (equal zyx and j <= i)
|
|
||||||
// latter excludes self-self interaction but allows superposed atoms
|
|
||||||
|
|
||||||
ibin = atom2bin[i];
|
ibin = atom2bin[i];
|
||||||
s = stencil_multi[itype];
|
|
||||||
distsq = distsq_multi[itype];
|
// loop through stencils for all collections
|
||||||
cutsq = cutneighsq[itype];
|
for (jcollection = 0; jcollection < ncollections; jcollection++) {
|
||||||
ns = nstencil_multi[itype];
|
|
||||||
for (k = 0; k < ns; k++) {
|
// if same collection use own bin
|
||||||
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
|
if (icollection == jcollection) jbin = ibin;
|
||||||
jtype = type[j];
|
else jbin = coord2bin(x[i], jcollection);
|
||||||
if (cutsq[jtype] < distsq[k]) continue;
|
|
||||||
if (x[j][2] < ztmp) continue;
|
// loop over all atoms in bins in stencil
|
||||||
if (x[j][2] == ztmp) {
|
// stencil is empty if i larger than j
|
||||||
if (x[j][1] < ytmp) continue;
|
// stencil is half if i same size as j
|
||||||
if (x[j][1] == ytmp) {
|
// stencil is full if i smaller than j
|
||||||
if (x[j][0] < xtmp) continue;
|
// if half: pairs for atoms j "below" i are excluded
|
||||||
if (x[j][0] == xtmp && j <= i) continue;
|
// below = lower z or (equal z and lower y) or (equal zy and lower x)
|
||||||
|
// (equal zyx and j <= i)
|
||||||
|
// latter excludes self-self interaction but allows superposed atoms
|
||||||
|
|
||||||
|
s = stencil_multi[icollection][jcollection];
|
||||||
|
ns = nstencil_multi[icollection][jcollection];
|
||||||
|
|
||||||
|
for (k = 0; k < ns; k++) {
|
||||||
|
js = binhead_multi[jcollection][jbin + s[k]];
|
||||||
|
for (j = js; j >= 0; j = bins[j]) {
|
||||||
|
|
||||||
|
// if same size (same collection), use half stencil
|
||||||
|
if(cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){
|
||||||
|
if (x[j][2] < ztmp) continue;
|
||||||
|
if (x[j][2] == ztmp) {
|
||||||
|
if (x[j][1] < ytmp) continue;
|
||||||
|
if (x[j][1] == ytmp) {
|
||||||
|
if (x[j][0] < xtmp) continue;
|
||||||
|
if (x[j][0] == xtmp && j <= i) continue;
|
||||||
|
}
|
||||||
|
}
|
||||||
}
|
}
|
||||||
}
|
|
||||||
|
|
||||||
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
jtype = type[j];
|
||||||
|
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
||||||
|
|
||||||
delx = xtmp - x[j][0];
|
delx = xtmp - x[j][0];
|
||||||
dely = ytmp - x[j][1];
|
dely = ytmp - x[j][1];
|
||||||
delz = ztmp - x[j][2];
|
delz = ztmp - x[j][2];
|
||||||
rsq = delx*delx + dely*dely + delz*delz;
|
rsq = delx*delx + dely*dely + delz*delz;
|
||||||
|
|
||||||
if (rsq <= cutneighsq[itype][jtype]) {
|
if (rsq <= cutneighsq[itype][jtype]) {
|
||||||
if (molecular != Atom::ATOMIC) {
|
if (molecular != Atom::ATOMIC) {
|
||||||
if (!moltemplate)
|
if (!moltemplate)
|
||||||
which = find_special(special[i],nspecial[i],tag[j]);
|
which = find_special(special[i],nspecial[i],tag[j]);
|
||||||
else if (imol >= 0)
|
else if (imol >= 0)
|
||||||
which = find_special(onemols[imol]->special[iatom],
|
which = find_special(onemols[imol]->special[iatom],
|
||||||
onemols[imol]->nspecial[iatom],
|
onemols[imol]->nspecial[iatom],
|
||||||
tag[j]-tagprev);
|
tag[j]-tagprev);
|
||||||
else which = 0;
|
else which = 0;
|
||||||
if (which == 0) neighptr[n++] = j;
|
if (which == 0) neighptr[n++] = j;
|
||||||
else if (domain->minimum_image_check(delx,dely,delz))
|
else if (domain->minimum_image_check(delx,dely,delz))
|
||||||
neighptr[n++] = j;
|
neighptr[n++] = j;
|
||||||
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
|
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
|
||||||
} else neighptr[n++] = j;
|
} else neighptr[n++] = j;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
ilist[inum++] = i;
|
ilist[inum++] = i;
|
||||||
|
|||||||
@ -40,8 +40,4 @@ class NPairHalfMultiNewtonTri : public NPair {
|
|||||||
|
|
||||||
/* ERROR/WARNING messages:
|
/* ERROR/WARNING messages:
|
||||||
|
|
||||||
E: Neighbor list overflow, boost neigh_modify one
|
|
||||||
|
|
||||||
UNDOCUMENTED
|
|
||||||
|
|
||||||
*/
|
*/
|
||||||
|
|||||||
135
src/npair_half_multi_old_newtoff.cpp
Normal file
135
src/npair_half_multi_old_newtoff.cpp
Normal file
@ -0,0 +1,135 @@
|
|||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
https://lammps.sandia.gov/, 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 "npair_half_multi_old_newtoff.h"
|
||||||
|
|
||||||
|
#include "atom.h"
|
||||||
|
#include "atom_vec.h"
|
||||||
|
#include "domain.h"
|
||||||
|
#include "error.h"
|
||||||
|
#include "molecule.h"
|
||||||
|
#include "my_page.h"
|
||||||
|
#include "neigh_list.h"
|
||||||
|
|
||||||
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
NPairHalfMultiOldNewtoff::NPairHalfMultiOldNewtoff(LAMMPS *lmp) : NPair(lmp) {}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
binned neighbor list construction with partial Newton's 3rd law
|
||||||
|
each owned atom i checks own bin and other bins in stencil
|
||||||
|
multi-type stencil is itype dependent and is distance checked
|
||||||
|
pair stored once if i,j are both owned and i < j
|
||||||
|
pair stored by me if j is ghost (also stored by proc owning j)
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void NPairHalfMultiOldNewtoff::build(NeighList *list)
|
||||||
|
{
|
||||||
|
int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate;
|
||||||
|
tagint tagprev;
|
||||||
|
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
||||||
|
int *neighptr,*s;
|
||||||
|
double *cutsq,*distsq;
|
||||||
|
|
||||||
|
double **x = atom->x;
|
||||||
|
int *type = atom->type;
|
||||||
|
int *mask = atom->mask;
|
||||||
|
tagint *tag = atom->tag;
|
||||||
|
tagint *molecule = atom->molecule;
|
||||||
|
tagint **special = atom->special;
|
||||||
|
int **nspecial = atom->nspecial;
|
||||||
|
int nlocal = atom->nlocal;
|
||||||
|
if (includegroup) nlocal = atom->nfirst;
|
||||||
|
|
||||||
|
int *molindex = atom->molindex;
|
||||||
|
int *molatom = atom->molatom;
|
||||||
|
Molecule **onemols = atom->avec->onemols;
|
||||||
|
if (molecular == Atom::TEMPLATE) moltemplate = 1;
|
||||||
|
else moltemplate = 0;
|
||||||
|
|
||||||
|
int *ilist = list->ilist;
|
||||||
|
int *numneigh = list->numneigh;
|
||||||
|
int **firstneigh = list->firstneigh;
|
||||||
|
MyPage<int> *ipage = list->ipage;
|
||||||
|
|
||||||
|
int inum = 0;
|
||||||
|
ipage->reset();
|
||||||
|
|
||||||
|
for (i = 0; i < nlocal; i++) {
|
||||||
|
n = 0;
|
||||||
|
neighptr = ipage->vget();
|
||||||
|
|
||||||
|
itype = type[i];
|
||||||
|
xtmp = x[i][0];
|
||||||
|
ytmp = x[i][1];
|
||||||
|
ztmp = x[i][2];
|
||||||
|
if (moltemplate) {
|
||||||
|
imol = molindex[i];
|
||||||
|
iatom = molatom[i];
|
||||||
|
tagprev = tag[i] - iatom - 1;
|
||||||
|
}
|
||||||
|
|
||||||
|
// loop over all atoms in other bins in stencil including self
|
||||||
|
// only store pair if i < j
|
||||||
|
// skip if i,j neighbor cutoff is less than bin distance
|
||||||
|
// stores own/own pairs only once
|
||||||
|
// stores own/ghost pairs on both procs
|
||||||
|
|
||||||
|
ibin = atom2bin[i];
|
||||||
|
s = stencil_multi_old[itype];
|
||||||
|
distsq = distsq_multi_old[itype];
|
||||||
|
cutsq = cutneighsq[itype];
|
||||||
|
ns = nstencil_multi_old[itype];
|
||||||
|
for (k = 0; k < ns; k++) {
|
||||||
|
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
|
||||||
|
if (j <= i) continue;
|
||||||
|
jtype = type[j];
|
||||||
|
if (cutsq[jtype] < distsq[k]) continue;
|
||||||
|
|
||||||
|
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
||||||
|
|
||||||
|
delx = xtmp - x[j][0];
|
||||||
|
dely = ytmp - x[j][1];
|
||||||
|
delz = ztmp - x[j][2];
|
||||||
|
rsq = delx*delx + dely*dely + delz*delz;
|
||||||
|
|
||||||
|
if (rsq <= cutneighsq[itype][jtype]) {
|
||||||
|
if (molecular != Atom::ATOMIC) {
|
||||||
|
if (!moltemplate)
|
||||||
|
which = find_special(special[i],nspecial[i],tag[j]);
|
||||||
|
else if (imol >= 0)
|
||||||
|
which = find_special(onemols[imol]->special[iatom],
|
||||||
|
onemols[imol]->nspecial[iatom],
|
||||||
|
tag[j]-tagprev);
|
||||||
|
else which = 0;
|
||||||
|
if (which == 0) neighptr[n++] = j;
|
||||||
|
else if (domain->minimum_image_check(delx,dely,delz))
|
||||||
|
neighptr[n++] = j;
|
||||||
|
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
|
||||||
|
} else neighptr[n++] = j;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
ilist[inum++] = i;
|
||||||
|
firstneigh[i] = neighptr;
|
||||||
|
numneigh[i] = n;
|
||||||
|
ipage->vgot(n);
|
||||||
|
if (ipage->status())
|
||||||
|
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
|
||||||
|
}
|
||||||
|
|
||||||
|
list->inum = inum;
|
||||||
|
}
|
||||||
47
src/npair_half_multi_old_newtoff.h
Normal file
47
src/npair_half_multi_old_newtoff.h
Normal file
@ -0,0 +1,47 @@
|
|||||||
|
/* -*- c++ -*- ----------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
https://lammps.sandia.gov/, 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.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#ifdef NPAIR_CLASS
|
||||||
|
|
||||||
|
NPairStyle(half/multi/old/newtoff,
|
||||||
|
NPairHalfMultiOldNewtoff,
|
||||||
|
NP_HALF | NP_MULTI_OLD | NP_NEWTOFF | NP_ORTHO | NP_TRI)
|
||||||
|
|
||||||
|
#else
|
||||||
|
|
||||||
|
#ifndef LMP_NPAIR_HALF_MULTI_OLD_NEWTOFF_H
|
||||||
|
#define LMP_NPAIR_HALF_MULTI_OLD_NEWTOFF_H
|
||||||
|
|
||||||
|
#include "npair.h"
|
||||||
|
|
||||||
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
|
class NPairHalfMultiOldNewtoff : public NPair {
|
||||||
|
public:
|
||||||
|
NPairHalfMultiOldNewtoff(class LAMMPS *);
|
||||||
|
~NPairHalfMultiOldNewtoff() {}
|
||||||
|
void build(class NeighList *);
|
||||||
|
};
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
#endif
|
||||||
|
#endif
|
||||||
|
|
||||||
|
/* ERROR/WARNING messages:
|
||||||
|
|
||||||
|
E: Neighbor list overflow, boost neigh_modify one
|
||||||
|
|
||||||
|
UNDOCUMENTED
|
||||||
|
|
||||||
|
*/
|
||||||
168
src/npair_half_multi_old_newton.cpp
Normal file
168
src/npair_half_multi_old_newton.cpp
Normal file
@ -0,0 +1,168 @@
|
|||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
https://lammps.sandia.gov/, 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 "npair_half_multi_old_newton.h"
|
||||||
|
|
||||||
|
#include "atom.h"
|
||||||
|
#include "atom_vec.h"
|
||||||
|
#include "domain.h"
|
||||||
|
#include "error.h"
|
||||||
|
#include "molecule.h"
|
||||||
|
#include "my_page.h"
|
||||||
|
#include "neigh_list.h"
|
||||||
|
|
||||||
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
NPairHalfMultiOldNewton::NPairHalfMultiOldNewton(LAMMPS *lmp) : NPair(lmp) {}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
binned neighbor list construction with full Newton's 3rd law
|
||||||
|
each owned atom i checks its own bin and other bins in Newton stencil
|
||||||
|
multi-type stencil is itype dependent and is distance checked
|
||||||
|
every pair stored exactly once by some processor
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void NPairHalfMultiOldNewton::build(NeighList *list)
|
||||||
|
{
|
||||||
|
int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate;
|
||||||
|
tagint tagprev;
|
||||||
|
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
||||||
|
int *neighptr,*s;
|
||||||
|
double *cutsq,*distsq;
|
||||||
|
|
||||||
|
double **x = atom->x;
|
||||||
|
int *type = atom->type;
|
||||||
|
int *mask = atom->mask;
|
||||||
|
tagint *tag = atom->tag;
|
||||||
|
tagint *molecule = atom->molecule;
|
||||||
|
tagint **special = atom->special;
|
||||||
|
int **nspecial = atom->nspecial;
|
||||||
|
int nlocal = atom->nlocal;
|
||||||
|
if (includegroup) nlocal = atom->nfirst;
|
||||||
|
|
||||||
|
int *molindex = atom->molindex;
|
||||||
|
int *molatom = atom->molatom;
|
||||||
|
Molecule **onemols = atom->avec->onemols;
|
||||||
|
if (molecular == Atom::TEMPLATE) moltemplate = 1;
|
||||||
|
else moltemplate = 0;
|
||||||
|
|
||||||
|
int *ilist = list->ilist;
|
||||||
|
int *numneigh = list->numneigh;
|
||||||
|
int **firstneigh = list->firstneigh;
|
||||||
|
MyPage<int> *ipage = list->ipage;
|
||||||
|
|
||||||
|
int inum = 0;
|
||||||
|
ipage->reset();
|
||||||
|
|
||||||
|
for (i = 0; i < nlocal; i++) {
|
||||||
|
n = 0;
|
||||||
|
neighptr = ipage->vget();
|
||||||
|
|
||||||
|
itype = type[i];
|
||||||
|
xtmp = x[i][0];
|
||||||
|
ytmp = x[i][1];
|
||||||
|
ztmp = x[i][2];
|
||||||
|
if (moltemplate) {
|
||||||
|
imol = molindex[i];
|
||||||
|
iatom = molatom[i];
|
||||||
|
tagprev = tag[i] - iatom - 1;
|
||||||
|
}
|
||||||
|
|
||||||
|
// loop over rest of atoms in i's bin, ghosts are at end of linked list
|
||||||
|
// if j is owned atom, store it, since j is beyond i in linked list
|
||||||
|
// if j is ghost, only store if j coords are "above and to the right" of i
|
||||||
|
|
||||||
|
for (j = bins[i]; j >= 0; j = bins[j]) {
|
||||||
|
if (j >= nlocal) {
|
||||||
|
if (x[j][2] < ztmp) continue;
|
||||||
|
if (x[j][2] == ztmp) {
|
||||||
|
if (x[j][1] < ytmp) continue;
|
||||||
|
if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
jtype = type[j];
|
||||||
|
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
||||||
|
|
||||||
|
delx = xtmp - x[j][0];
|
||||||
|
dely = ytmp - x[j][1];
|
||||||
|
delz = ztmp - x[j][2];
|
||||||
|
rsq = delx*delx + dely*dely + delz*delz;
|
||||||
|
|
||||||
|
if (rsq <= cutneighsq[itype][jtype]) {
|
||||||
|
if (molecular != Atom::ATOMIC) {
|
||||||
|
if (!moltemplate)
|
||||||
|
which = find_special(special[i],nspecial[i],tag[j]);
|
||||||
|
else if (imol >= 0)
|
||||||
|
which = find_special(onemols[imol]->special[iatom],
|
||||||
|
onemols[imol]->nspecial[iatom],
|
||||||
|
tag[j]-tagprev);
|
||||||
|
else which = 0;
|
||||||
|
if (which == 0) neighptr[n++] = j;
|
||||||
|
else if (domain->minimum_image_check(delx,dely,delz))
|
||||||
|
neighptr[n++] = j;
|
||||||
|
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
|
||||||
|
} else neighptr[n++] = j;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
// loop over all atoms in other bins in stencil, store every pair
|
||||||
|
// skip if i,j neighbor cutoff is less than bin distance
|
||||||
|
|
||||||
|
ibin = atom2bin[i];
|
||||||
|
s = stencil_multi_old[itype];
|
||||||
|
distsq = distsq_multi_old[itype];
|
||||||
|
cutsq = cutneighsq[itype];
|
||||||
|
ns = nstencil_multi_old[itype];
|
||||||
|
for (k = 0; k < ns; k++) {
|
||||||
|
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
|
||||||
|
jtype = type[j];
|
||||||
|
if (cutsq[jtype] < distsq[k]) continue;
|
||||||
|
|
||||||
|
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
||||||
|
|
||||||
|
delx = xtmp - x[j][0];
|
||||||
|
dely = ytmp - x[j][1];
|
||||||
|
delz = ztmp - x[j][2];
|
||||||
|
rsq = delx*delx + dely*dely + delz*delz;
|
||||||
|
|
||||||
|
if (rsq <= cutneighsq[itype][jtype]) {
|
||||||
|
if (molecular != Atom::ATOMIC) {
|
||||||
|
if (!moltemplate)
|
||||||
|
which = find_special(special[i],nspecial[i],tag[j]);
|
||||||
|
else if (imol >= 0)
|
||||||
|
which = find_special(onemols[imol]->special[iatom],
|
||||||
|
onemols[imol]->nspecial[iatom],
|
||||||
|
tag[j]-tagprev);
|
||||||
|
else which = 0;
|
||||||
|
if (which == 0) neighptr[n++] = j;
|
||||||
|
else if (domain->minimum_image_check(delx,dely,delz))
|
||||||
|
neighptr[n++] = j;
|
||||||
|
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
|
||||||
|
} else neighptr[n++] = j;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
ilist[inum++] = i;
|
||||||
|
firstneigh[i] = neighptr;
|
||||||
|
numneigh[i] = n;
|
||||||
|
ipage->vgot(n);
|
||||||
|
if (ipage->status())
|
||||||
|
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
|
||||||
|
}
|
||||||
|
|
||||||
|
list->inum = inum;
|
||||||
|
}
|
||||||
47
src/npair_half_multi_old_newton.h
Normal file
47
src/npair_half_multi_old_newton.h
Normal file
@ -0,0 +1,47 @@
|
|||||||
|
/* -*- c++ -*- ----------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
https://lammps.sandia.gov/, 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.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#ifdef NPAIR_CLASS
|
||||||
|
|
||||||
|
NPairStyle(half/multi/old/newton,
|
||||||
|
NPairHalfMultiOldNewton,
|
||||||
|
NP_HALF | NP_MULTI_OLD | NP_NEWTON | NP_ORTHO)
|
||||||
|
|
||||||
|
#else
|
||||||
|
|
||||||
|
#ifndef LMP_NPAIR_HALF_MULTI_OLD_NEWTON_H
|
||||||
|
#define LMP_NPAIR_HALF_MULTI_OLD_NEWTON_H
|
||||||
|
|
||||||
|
#include "npair.h"
|
||||||
|
|
||||||
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
|
class NPairHalfMultiOldNewton : public NPair {
|
||||||
|
public:
|
||||||
|
NPairHalfMultiOldNewton(class LAMMPS *);
|
||||||
|
~NPairHalfMultiOldNewton() {}
|
||||||
|
void build(class NeighList *);
|
||||||
|
};
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
#endif
|
||||||
|
#endif
|
||||||
|
|
||||||
|
/* ERROR/WARNING messages:
|
||||||
|
|
||||||
|
E: Neighbor list overflow, boost neigh_modify one
|
||||||
|
|
||||||
|
UNDOCUMENTED
|
||||||
|
|
||||||
|
*/
|
||||||
143
src/npair_half_multi_old_newton_tri.cpp
Normal file
143
src/npair_half_multi_old_newton_tri.cpp
Normal file
@ -0,0 +1,143 @@
|
|||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
https://lammps.sandia.gov/, 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 "npair_half_multi_old_newton_tri.h"
|
||||||
|
|
||||||
|
#include "atom.h"
|
||||||
|
#include "atom_vec.h"
|
||||||
|
#include "domain.h"
|
||||||
|
#include "error.h"
|
||||||
|
#include "molecule.h"
|
||||||
|
#include "my_page.h"
|
||||||
|
#include "neigh_list.h"
|
||||||
|
|
||||||
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
NPairHalfMultiOldNewtonTri::NPairHalfMultiOldNewtonTri(LAMMPS *lmp) : NPair(lmp) {}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
binned neighbor list construction with Newton's 3rd law for triclinic
|
||||||
|
each owned atom i checks its own bin and other bins in triclinic stencil
|
||||||
|
multi-type stencil is itype dependent and is distance checked
|
||||||
|
every pair stored exactly once by some processor
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void NPairHalfMultiOldNewtonTri::build(NeighList *list)
|
||||||
|
{
|
||||||
|
int i,j,k,n,itype,jtype,ibin,which,ns,imol,iatom,moltemplate;
|
||||||
|
tagint tagprev;
|
||||||
|
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
||||||
|
int *neighptr,*s;
|
||||||
|
double *cutsq,*distsq;
|
||||||
|
|
||||||
|
double **x = atom->x;
|
||||||
|
int *type = atom->type;
|
||||||
|
int *mask = atom->mask;
|
||||||
|
tagint *tag = atom->tag;
|
||||||
|
tagint *molecule = atom->molecule;
|
||||||
|
tagint **special = atom->special;
|
||||||
|
int **nspecial = atom->nspecial;
|
||||||
|
int nlocal = atom->nlocal;
|
||||||
|
if (includegroup) nlocal = atom->nfirst;
|
||||||
|
|
||||||
|
int *molindex = atom->molindex;
|
||||||
|
int *molatom = atom->molatom;
|
||||||
|
Molecule **onemols = atom->avec->onemols;
|
||||||
|
if (molecular == Atom::TEMPLATE) moltemplate = 1;
|
||||||
|
else moltemplate = 0;
|
||||||
|
|
||||||
|
int *ilist = list->ilist;
|
||||||
|
int *numneigh = list->numneigh;
|
||||||
|
int **firstneigh = list->firstneigh;
|
||||||
|
MyPage<int> *ipage = list->ipage;
|
||||||
|
|
||||||
|
int inum = 0;
|
||||||
|
ipage->reset();
|
||||||
|
|
||||||
|
for (i = 0; i < nlocal; i++) {
|
||||||
|
n = 0;
|
||||||
|
neighptr = ipage->vget();
|
||||||
|
|
||||||
|
itype = type[i];
|
||||||
|
xtmp = x[i][0];
|
||||||
|
ytmp = x[i][1];
|
||||||
|
ztmp = x[i][2];
|
||||||
|
if (moltemplate) {
|
||||||
|
imol = molindex[i];
|
||||||
|
iatom = molatom[i];
|
||||||
|
tagprev = tag[i] - iatom - 1;
|
||||||
|
}
|
||||||
|
|
||||||
|
// loop over all atoms in bins, including self, in stencil
|
||||||
|
// skip if i,j neighbor cutoff is less than bin distance
|
||||||
|
// bins below self are excluded from stencil
|
||||||
|
// pairs for atoms j "below" i are excluded
|
||||||
|
// below = lower z or (equal z and lower y) or (equal zy and lower x)
|
||||||
|
// (equal zyx and j <= i)
|
||||||
|
// latter excludes self-self interaction but allows superposed atoms
|
||||||
|
|
||||||
|
ibin = atom2bin[i];
|
||||||
|
s = stencil_multi_old[itype];
|
||||||
|
distsq = distsq_multi_old[itype];
|
||||||
|
cutsq = cutneighsq[itype];
|
||||||
|
ns = nstencil_multi_old[itype];
|
||||||
|
for (k = 0; k < ns; k++) {
|
||||||
|
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
|
||||||
|
jtype = type[j];
|
||||||
|
if (cutsq[jtype] < distsq[k]) continue;
|
||||||
|
if (x[j][2] < ztmp) continue;
|
||||||
|
if (x[j][2] == ztmp) {
|
||||||
|
if (x[j][1] < ytmp) continue;
|
||||||
|
if (x[j][1] == ytmp) {
|
||||||
|
if (x[j][0] < xtmp) continue;
|
||||||
|
if (x[j][0] == xtmp && j <= i) continue;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
||||||
|
|
||||||
|
delx = xtmp - x[j][0];
|
||||||
|
dely = ytmp - x[j][1];
|
||||||
|
delz = ztmp - x[j][2];
|
||||||
|
rsq = delx*delx + dely*dely + delz*delz;
|
||||||
|
|
||||||
|
if (rsq <= cutneighsq[itype][jtype]) {
|
||||||
|
if (molecular != Atom::ATOMIC) {
|
||||||
|
if (!moltemplate)
|
||||||
|
which = find_special(special[i],nspecial[i],tag[j]);
|
||||||
|
else if (imol >= 0)
|
||||||
|
which = find_special(onemols[imol]->special[iatom],
|
||||||
|
onemols[imol]->nspecial[iatom],
|
||||||
|
tag[j]-tagprev);
|
||||||
|
else which = 0;
|
||||||
|
if (which == 0) neighptr[n++] = j;
|
||||||
|
else if (domain->minimum_image_check(delx,dely,delz))
|
||||||
|
neighptr[n++] = j;
|
||||||
|
else if (which > 0) neighptr[n++] = j ^ (which << SBBITS);
|
||||||
|
} else neighptr[n++] = j;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
ilist[inum++] = i;
|
||||||
|
firstneigh[i] = neighptr;
|
||||||
|
numneigh[i] = n;
|
||||||
|
ipage->vgot(n);
|
||||||
|
if (ipage->status())
|
||||||
|
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
|
||||||
|
}
|
||||||
|
|
||||||
|
list->inum = inum;
|
||||||
|
}
|
||||||
47
src/npair_half_multi_old_newton_tri.h
Normal file
47
src/npair_half_multi_old_newton_tri.h
Normal file
@ -0,0 +1,47 @@
|
|||||||
|
/* -*- c++ -*- ----------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
https://lammps.sandia.gov/, 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.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#ifdef NPAIR_CLASS
|
||||||
|
|
||||||
|
NPairStyle(half/multi/old/newton/tri,
|
||||||
|
NPairHalfMultiOldNewtonTri,
|
||||||
|
NP_HALF | NP_MULTI_OLD | NP_NEWTON | NP_TRI)
|
||||||
|
|
||||||
|
#else
|
||||||
|
|
||||||
|
#ifndef LMP_NPAIR_HALF_MULTI_OLD_NEWTON_TRI_H
|
||||||
|
#define LMP_NPAIR_HALF_MULTI_OLD_NEWTON_TRI_H
|
||||||
|
|
||||||
|
#include "npair.h"
|
||||||
|
|
||||||
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
|
class NPairHalfMultiOldNewtonTri : public NPair {
|
||||||
|
public:
|
||||||
|
NPairHalfMultiOldNewtonTri(class LAMMPS *);
|
||||||
|
~NPairHalfMultiOldNewtonTri() {}
|
||||||
|
void build(class NeighList *);
|
||||||
|
};
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
#endif
|
||||||
|
#endif
|
||||||
|
|
||||||
|
/* ERROR/WARNING messages:
|
||||||
|
|
||||||
|
E: Neighbor list overflow, boost neigh_modify one
|
||||||
|
|
||||||
|
UNDOCUMENTED
|
||||||
|
|
||||||
|
*/
|
||||||
@ -5,17 +5,19 @@
|
|||||||
|
|
||||||
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
Copyright (2003) Sandia Corporation. Under the terms of Contract
|
||||||
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
|
||||||
certain rights in this software. This software is distributed under
|
es certain rights in this software. This software is distributed under
|
||||||
the GNU General Public License.
|
the GNU General Public License.
|
||||||
|
|
||||||
See the README file in the top-level LAMMPS directory.
|
See the README file in the top-level LAMMPS directory.
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#include <string.h>
|
||||||
#include "npair_half_size_multi_newtoff.h"
|
#include "npair_half_size_multi_newtoff.h"
|
||||||
|
|
||||||
#include "atom.h"
|
#include "atom.h"
|
||||||
#include "error.h"
|
#include "error.h"
|
||||||
#include "my_page.h"
|
#include "my_page.h"
|
||||||
|
#include "neighbor.h"
|
||||||
#include "neigh_list.h"
|
#include "neigh_list.h"
|
||||||
|
|
||||||
using namespace LAMMPS_NS;
|
using namespace LAMMPS_NS;
|
||||||
@ -27,20 +29,21 @@ NPairHalfSizeMultiNewtoff::NPairHalfSizeMultiNewtoff(LAMMPS *lmp) : NPair(lmp) {
|
|||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
size particles
|
size particles
|
||||||
binned neighbor list construction with partial Newton's 3rd law
|
binned neighbor list construction with partial Newton's 3rd law
|
||||||
|
multi stencil is icollection-jcollection dependent
|
||||||
each owned atom i checks own bin and other bins in stencil
|
each owned atom i checks own bin and other bins in stencil
|
||||||
multi-type stencil is itype dependent and is distance checked
|
|
||||||
pair stored once if i,j are both owned and i < j
|
pair stored once if i,j are both owned and i < j
|
||||||
pair stored by me if j is ghost (also stored by proc owning j)
|
pair stored by me if j is ghost (also stored by proc owning j)
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
void NPairHalfSizeMultiNewtoff::build(NeighList *list)
|
void NPairHalfSizeMultiNewtoff::build(NeighList *list)
|
||||||
{
|
{
|
||||||
int i,j,k,n,itype,jtype,ibin,ns;
|
int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,ns;
|
||||||
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
||||||
double radi,radsum,cutdistsq;
|
double radi,radsum,cutdistsq;
|
||||||
int *neighptr,*s;
|
int *neighptr,*s;
|
||||||
double *cutsq,*distsq;
|
int js;
|
||||||
|
|
||||||
|
int *collection = neighbor->collection;
|
||||||
double **x = atom->x;
|
double **x = atom->x;
|
||||||
double *radius = atom->radius;
|
double *radius = atom->radius;
|
||||||
int *type = atom->type;
|
int *type = atom->type;
|
||||||
@ -63,45 +66,53 @@ void NPairHalfSizeMultiNewtoff::build(NeighList *list)
|
|||||||
for (i = 0; i < nlocal; i++) {
|
for (i = 0; i < nlocal; i++) {
|
||||||
n = 0;
|
n = 0;
|
||||||
neighptr = ipage->vget();
|
neighptr = ipage->vget();
|
||||||
|
|
||||||
itype = type[i];
|
itype = type[i];
|
||||||
|
icollection = collection[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];
|
||||||
radi = radius[i];
|
radi = radius[i];
|
||||||
|
|
||||||
// loop over all atoms in other bins in stencil including self
|
|
||||||
// only store pair if i < j
|
|
||||||
// skip if i,j neighbor cutoff is less than bin distance
|
|
||||||
// stores own/own pairs only once
|
|
||||||
// stores own/ghost pairs on both procs
|
|
||||||
|
|
||||||
ibin = atom2bin[i];
|
ibin = atom2bin[i];
|
||||||
s = stencil_multi[itype];
|
|
||||||
distsq = distsq_multi[itype];
|
|
||||||
cutsq = cutneighsq[itype];
|
|
||||||
ns = nstencil_multi[itype];
|
|
||||||
for (k = 0; k < ns; k++) {
|
|
||||||
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
|
|
||||||
if (j <= i) continue;
|
|
||||||
jtype = type[j];
|
|
||||||
if (cutsq[jtype] < distsq[k]) continue;
|
|
||||||
|
|
||||||
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
// loop through stencils for all collections
|
||||||
|
for (jcollection = 0; jcollection < ncollections; jcollection++) {
|
||||||
|
|
||||||
delx = xtmp - x[j][0];
|
// if same collection use own bin
|
||||||
dely = ytmp - x[j][1];
|
if (icollection == jcollection) jbin = ibin;
|
||||||
delz = ztmp - x[j][2];
|
else jbin = coord2bin(x[i], jcollection);
|
||||||
rsq = delx*delx + dely*dely + delz*delz;
|
|
||||||
radsum = radi + radius[j];
|
|
||||||
cutdistsq = (radsum+skin) * (radsum+skin);
|
|
||||||
|
|
||||||
if (rsq <= cutdistsq) {
|
// loop over all atoms in other bins in stencil including self
|
||||||
if (history && rsq < radsum*radsum)
|
// only store pair if i < j
|
||||||
neighptr[n++] = j ^ mask_history;
|
// stores own/own pairs only once
|
||||||
else
|
// stores own/ghost pairs on both procs
|
||||||
neighptr[n++] = j;
|
// use full stencil for all collection combinations
|
||||||
}
|
|
||||||
|
s = stencil_multi[icollection][jcollection];
|
||||||
|
ns = nstencil_multi[icollection][jcollection];
|
||||||
|
|
||||||
|
for (k = 0; k < ns; k++) {
|
||||||
|
js = binhead_multi[jcollection][jbin + s[k]];
|
||||||
|
for (j = js; j >= 0; j = bins[j]) {
|
||||||
|
if (j <= i) continue;
|
||||||
|
|
||||||
|
jtype = type[j];
|
||||||
|
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
||||||
|
|
||||||
|
delx = xtmp - x[j][0];
|
||||||
|
dely = ytmp - x[j][1];
|
||||||
|
delz = ztmp - x[j][2];
|
||||||
|
rsq = delx*delx + dely*dely + delz*delz;
|
||||||
|
radsum = radi + radius[j];
|
||||||
|
cutdistsq = (radsum+skin) * (radsum+skin);
|
||||||
|
|
||||||
|
if (rsq <= cutdistsq) {
|
||||||
|
if (history && rsq < radsum*radsum)
|
||||||
|
neighptr[n++] = j ^ mask_history;
|
||||||
|
else
|
||||||
|
neighptr[n++] = j;
|
||||||
|
}
|
||||||
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|||||||
@ -43,4 +43,5 @@ class NPairHalfSizeMultiNewtoff : public NPair {
|
|||||||
E: Neighbor list overflow, boost neigh_modify one
|
E: Neighbor list overflow, boost neigh_modify one
|
||||||
|
|
||||||
UNDOCUMENTED
|
UNDOCUMENTED
|
||||||
|
|
||||||
*/
|
*/
|
||||||
|
|||||||
@ -16,6 +16,7 @@
|
|||||||
#include "atom.h"
|
#include "atom.h"
|
||||||
#include "error.h"
|
#include "error.h"
|
||||||
#include "my_page.h"
|
#include "my_page.h"
|
||||||
|
#include "neighbor.h"
|
||||||
#include "neigh_list.h"
|
#include "neigh_list.h"
|
||||||
|
|
||||||
using namespace LAMMPS_NS;
|
using namespace LAMMPS_NS;
|
||||||
@ -27,19 +28,19 @@ NPairHalfSizeMultiNewton::NPairHalfSizeMultiNewton(LAMMPS *lmp) : NPair(lmp) {}
|
|||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
size particles
|
size particles
|
||||||
binned neighbor list construction with full Newton's 3rd law
|
binned neighbor list construction with full Newton's 3rd law
|
||||||
|
multi stencil is icollection-jcollection dependent
|
||||||
each owned atom i checks its own bin and other bins in Newton stencil
|
each owned atom i checks its own bin and other bins in Newton stencil
|
||||||
multi-type stencil is itype dependent and is distance checked
|
|
||||||
every pair stored exactly once by some processor
|
every pair stored exactly once by some processor
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
void NPairHalfSizeMultiNewton::build(NeighList *list)
|
void NPairHalfSizeMultiNewton::build(NeighList *list)
|
||||||
{
|
{
|
||||||
int i,j,k,n,itype,jtype,ibin,ns;
|
int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,ns,js;
|
||||||
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
||||||
double radi,radsum,cutdistsq;
|
double radi,radsum,cutdistsq;
|
||||||
int *neighptr,*s;
|
int *neighptr,*s;
|
||||||
double *cutsq,*distsq;
|
|
||||||
|
|
||||||
|
int *collection = neighbor->collection;
|
||||||
double **x = atom->x;
|
double **x = atom->x;
|
||||||
double *radius = atom->radius;
|
double *radius = atom->radius;
|
||||||
int *type = atom->type;
|
int *type = atom->type;
|
||||||
@ -62,73 +63,96 @@ void NPairHalfSizeMultiNewton::build(NeighList *list)
|
|||||||
for (i = 0; i < nlocal; i++) {
|
for (i = 0; i < nlocal; i++) {
|
||||||
n = 0;
|
n = 0;
|
||||||
neighptr = ipage->vget();
|
neighptr = ipage->vget();
|
||||||
|
|
||||||
itype = type[i];
|
itype = type[i];
|
||||||
|
icollection = collection[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];
|
||||||
radi = radius[i];
|
radi = radius[i];
|
||||||
|
|
||||||
// loop over rest of atoms in i's bin, ghosts are at end of linked list
|
|
||||||
// if j is owned atom, store it, since j is beyond i in linked list
|
|
||||||
// if j is ghost, only store if j coords are "above and to the right" of i
|
|
||||||
|
|
||||||
for (j = bins[i]; j >= 0; j = bins[j]) {
|
|
||||||
if (j >= nlocal) {
|
|
||||||
if (x[j][2] < ztmp) continue;
|
|
||||||
if (x[j][2] == ztmp) {
|
|
||||||
if (x[j][1] < ytmp) continue;
|
|
||||||
if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
jtype = type[j];
|
|
||||||
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
|
||||||
|
|
||||||
delx = xtmp - x[j][0];
|
|
||||||
dely = ytmp - x[j][1];
|
|
||||||
delz = ztmp - x[j][2];
|
|
||||||
rsq = delx*delx + dely*dely + delz*delz;
|
|
||||||
radsum = radi + radius[j];
|
|
||||||
cutdistsq = (radsum+skin) * (radsum+skin);
|
|
||||||
|
|
||||||
if (rsq <= cutdistsq) {
|
|
||||||
if (history && rsq < radsum*radsum)
|
|
||||||
neighptr[n++] = j ^ mask_history;
|
|
||||||
else
|
|
||||||
neighptr[n++] = j;
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
// loop over all atoms in other bins in stencil, store every pair
|
|
||||||
// skip if i,j neighbor cutoff is less than bin distance
|
|
||||||
|
|
||||||
ibin = atom2bin[i];
|
ibin = atom2bin[i];
|
||||||
s = stencil_multi[itype];
|
|
||||||
distsq = distsq_multi[itype];
|
|
||||||
cutsq = cutneighsq[itype];
|
|
||||||
ns = nstencil_multi[itype];
|
|
||||||
for (k = 0; k < ns; k++) {
|
|
||||||
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
|
|
||||||
jtype = type[j];
|
|
||||||
if (cutsq[jtype] < distsq[k]) continue;
|
|
||||||
|
|
||||||
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
// loop through stencils for all collections
|
||||||
|
for (jcollection = 0; jcollection < ncollections; jcollection++) {
|
||||||
|
|
||||||
delx = xtmp - x[j][0];
|
// if same collection use own bin
|
||||||
dely = ytmp - x[j][1];
|
if (icollection == jcollection) jbin = ibin;
|
||||||
delz = ztmp - x[j][2];
|
else jbin = coord2bin(x[i], jcollection);
|
||||||
rsq = delx*delx + dely*dely + delz*delz;
|
|
||||||
radsum = radi + radius[j];
|
|
||||||
cutdistsq = (radsum+skin) * (radsum+skin);
|
|
||||||
|
|
||||||
if (rsq <= cutdistsq) {
|
// if same size: uses half stencil so check central bin
|
||||||
if (history && rsq < radsum*radsum)
|
if (cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){
|
||||||
neighptr[n++] = j ^ mask_history;
|
|
||||||
else
|
if (icollection == jcollection) js = bins[i];
|
||||||
neighptr[n++] = j;
|
else js = binhead_multi[jcollection][jbin];
|
||||||
|
|
||||||
|
// if same collection,
|
||||||
|
// if j is owned atom, store it, since j is beyond i in linked list
|
||||||
|
// if j is ghost, only store if j coords are "above and to the right" of i
|
||||||
|
|
||||||
|
// if different collections,
|
||||||
|
// if j is owned atom, store it if j > i
|
||||||
|
// if j is ghost, only store if j coords are "above and to the right" of i
|
||||||
|
|
||||||
|
for (j = js; j >= 0; j = bins[j]) {
|
||||||
|
if ((icollection != jcollection) && (j < i)) continue;
|
||||||
|
|
||||||
|
if (j >= nlocal) {
|
||||||
|
if (x[j][2] < ztmp) continue;
|
||||||
|
if (x[j][2] == ztmp) {
|
||||||
|
if (x[j][1] < ytmp) continue;
|
||||||
|
if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
jtype = type[j];
|
||||||
|
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
||||||
|
|
||||||
|
delx = xtmp - x[j][0];
|
||||||
|
dely = ytmp - x[j][1];
|
||||||
|
delz = ztmp - x[j][2];
|
||||||
|
rsq = delx*delx + dely*dely + delz*delz;
|
||||||
|
radsum = radi + radius[j];
|
||||||
|
cutdistsq = (radsum+skin) * (radsum+skin);
|
||||||
|
|
||||||
|
if (rsq <= cutdistsq) {
|
||||||
|
if (history && rsq < radsum*radsum)
|
||||||
|
neighptr[n++] = j ^ mask_history;
|
||||||
|
else
|
||||||
|
neighptr[n++] = j;
|
||||||
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
// for all collections, loop over all atoms in other bins in stencil, store every pair
|
||||||
|
// stencil is empty if i larger than j
|
||||||
|
// stencil is half if i same size as j
|
||||||
|
// stencil is full if i smaller than j
|
||||||
|
|
||||||
|
s = stencil_multi[icollection][jcollection];
|
||||||
|
ns = nstencil_multi[icollection][jcollection];
|
||||||
|
|
||||||
|
for (k = 0; k < ns; k++) {
|
||||||
|
js = binhead_multi[jcollection][jbin + s[k]];
|
||||||
|
for (j = js; j >= 0; j = bins[j]) {
|
||||||
|
|
||||||
|
jtype = type[j];
|
||||||
|
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
||||||
|
|
||||||
|
delx = xtmp - x[j][0];
|
||||||
|
dely = ytmp - x[j][1];
|
||||||
|
delz = ztmp - x[j][2];
|
||||||
|
rsq = delx*delx + dely*dely + delz*delz;
|
||||||
|
radsum = radi + radius[j];
|
||||||
|
cutdistsq = (radsum+skin) * (radsum+skin);
|
||||||
|
|
||||||
|
if (rsq <= cutdistsq) {
|
||||||
|
if (history && rsq < radsum*radsum)
|
||||||
|
neighptr[n++] = j ^ mask_history;
|
||||||
|
else
|
||||||
|
neighptr[n++] = j;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
ilist[inum++] = i;
|
ilist[inum++] = i;
|
||||||
|
|||||||
@ -43,4 +43,5 @@ class NPairHalfSizeMultiNewton : public NPair {
|
|||||||
E: Neighbor list overflow, boost neigh_modify one
|
E: Neighbor list overflow, boost neigh_modify one
|
||||||
|
|
||||||
UNDOCUMENTED
|
UNDOCUMENTED
|
||||||
|
|
||||||
*/
|
*/
|
||||||
|
|||||||
@ -16,6 +16,7 @@
|
|||||||
#include "atom.h"
|
#include "atom.h"
|
||||||
#include "error.h"
|
#include "error.h"
|
||||||
#include "my_page.h"
|
#include "my_page.h"
|
||||||
|
#include "neighbor.h"
|
||||||
#include "neigh_list.h"
|
#include "neigh_list.h"
|
||||||
|
|
||||||
using namespace LAMMPS_NS;
|
using namespace LAMMPS_NS;
|
||||||
@ -25,20 +26,21 @@ using namespace LAMMPS_NS;
|
|||||||
NPairHalfSizeMultiNewtonTri::NPairHalfSizeMultiNewtonTri(LAMMPS *lmp) : NPair(lmp) {}
|
NPairHalfSizeMultiNewtonTri::NPairHalfSizeMultiNewtonTri(LAMMPS *lmp) : NPair(lmp) {}
|
||||||
|
|
||||||
/* ----------------------------------------------------------------------
|
/* ----------------------------------------------------------------------
|
||||||
|
size particles
|
||||||
binned neighbor list construction with Newton's 3rd law for triclinic
|
binned neighbor list construction with Newton's 3rd law for triclinic
|
||||||
|
multi stencil is icollection-jcollection dependent
|
||||||
each owned atom i checks its own bin and other bins in triclinic stencil
|
each owned atom i checks its own bin and other bins in triclinic stencil
|
||||||
multi-type stencil is itype dependent and is distance checked
|
|
||||||
every pair stored exactly once by some processor
|
every pair stored exactly once by some processor
|
||||||
------------------------------------------------------------------------- */
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
void NPairHalfSizeMultiNewtonTri::build(NeighList *list)
|
void NPairHalfSizeMultiNewtonTri::build(NeighList *list)
|
||||||
{
|
{
|
||||||
int i,j,k,n,itype,jtype,ibin,ns;
|
int i,j,k,n,itype,jtype,icollection,jcollection,ibin,jbin,ns,js;
|
||||||
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
||||||
double radi,radsum,cutdistsq;
|
double radi,radsum,cutdistsq;
|
||||||
int *neighptr,*s;
|
int *neighptr,*s;
|
||||||
double *cutsq,*distsq;
|
|
||||||
|
|
||||||
|
int *collection = neighbor->collection;
|
||||||
double **x = atom->x;
|
double **x = atom->x;
|
||||||
double *radius = atom->radius;
|
double *radius = atom->radius;
|
||||||
int *type = atom->type;
|
int *type = atom->type;
|
||||||
@ -61,56 +63,68 @@ void NPairHalfSizeMultiNewtonTri::build(NeighList *list)
|
|||||||
for (i = 0; i < nlocal; i++) {
|
for (i = 0; i < nlocal; i++) {
|
||||||
n = 0;
|
n = 0;
|
||||||
neighptr = ipage->vget();
|
neighptr = ipage->vget();
|
||||||
|
|
||||||
itype = type[i];
|
itype = type[i];
|
||||||
|
icollection = collection[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];
|
||||||
radi = radius[i];
|
radi = radius[i];
|
||||||
|
|
||||||
|
|
||||||
// loop over all atoms in bins, including self, in stencil
|
|
||||||
// skip if i,j neighbor cutoff is less than bin distance
|
|
||||||
// bins below self are excluded from stencil
|
|
||||||
// pairs for atoms j "below" i are excluded
|
|
||||||
// below = lower z or (equal z and lower y) or (equal zy and lower x)
|
|
||||||
// (equal zyx and j <= i)
|
|
||||||
// latter excludes self-self interaction but allows superposed atoms
|
|
||||||
|
|
||||||
ibin = atom2bin[i];
|
ibin = atom2bin[i];
|
||||||
s = stencil_multi[itype];
|
|
||||||
distsq = distsq_multi[itype];
|
// loop through stencils for all collections
|
||||||
cutsq = cutneighsq[itype];
|
for (jcollection = 0; jcollection < ncollections; jcollection++) {
|
||||||
ns = nstencil_multi[itype];
|
|
||||||
for (k = 0; k < ns; k++) {
|
// if same collection use own bin
|
||||||
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
|
if (icollection == jcollection) jbin = ibin;
|
||||||
jtype = type[j];
|
else jbin = coord2bin(x[i], jcollection);
|
||||||
if (cutsq[jtype] < distsq[k]) continue;
|
|
||||||
if (x[j][2] < ztmp) continue;
|
// loop over all atoms in bins in stencil
|
||||||
if (x[j][2] == ztmp) {
|
// stencil is empty if i larger than j
|
||||||
if (x[j][1] < ytmp) continue;
|
// stencil is half if i same size as j
|
||||||
if (x[j][1] == ytmp) {
|
// stencil is full if i smaller than j
|
||||||
if (x[j][0] < xtmp) continue;
|
// if half: pairs for atoms j "below" i are excluded
|
||||||
if (x[j][0] == xtmp && j <= i) continue;
|
// below = lower z or (equal z and lower y) or (equal zy and lower x)
|
||||||
|
// (equal zyx and j <= i)
|
||||||
|
// latter excludes self-self interaction but allows superposed atoms
|
||||||
|
|
||||||
|
s = stencil_multi[icollection][jcollection];
|
||||||
|
ns = nstencil_multi[icollection][jcollection];
|
||||||
|
|
||||||
|
for (k = 0; k < ns; k++) {
|
||||||
|
js = binhead_multi[jcollection][jbin + s[k]];
|
||||||
|
for (j = js; j >= 0; j = bins[j]) {
|
||||||
|
|
||||||
|
// if same size (same collection), use half stencil
|
||||||
|
if (cutcollectionsq[icollection][icollection] == cutcollectionsq[jcollection][jcollection]){
|
||||||
|
if (x[j][2] < ztmp) continue;
|
||||||
|
if (x[j][2] == ztmp) {
|
||||||
|
if (x[j][1] < ytmp) continue;
|
||||||
|
if (x[j][1] == ytmp) {
|
||||||
|
if (x[j][0] < xtmp) continue;
|
||||||
|
if (x[j][0] == xtmp && j <= i) continue;
|
||||||
|
}
|
||||||
|
}
|
||||||
}
|
}
|
||||||
}
|
|
||||||
|
|
||||||
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
jtype = type[j];
|
||||||
|
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
||||||
|
|
||||||
delx = xtmp - x[j][0];
|
delx = xtmp - x[j][0];
|
||||||
dely = ytmp - x[j][1];
|
dely = ytmp - x[j][1];
|
||||||
delz = ztmp - x[j][2];
|
delz = ztmp - x[j][2];
|
||||||
rsq = delx*delx + dely*dely + delz*delz;
|
rsq = delx*delx + dely*dely + delz*delz;
|
||||||
radsum = radi + radius[j];
|
radsum = radi + radius[j];
|
||||||
cutdistsq = (radsum+skin) * (radsum+skin);
|
cutdistsq = (radsum+skin) * (radsum+skin);
|
||||||
|
|
||||||
if (rsq <= cutdistsq) {
|
if (rsq <= cutdistsq) {
|
||||||
if (history && rsq < radsum*radsum)
|
if (history && rsq < radsum*radsum)
|
||||||
neighptr[n++] = j ^ mask_history;
|
neighptr[n++] = j ^ mask_history;
|
||||||
else
|
else
|
||||||
neighptr[n++] = j;
|
neighptr[n++] = j;
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
ilist[inum++] = i;
|
ilist[inum++] = i;
|
||||||
|
|||||||
@ -43,4 +43,5 @@ class NPairHalfSizeMultiNewtonTri : public NPair {
|
|||||||
E: Neighbor list overflow, boost neigh_modify one
|
E: Neighbor list overflow, boost neigh_modify one
|
||||||
|
|
||||||
UNDOCUMENTED
|
UNDOCUMENTED
|
||||||
|
|
||||||
*/
|
*/
|
||||||
|
|||||||
118
src/npair_half_size_multi_old_newtoff.cpp
Normal file
118
src/npair_half_size_multi_old_newtoff.cpp
Normal file
@ -0,0 +1,118 @@
|
|||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
https://lammps.sandia.gov/, 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 "npair_half_size_multi_old_newtoff.h"
|
||||||
|
|
||||||
|
#include "atom.h"
|
||||||
|
#include "error.h"
|
||||||
|
#include "molecule.h"
|
||||||
|
#include "my_page.h"
|
||||||
|
#include "neigh_list.h"
|
||||||
|
|
||||||
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
NPairHalfSizeMultiOldNewtoff::NPairHalfSizeMultiOldNewtoff(LAMMPS *lmp) : NPair(lmp) {}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
size particles
|
||||||
|
binned neighbor list construction with partial Newton's 3rd law
|
||||||
|
each owned atom i checks own bin and other bins in stencil
|
||||||
|
multi-type stencil is itype dependent and is distance checked
|
||||||
|
pair stored once if i,j are both owned and i < j
|
||||||
|
pair stored by me if j is ghost (also stored by proc owning j)
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void NPairHalfSizeMultiOldNewtoff::build(NeighList *list)
|
||||||
|
{
|
||||||
|
int i,j,k,n,itype,jtype,ibin,ns;
|
||||||
|
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
||||||
|
double radi,radsum,cutdistsq;
|
||||||
|
int *neighptr,*s;
|
||||||
|
double *cutsq,*distsq;
|
||||||
|
|
||||||
|
double **x = atom->x;
|
||||||
|
double *radius = atom->radius;
|
||||||
|
int *type = atom->type;
|
||||||
|
int *mask = atom->mask;
|
||||||
|
tagint *molecule = atom->molecule;
|
||||||
|
int nlocal = atom->nlocal;
|
||||||
|
if (includegroup) nlocal = atom->nfirst;
|
||||||
|
|
||||||
|
int history = list->history;
|
||||||
|
int *ilist = list->ilist;
|
||||||
|
int *numneigh = list->numneigh;
|
||||||
|
int **firstneigh = list->firstneigh;
|
||||||
|
MyPage<int> *ipage = list->ipage;
|
||||||
|
|
||||||
|
int mask_history = 3 << SBBITS;
|
||||||
|
|
||||||
|
int inum = 0;
|
||||||
|
ipage->reset();
|
||||||
|
|
||||||
|
for (i = 0; i < nlocal; i++) {
|
||||||
|
n = 0;
|
||||||
|
neighptr = ipage->vget();
|
||||||
|
|
||||||
|
itype = type[i];
|
||||||
|
xtmp = x[i][0];
|
||||||
|
ytmp = x[i][1];
|
||||||
|
ztmp = x[i][2];
|
||||||
|
radi = radius[i];
|
||||||
|
|
||||||
|
// loop over all atoms in other bins in stencil including self
|
||||||
|
// only store pair if i < j
|
||||||
|
// skip if i,j neighbor cutoff is less than bin distance
|
||||||
|
// stores own/own pairs only once
|
||||||
|
// stores own/ghost pairs on both procs
|
||||||
|
|
||||||
|
ibin = atom2bin[i];
|
||||||
|
s = stencil_multi_old[itype];
|
||||||
|
distsq = distsq_multi_old[itype];
|
||||||
|
cutsq = cutneighsq[itype];
|
||||||
|
ns = nstencil_multi_old[itype];
|
||||||
|
for (k = 0; k < ns; k++) {
|
||||||
|
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
|
||||||
|
if (j <= i) continue;
|
||||||
|
jtype = type[j];
|
||||||
|
if (cutsq[jtype] < distsq[k]) continue;
|
||||||
|
|
||||||
|
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
||||||
|
|
||||||
|
delx = xtmp - x[j][0];
|
||||||
|
dely = ytmp - x[j][1];
|
||||||
|
delz = ztmp - x[j][2];
|
||||||
|
rsq = delx*delx + dely*dely + delz*delz;
|
||||||
|
radsum = radi + radius[j];
|
||||||
|
cutdistsq = (radsum+skin) * (radsum+skin);
|
||||||
|
|
||||||
|
if (rsq <= cutdistsq) {
|
||||||
|
if (history && rsq < radsum*radsum)
|
||||||
|
neighptr[n++] = j ^ mask_history;
|
||||||
|
else
|
||||||
|
neighptr[n++] = j;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
ilist[inum++] = i;
|
||||||
|
firstneigh[i] = neighptr;
|
||||||
|
numneigh[i] = n;
|
||||||
|
ipage->vgot(n);
|
||||||
|
if (ipage->status())
|
||||||
|
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
|
||||||
|
}
|
||||||
|
|
||||||
|
list->inum = inum;
|
||||||
|
}
|
||||||
46
src/npair_half_size_multi_old_newtoff.h
Normal file
46
src/npair_half_size_multi_old_newtoff.h
Normal file
@ -0,0 +1,46 @@
|
|||||||
|
/* -*- c++ -*- ----------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
https://lammps.sandia.gov/, 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.
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
#ifdef NPAIR_CLASS
|
||||||
|
|
||||||
|
NPairStyle(half/size/multi/old/newtoff,
|
||||||
|
NPairHalfSizeMultiOldNewtoff,
|
||||||
|
NP_HALF | NP_SIZE | NP_MULTI_OLD | NP_NEWTOFF | NP_ORTHO | NP_TRI)
|
||||||
|
|
||||||
|
#else
|
||||||
|
|
||||||
|
#ifndef LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTOFF_H
|
||||||
|
#define LMP_NPAIR_HALF_SIZE_MULTI_OLD_NEWTOFF_H
|
||||||
|
|
||||||
|
#include "npair.h"
|
||||||
|
|
||||||
|
namespace LAMMPS_NS {
|
||||||
|
|
||||||
|
class NPairHalfSizeMultiOldNewtoff : public NPair {
|
||||||
|
public:
|
||||||
|
NPairHalfSizeMultiOldNewtoff(class LAMMPS *);
|
||||||
|
~NPairHalfSizeMultiOldNewtoff() {}
|
||||||
|
void build(class NeighList *);
|
||||||
|
};
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
#endif
|
||||||
|
#endif
|
||||||
|
|
||||||
|
/* ERROR/WARNING messages:
|
||||||
|
|
||||||
|
E: Neighbor list overflow, boost neigh_modify one
|
||||||
|
|
||||||
|
UNDOCUMENTED
|
||||||
|
*/
|
||||||
144
src/npair_half_size_multi_old_newton.cpp
Normal file
144
src/npair_half_size_multi_old_newton.cpp
Normal file
@ -0,0 +1,144 @@
|
|||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
LAMMPS - Large-scale Atomic/Molecular Massively Parallel Simulator
|
||||||
|
https://lammps.sandia.gov/, 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 "npair_half_size_multi_old_newton.h"
|
||||||
|
|
||||||
|
#include "atom.h"
|
||||||
|
#include "error.h"
|
||||||
|
#include "molecule.h"
|
||||||
|
#include "my_page.h"
|
||||||
|
#include "neigh_list.h"
|
||||||
|
|
||||||
|
using namespace LAMMPS_NS;
|
||||||
|
|
||||||
|
/* ---------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
NPairHalfSizeMultiOldNewton::NPairHalfSizeMultiOldNewton(LAMMPS *lmp) : NPair(lmp) {}
|
||||||
|
|
||||||
|
/* ----------------------------------------------------------------------
|
||||||
|
size particles
|
||||||
|
binned neighbor list construction with full Newton's 3rd law
|
||||||
|
each owned atom i checks its own bin and other bins in Newton stencil
|
||||||
|
multi-type stencil is itype dependent and is distance checked
|
||||||
|
every pair stored exactly once by some processor
|
||||||
|
------------------------------------------------------------------------- */
|
||||||
|
|
||||||
|
void NPairHalfSizeMultiOldNewton::build(NeighList *list)
|
||||||
|
{
|
||||||
|
int i,j,k,n,itype,jtype,ibin,ns;
|
||||||
|
double xtmp,ytmp,ztmp,delx,dely,delz,rsq;
|
||||||
|
double radi,radsum,cutdistsq;
|
||||||
|
int *neighptr,*s;
|
||||||
|
double *cutsq,*distsq;
|
||||||
|
|
||||||
|
double **x = atom->x;
|
||||||
|
double *radius = atom->radius;
|
||||||
|
int *type = atom->type;
|
||||||
|
int *mask = atom->mask;
|
||||||
|
tagint *molecule = atom->molecule;
|
||||||
|
int nlocal = atom->nlocal;
|
||||||
|
if (includegroup) nlocal = atom->nfirst;
|
||||||
|
|
||||||
|
int history = list->history;
|
||||||
|
int *ilist = list->ilist;
|
||||||
|
int *numneigh = list->numneigh;
|
||||||
|
int **firstneigh = list->firstneigh;
|
||||||
|
MyPage<int> *ipage = list->ipage;
|
||||||
|
|
||||||
|
int mask_history = 3 << SBBITS;
|
||||||
|
|
||||||
|
int inum = 0;
|
||||||
|
ipage->reset();
|
||||||
|
|
||||||
|
for (i = 0; i < nlocal; i++) {
|
||||||
|
n = 0;
|
||||||
|
neighptr = ipage->vget();
|
||||||
|
|
||||||
|
itype = type[i];
|
||||||
|
xtmp = x[i][0];
|
||||||
|
ytmp = x[i][1];
|
||||||
|
ztmp = x[i][2];
|
||||||
|
radi = radius[i];
|
||||||
|
|
||||||
|
// loop over rest of atoms in i's bin, ghosts are at end of linked list
|
||||||
|
// if j is owned atom, store it, since j is beyond i in linked list
|
||||||
|
// if j is ghost, only store if j coords are "above and to the right" of i
|
||||||
|
|
||||||
|
for (j = bins[i]; j >= 0; j = bins[j]) {
|
||||||
|
if (j >= nlocal) {
|
||||||
|
if (x[j][2] < ztmp) continue;
|
||||||
|
if (x[j][2] == ztmp) {
|
||||||
|
if (x[j][1] < ytmp) continue;
|
||||||
|
if (x[j][1] == ytmp && x[j][0] < xtmp) continue;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
jtype = type[j];
|
||||||
|
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
||||||
|
|
||||||
|
delx = xtmp - x[j][0];
|
||||||
|
dely = ytmp - x[j][1];
|
||||||
|
delz = ztmp - x[j][2];
|
||||||
|
rsq = delx*delx + dely*dely + delz*delz;
|
||||||
|
radsum = radi + radius[j];
|
||||||
|
cutdistsq = (radsum+skin) * (radsum+skin);
|
||||||
|
|
||||||
|
if (rsq <= cutdistsq) {
|
||||||
|
if (history && rsq < radsum*radsum)
|
||||||
|
neighptr[n++] = j ^ mask_history;
|
||||||
|
else
|
||||||
|
neighptr[n++] = j;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
// loop over all atoms in other bins in stencil, store every pair
|
||||||
|
// skip if i,j neighbor cutoff is less than bin distance
|
||||||
|
|
||||||
|
ibin = atom2bin[i];
|
||||||
|
s = stencil_multi_old[itype];
|
||||||
|
distsq = distsq_multi_old[itype];
|
||||||
|
cutsq = cutneighsq[itype];
|
||||||
|
ns = nstencil_multi_old[itype];
|
||||||
|
for (k = 0; k < ns; k++) {
|
||||||
|
for (j = binhead[ibin+s[k]]; j >= 0; j = bins[j]) {
|
||||||
|
jtype = type[j];
|
||||||
|
if (cutsq[jtype] < distsq[k]) continue;
|
||||||
|
|
||||||
|
if (exclude && exclusion(i,j,itype,jtype,mask,molecule)) continue;
|
||||||
|
|
||||||
|
delx = xtmp - x[j][0];
|
||||||
|
dely = ytmp - x[j][1];
|
||||||
|
delz = ztmp - x[j][2];
|
||||||
|
rsq = delx*delx + dely*dely + delz*delz;
|
||||||
|
radsum = radi + radius[j];
|
||||||
|
cutdistsq = (radsum+skin) * (radsum+skin);
|
||||||
|
|
||||||
|
if (rsq <= cutdistsq) {
|
||||||
|
if (history && rsq < radsum*radsum)
|
||||||
|
neighptr[n++] = j ^ mask_history;
|
||||||
|
else
|
||||||
|
neighptr[n++] = j;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
ilist[inum++] = i;
|
||||||
|
firstneigh[i] = neighptr;
|
||||||
|
numneigh[i] = n;
|
||||||
|
ipage->vgot(n);
|
||||||
|
if (ipage->status())
|
||||||
|
error->one(FLERR,"Neighbor list overflow, boost neigh_modify one");
|
||||||
|
}
|
||||||
|
|
||||||
|
list->inum = inum;
|
||||||
|
}
|
||||||
Some files were not shown because too many files have changed in this diff Show More
Reference in New Issue
Block a user