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fix ave/chunk fixes, 2d disc option, fix_modify dynamic/dof

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This commit is contained in:
Steve Plimpton
2017-03-23 15:31:27 -06:00
parent dcede304df
commit 44841f6891
42 changed files with 316 additions and 154 deletions
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50
doc/src/Section_python.txt
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@ -594,10 +594,10 @@ flag = lmp.set_variable(name,value) # set existing named string-style vari
value = lmp.get_thermo(name) # return current value of a thermo keyword
natoms = lmp.get_natoms() # total # of atoms as int
data = lmp.gather_atoms(name,type,count) # return atom attribute of all atoms gathered into data, ordered by atom ID
data = lmp.gather_atoms(name,type,count) # return per-atom property of all atoms gathered into data, ordered by atom ID
# name = "x", "charge", "type", etc
# count = # of per-atom values, 1 or 3, etc
lmp.scatter_atoms(name,type,count,data) # scatter atom attribute of all atoms from data, ordered by atom ID
lmp.scatter_atoms(name,type,count,data) # scatter per-atom property to all atoms from data, ordered by atom ID
# name = "x", "charge", "type", etc
# count = # of per-atom values, 1 or 3, etc :pre
@ -656,10 +656,10 @@ argument.
For extract_atom(), a pointer to internal LAMMPS atom-based data is
returned, which you can use via normal Python subscripting. See the
extract() method in the src/atom.cpp file for a list of valid names.
Again, new names could easily be added. A pointer to a vector of
doubles or integers, or a pointer to an array of doubles (double **)
or integers (int **) is returned. You need to specify the appropriate
data type via the type argument.
Again, new names could easily be added if the property you want is not
listed. A pointer to a vector of doubles or integers, or a pointer to
an array of doubles (double **) or integers (int **) is returned. You
need to specify the appropriate data type via the type argument.
For extract_compute() and extract_fix(), the global, per-atom, or
local data calculated by the compute or fix can be accessed. What is
@ -689,12 +689,16 @@ specified group.
The get_natoms() method returns the total number of atoms in the
simulation, as an int.
The gather_atoms() method returns a ctypes vector of ints or doubles
as specified by type, of length count*natoms, for the property of all
the atoms in the simulation specified by name, ordered by count and
then by atom ID. The vector can be used via normal Python
subscripting. If atom IDs are not consecutively ordered within
LAMMPS, a None is returned as indication of an error.
The gather_atoms() method allows any per-atom property (coordinates,
velocities, etc) to be extracted from LAMMPS. It returns a ctypes
vector of ints or doubles as specified by type, of length
count*natoms, for the named property for all atoms in the simulation.
The data is ordered by count and then by atom ID. See the extract()
method in the src/atom.cpp file for a list of valid names. Again, new
names could easily be added if the property you want is missing. The
vector can be used via normal Python subscripting. If atom IDs are
not consecutively ordered within LAMMPS, a None is returned as
indication of an error.
Note that the data structure gather_atoms("x") returns is different
from the data structure returned by extract_atom("x") in four ways.
@ -711,14 +715,18 @@ assigning a new values to the extract_atom() array. To do this with
the gather_atoms() vector, you need to change values in the vector,
then invoke the scatter_atoms() method.
The scatter_atoms() method takes a vector of ints or doubles as
specified by type, of length count*natoms, for the property of all the
atoms in the simulation specified by name, ordered by bount and then
by atom ID. It uses the vector of data to overwrite the corresponding
properties for each atom inside LAMMPS. This requires LAMMPS to have
its "map" option enabled; see the "atom_modify"_atom_modify.html
command for details. If it is not, or if atom IDs are not
consecutively ordered, no coordinates are reset.
The scatter_atoms() method allows any per-atom property (coordinates,
velocities, etc) to be inserted into LAMMPS, overwriting the current
property. It takes a vector of ints or doubles as specified by type,
of length count*natoms, for the named property for all atoms in the
simulation. The data should be ordered by count and then by atom ID.
See the extract() method in the src/atom.cpp file for a list of valid
names. Again, new names could easily be added if the property you
want is missing. It uses the vector of data to overwrite the
corresponding properties for each atom inside LAMMPS. This requires
LAMMPS to have its "map" option enabled; see the
"atom_modify"_atom_modify.html command for details. If it is not, or
if atom IDs are not consecutively ordered, no coordinates are reset.
The array of coordinates passed to scatter_atoms() must be a ctypes
vector of ints or doubles, allocated and initialized something like
@ -734,7 +742,7 @@ x\[2\] = z coord of atom with ID 1
x\[3\] = x coord of atom with ID 2
...
x\[n3-1\] = z coord of atom with ID natoms
lmp.scatter_coords("x",1,3,x) :pre
lmp.scatter_atoms("x",1,3,x) :pre
Alternatively, you can just change values in the vector returned by
gather_atoms("x",1,3), since it is a ctypes vector of doubles.