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106
doc/Section_python.html
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@ -335,16 +335,9 @@ Python on a single processor, not in parallel.
the source code for which is in python/lammps.py, which creates a the source code for which is in python/lammps.py, which creates a
"lammps" object, with a set of methods that can be invoked on that "lammps" object, with a set of methods that can be invoked on that
object. The sample Python code below assumes you have first imported object. The sample Python code below assumes you have first imported
the "lammps" module in your Python script. You can also include its the "lammps" module in your Python script, as follows:
settings as follows, which are useful in test return values from some
of the methods described below:
</P> </P>
<PRE>from lammps import lammps <PRE>from lammps import lammps
from lammps import LMPINT as INT
from lammps import LMPDOUBLE as DOUBLE
from lammps import LMPIPTR as IPTR
from lammps import LMPDPTR as DPTR
from lammps import LMPDPTRPTR as DPTRPTR
</PRE> </PRE>
<P>These are the methods defined by the lammps module. If you look <P>These are the methods defined by the lammps module. If you look
at the file src/library.cpp you will see that they correspond at the file src/library.cpp you will see that they correspond
@ -362,16 +355,20 @@ lmp = lammps("g++",list)
lmp.command(cmd) # invoke a single LAMMPS command, cmd = "run 100" lmp.command(cmd) # invoke a single LAMMPS command, cmd = "run 100"
</PRE> </PRE>
<PRE>xlo = lmp.extract_global(name,type) # extract a global quantity <PRE>xlo = lmp.extract_global(name,type) # extract a global quantity
# name = "boxxlo", "nlocal", etc # name = "boxxlo", "nlocal", etc
# type = INT or DOUBLE # type = 0 = int
# 1 = double
</PRE> </PRE>
<PRE>coords = lmp.extract_atom(name,type) # extract a per-atom quantity <PRE>coords = lmp.extract_atom(name,type) # extract a per-atom quantity
# name = "x", "type", etc # name = "x", "type", etc
# type = IPTR or DPTR or DPTRPTR # type = 0 = vector of ints
# 1 = array of ints
# 2 = vector of doubles
# 3 = array of doubles
</PRE> </PRE>
<PRE>eng = lmp.extract_compute(id,style,type) # extract value(s) from a compute <PRE>eng = lmp.extract_compute(id,style,type) # extract value(s) from a compute
v3 = lmp.extract_fix(id,style,type,i,j) # extract value(s) from a fix v3 = lmp.extract_fix(id,style,type,i,j) # extract value(s) from a fix
# id = ID of compute or fix # id = ID of compute or fix
# style = 0 = global data # style = 0 = global data
# 1 = per-atom data # 1 = per-atom data
# 2 = local data # 2 = local data
@ -387,8 +384,12 @@ v3 = lmp.extract_fix(id,style,type,i,j) # extract value(s) from a fix
# 1 = atom-style variable # 1 = atom-style variable
</PRE> </PRE>
<PRE>natoms = lmp.get_natoms() # total # of atoms as int <PRE>natoms = lmp.get_natoms() # total # of atoms as int
x = lmp.get_coords() # return coords of all atoms in x data = lmp.gather_atoms(name,type,count) # return atom attribute of all atoms gathered into data, ordered by atom ID
lmp.put_coords(x) # set all atom coords via x # 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
# name = "x", "charge", "type", etc
# count = # of per-atom values, 1 or 3, etc
</PRE> </PRE>
<HR> <HR>
@ -427,8 +428,8 @@ 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. 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 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 **) doubles or integers, or a pointer to an array of doubles (double **)
is returned. You need to specify the appropriate data type via the or integers (int **) is returned. You need to specify the appropriate
type argument. data type via the type argument.
</P> </P>
<P>For extract_compute() and extract_fix(), the global, per-atom, or <P>For extract_compute() and extract_fix(), the global, per-atom, or
local data calulated by the compute or fix can be accessed. What is local data calulated by the compute or fix can be accessed. What is
@ -456,58 +457,57 @@ Python subscripting. The values will be zero for atoms not in the
specified group. specified group.
</P> </P>
<P>The get_natoms() method returns the total number of atoms in the <P>The get_natoms() method returns the total number of atoms in the
simulation, as an int. Note that extract_global("natoms") returns the simulation, as an int.
same value, but as a double, which is the way LAMMPS stores it to
allow for systems with more atoms than can be stored in an int (> 2
billion).
</P> </P>
<P>The get_coords() method returns an ctypes vector of doubles of length <P>The gather_atoms() method returns a ctypes vector of ints or doubles
3*natoms, for the coordinates of all the atoms in the simulation, as specified by type, of length count*natoms, for the property of all
ordered by x,y,z and then by atom ID (see code for put_coords() the atoms in the simulation specified by name, ordered by count and
below). The array can be used via normal Python subscripting. If then by atom ID. The vector can be used via normal Python
atom IDs are not consecutively ordered within LAMMPS, a None is subscripting. If atom IDs are not consecutively ordered within
returned as indication of an error. LAMMPS, a None is returned as indication of an error.
</P> </P>
<P>Note that the data structure get_coords() returns is different from <P>Note that the data structure gather_atoms("x") returns is different
the data structure returned by extract_atom("x") in four ways. (1) from the data structure returned by extract_atom("x") in four ways.
Get_coords() returns a vector which you index as x[i]; (1) Gather_atoms() returns a vector which you index as x[i];
extract_atom() returns an array which you index as x[i][j]. (2) extract_atom() returns an array which you index as x[i][j]. (2)
Get_coords() orders the atoms by atom ID while extract_atom() does Gather_atoms() orders the atoms by atom ID while extract_atom() does
not. (3) Get_coords() returns a list of all atoms in the simulation; not. (3) Gathert_atoms() returns a list of all atoms in the
extract_atoms() returns just the atoms local to each processor. (4) simulation; extract_atoms() returns just the atoms local to each
Finally, the get_coords() data structure is a copy of the atom coords processor. (4) Finally, the gather_atoms() data structure is a copy
stored internally in LAMMPS, whereas extract_atom returns an array of the atom coords stored internally in LAMMPS, whereas extract_atom()
that points directly to the internal data. This means you can change returns an array that effectively points directly to the internal
values inside LAMMPS from Python by assigning a new values to the data. This means you can change values inside LAMMPS from Python by
extract_atom() array. To do this with the get_atoms() vector, you assigning a new values to the extract_atom() array. To do this with
need to change values in the vector, then invoke the put_coords() the gather_atoms() vector, you need to change values in the vector,
method. then invoke the scatter_atoms() method.
</P> </P>
<P>The put_coords() method takes a vector of coordinates for all atoms in <P>The scatter_atoms() method takes a vector of ints or doubles as
the simulation, assumed to be ordered by x,y,z and then by atom ID, specified by type, of length count*natoms, for the property of all the
and uses the values to overwrite the corresponding coordinates for atoms in the simulation specified by name, ordered by bount and then
each atom inside LAMMPS. This requires LAMMPS to have its "map" by atom ID. It uses the vector of data to overwrite the corresponding
option enabled; see the <A HREF = "atom_modify.html">atom_modify</A> command for properties for each atom inside LAMMPS. This requires LAMMPS to have
details. If it is not or if atom IDs are not consecutively ordered, its "map" option enabled; see the <A HREF = "atom_modify.html">atom_modify</A>
no coordinates are reset, command for details. If it is not, or if atom IDs are not
consecutively ordered, no coordinates are reset.
</P> </P>
<P>The array of coordinates passed to put_coords() must be a ctypes <P>The array of coordinates passed to scatter_atoms() must be a ctypes
vector of doubles, allocated and initialized something like this: vector of ints or doubles, allocated and initialized something like
this:
</P> </P>
<PRE>from ctypes import * <PRE>from ctypes import *
natoms = lmp.get_atoms() natoms = lmp.get_natoms()
n3 = 3*natoms n3 = 3*natoms
x = (c_double*n3)() x = (n3*c_double)()
x<B>0</B> = x coord of atom with ID 1 x<B>0</B> = x coord of atom with ID 1
x<B>1</B> = y coord of atom with ID 1 x<B>1</B> = y coord of atom with ID 1
x<B>2</B> = z coord of atom with ID 1 x<B>2</B> = z coord of atom with ID 1
x<B>3</B> = x coord of atom with ID 2 x<B>3</B> = x coord of atom with ID 2
... ...
x<B>n3-1</B> = z coord of atom with ID natoms x<B>n3-1</B> = z coord of atom with ID natoms
lmp.put_coords(x) lmp.scatter_coords("x",1,3,x)
</PRE> </PRE>
<P>Alternatively, you can just change values in the vector returned by <P>Alternatively, you can just change values in the vector returned by
get_coords(), since it is a ctypes vector of doubles. gather_atoms("x",1,3), since it is a ctypes vector of doubles.
</P> </P>
<HR> <HR>

108
doc/Section_python.txt
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@ -330,16 +330,9 @@ The Python interface to LAMMPS consists of a Python "lammps" module,
the source code for which is in python/lammps.py, which creates a the source code for which is in python/lammps.py, which creates a
"lammps" object, with a set of methods that can be invoked on that "lammps" object, with a set of methods that can be invoked on that
object. The sample Python code below assumes you have first imported object. The sample Python code below assumes you have first imported
the "lammps" module in your Python script. You can also include its the "lammps" module in your Python script, as follows:
settings as follows, which are useful in test return values from some
of the methods described below:
from lammps import lammps from lammps import lammps :pre
from lammps import LMPINT as INT
from lammps import LMPDOUBLE as DOUBLE
from lammps import LMPIPTR as IPTR
from lammps import LMPDPTR as DPTR
from lammps import LMPDPTRPTR as DPTRPTR :pre
These are the methods defined by the lammps module. If you look These are the methods defined by the lammps module. If you look
at the file src/library.cpp you will see that they correspond at the file src/library.cpp you will see that they correspond
@ -357,16 +350,20 @@ lmp.file(file) # run an entire input script, file = "in.lj"
lmp.command(cmd) # invoke a single LAMMPS command, cmd = "run 100" :pre lmp.command(cmd) # invoke a single LAMMPS command, cmd = "run 100" :pre
xlo = lmp.extract_global(name,type) # extract a global quantity xlo = lmp.extract_global(name,type) # extract a global quantity
# name = "boxxlo", "nlocal", etc # name = "boxxlo", "nlocal", etc
# type = INT or DOUBLE :pre # type = 0 = int
# 1 = double :pre
coords = lmp.extract_atom(name,type) # extract a per-atom quantity coords = lmp.extract_atom(name,type) # extract a per-atom quantity
# name = "x", "type", etc # name = "x", "type", etc
# type = IPTR or DPTR or DPTRPTR :pre # type = 0 = vector of ints
# 1 = array of ints
# 2 = vector of doubles
# 3 = array of doubles :pre
eng = lmp.extract_compute(id,style,type) # extract value(s) from a compute eng = lmp.extract_compute(id,style,type) # extract value(s) from a compute
v3 = lmp.extract_fix(id,style,type,i,j) # extract value(s) from a fix v3 = lmp.extract_fix(id,style,type,i,j) # extract value(s) from a fix
# id = ID of compute or fix # id = ID of compute or fix
# style = 0 = global data # style = 0 = global data
# 1 = per-atom data # 1 = per-atom data
# 2 = local data # 2 = local data
@ -382,8 +379,12 @@ var = lmp.extract_variable(name,group,flag) # extract value(s) from a variable
# 1 = atom-style variable :pre # 1 = atom-style variable :pre
natoms = lmp.get_natoms() # total # of atoms as int natoms = lmp.get_natoms() # total # of atoms as int
x = lmp.get_coords() # return coords of all atoms in x data = lmp.gather_atoms(name,type,count) # return atom attribute of all atoms gathered into data, ordered by atom ID
lmp.put_coords(x) # set all atom coords via x :pre # 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
# name = "x", "charge", "type", etc
# count = # of per-atom values, 1 or 3, etc :pre
:line :line
@ -422,8 +423,8 @@ 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. 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 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 **) doubles or integers, or a pointer to an array of doubles (double **)
is returned. You need to specify the appropriate data type via the or integers (int **) is returned. You need to specify the appropriate
type argument. data type via the type argument.
For extract_compute() and extract_fix(), the global, per-atom, or For extract_compute() and extract_fix(), the global, per-atom, or
local data calulated by the compute or fix can be accessed. What is local data calulated by the compute or fix can be accessed. What is
@ -451,58 +452,57 @@ Python subscripting. The values will be zero for atoms not in the
specified group. specified group.
The get_natoms() method returns the total number of atoms in the The get_natoms() method returns the total number of atoms in the
simulation, as an int. Note that extract_global("natoms") returns the simulation, as an int.
same value, but as a double, which is the way LAMMPS stores it to
allow for systems with more atoms than can be stored in an int (> 2
billion).
The get_coords() method returns an ctypes vector of doubles of length The gather_atoms() method returns a ctypes vector of ints or doubles
3*natoms, for the coordinates of all the atoms in the simulation, as specified by type, of length count*natoms, for the property of all
ordered by x,y,z and then by atom ID (see code for put_coords() the atoms in the simulation specified by name, ordered by count and
below). The array can be used via normal Python subscripting. If then by atom ID. The vector can be used via normal Python
atom IDs are not consecutively ordered within LAMMPS, a None is subscripting. If atom IDs are not consecutively ordered within
returned as indication of an error. LAMMPS, a None is returned as indication of an error.
Note that the data structure get_coords() returns is different from Note that the data structure gather_atoms("x") returns is different
the data structure returned by extract_atom("x") in four ways. (1) from the data structure returned by extract_atom("x") in four ways.
Get_coords() returns a vector which you index as x\[i\]; (1) Gather_atoms() returns a vector which you index as x\[i\];
extract_atom() returns an array which you index as x\[i\]\[j\]. (2) extract_atom() returns an array which you index as x\[i\]\[j\]. (2)
Get_coords() orders the atoms by atom ID while extract_atom() does Gather_atoms() orders the atoms by atom ID while extract_atom() does
not. (3) Get_coords() returns a list of all atoms in the simulation; not. (3) Gathert_atoms() returns a list of all atoms in the
extract_atoms() returns just the atoms local to each processor. (4) simulation; extract_atoms() returns just the atoms local to each
Finally, the get_coords() data structure is a copy of the atom coords processor. (4) Finally, the gather_atoms() data structure is a copy
stored internally in LAMMPS, whereas extract_atom returns an array of the atom coords stored internally in LAMMPS, whereas extract_atom()
that points directly to the internal data. This means you can change returns an array that effectively points directly to the internal
values inside LAMMPS from Python by assigning a new values to the data. This means you can change values inside LAMMPS from Python by
extract_atom() array. To do this with the get_atoms() vector, you assigning a new values to the extract_atom() array. To do this with
need to change values in the vector, then invoke the put_coords() the gather_atoms() vector, you need to change values in the vector,
method. then invoke the scatter_atoms() method.
The put_coords() method takes a vector of coordinates for all atoms in The scatter_atoms() method takes a vector of ints or doubles as
the simulation, assumed to be ordered by x,y,z and then by atom ID, specified by type, of length count*natoms, for the property of all the
and uses the values to overwrite the corresponding coordinates for atoms in the simulation specified by name, ordered by bount and then
each atom inside LAMMPS. This requires LAMMPS to have its "map" by atom ID. It uses the vector of data to overwrite the corresponding
option enabled; see the "atom_modify"_atom_modify.html command for properties for each atom inside LAMMPS. This requires LAMMPS to have
details. If it is not or if atom IDs are not consecutively ordered, its "map" option enabled; see the "atom_modify"_atom_modify.html
no coordinates are reset, 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 put_coords() must be a ctypes The array of coordinates passed to scatter_atoms() must be a ctypes
vector of doubles, allocated and initialized something like this: vector of ints or doubles, allocated and initialized something like
this:
from ctypes import * from ctypes import *
natoms = lmp.get_atoms() natoms = lmp.get_natoms()
n3 = 3*natoms n3 = 3*natoms
x = (c_double*n3)() x = (n3*c_double)()
x[0] = x coord of atom with ID 1 x[0] = x coord of atom with ID 1
x[1] = y coord of atom with ID 1 x[1] = y coord of atom with ID 1
x[2] = z coord of atom with ID 1 x[2] = z coord of atom with ID 1
x[3] = x coord of atom with ID 2 x[3] = x coord of atom with ID 2
... ...
x[n3-1] = z coord of atom with ID natoms x[n3-1] = z coord of atom with ID natoms
lmp.put_coords(x) :pre lmp.scatter_coords("x",1,3,x) :pre
Alternatively, you can just change values in the vector returned by Alternatively, you can just change values in the vector returned by
get_coords(), since it is a ctypes vector of doubles. gather_atoms("x",1,3), since it is a ctypes vector of doubles.
:line :line