move versionadded tags to the top, replace some missed TBD with version info
This commit is contained in:
Axel Kohlmeyer
@ -506,9 +506,9 @@ class lammps(object):
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def error(self, error_type, error_text):
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"""Forward error to the LAMMPS Error class.
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This is a wrapper around the :cpp:func:`lammps_error` function of the C-library interface.
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.. versionadded:: 3Nov2022
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.. versionadded:: TBD
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This is a wrapper around the :cpp:func:`lammps_error` function of the C-library interface.
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:param error_type:
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:type error_type: int
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@ -1343,6 +1343,8 @@ class lammps(object):
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def gather_bonds(self):
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"""Retrieve global list of bonds
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.. versionadded:: 28Jul2021
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This is a wrapper around the :cpp:func:`lammps_gather_bonds`
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function of the C-library interface.
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@ -1350,8 +1352,6 @@ class lammps(object):
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flat list of ctypes integer values with the bond type, bond atom1,
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bond atom2 for each bond.
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.. versionadded:: 28Jul2021
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:return: a tuple with the number of bonds and a list of c_int or c_long
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:rtype: (int, 3*nbonds*c_tagint)
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"""
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@ -1366,6 +1366,8 @@ class lammps(object):
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def gather_angles(self):
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"""Retrieve global list of angles
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.. versionadded:: 8Feb2023
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This is a wrapper around the :cpp:func:`lammps_gather_angles`
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function of the C-library interface.
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@ -1373,8 +1375,6 @@ class lammps(object):
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flat list of ctypes integer values with the angle type, angle atom1,
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angle atom2, angle atom3 for each angle.
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.. versionadded:: TBD
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:return: a tuple with the number of angles and a list of c_int or c_long
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:rtype: (int, 4*nangles*c_tagint)
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"""
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@ -1389,6 +1389,8 @@ class lammps(object):
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def gather_dihedrals(self):
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"""Retrieve global list of dihedrals
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.. versionadded:: 8Feb2023
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This is a wrapper around the :cpp:func:`lammps_gather_dihedrals`
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function of the C-library interface.
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@ -1396,8 +1398,6 @@ class lammps(object):
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flat list of ctypes integer values with the dihedral type, dihedral atom1,
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dihedral atom2, dihedral atom3, dihedral atom4 for each dihedral.
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.. versionadded:: TBD
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:return: a tuple with the number of dihedrals and a list of c_int or c_long
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:rtype: (int, 5*ndihedrals*c_tagint)
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"""
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@ -1412,6 +1412,8 @@ class lammps(object):
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def gather_impropers(self):
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"""Retrieve global list of impropers
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.. versionadded:: 8Feb2023
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This is a wrapper around the :cpp:func:`lammps_gather_impropers`
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function of the C-library interface.
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@ -1419,8 +1421,6 @@ class lammps(object):
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flat list of ctypes integer values with the improper type, improper atom1,
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improper atom2, improper atom3, improper atom4 for each improper.
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.. versionadded:: TBD
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:return: a tuple with the number of impropers and a list of c_int or c_long
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:rtype: (int, 5*nimpropers*c_tagint)
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"""
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@ -1659,13 +1659,13 @@ class lammps(object):
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def is_running(self):
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""" Report whether being called from a function during a run or a minimization
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.. versionadded:: 9Oct2020
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Various LAMMPS commands must not be called during an ongoing
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run or minimization. This property allows to check for that.
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This is a wrapper around the :cpp:func:`lammps_is_running`
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function of the library interface.
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.. versionadded:: 9Oct2020
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:return: True when called during a run otherwise false
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:rtype: bool
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"""
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@ -1676,12 +1676,13 @@ class lammps(object):
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def force_timeout(self):
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""" Trigger an immediate timeout, i.e. a "soft stop" of a run.
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.. versionadded:: 9Oct2020
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This function allows to cleanly stop an ongoing run or minimization
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at the next loop iteration.
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This is a wrapper around the :cpp:func:`lammps_force_timeout`
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function of the library interface.
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.. versionadded:: 9Oct2020
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"""
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self.lib.lammps_force_timeout(self.lmp)
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@ -1764,11 +1765,11 @@ class lammps(object):
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def has_package(self, name):
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""" Report if the named package has been enabled in the LAMMPS shared library.
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.. versionadded:: 3Nov2022
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This is a wrapper around the :cpp:func:`lammps_config_has_package`
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function of the library interface.
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.. versionadded:: TBD
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:param name: name of the package
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:type name: string
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@ -1908,11 +1909,11 @@ class lammps(object):
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def has_id(self, category, name):
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"""Returns whether a given ID name is available in a given category
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.. versionadded:: 9Oct2020
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This is a wrapper around the function :cpp:func:`lammps_has_id`
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of the library interface.
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.. versionadded:: 9Oct2020
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:param category: name of category
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:type category: string
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:param name: name of the ID
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@ -1928,11 +1929,11 @@ class lammps(object):
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def available_ids(self, category):
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"""Returns a list of IDs available for a given category
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.. versionadded:: 9Oct2020
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This is a wrapper around the functions :cpp:func:`lammps_id_count()`
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and :cpp:func:`lammps_id_name()` of the library interface.
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.. versionadded:: 9Oct2020
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:param category: name of category
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:type category: string
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@ -1955,11 +1956,11 @@ class lammps(object):
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def available_plugins(self, category):
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"""Returns a list of plugins available for a given category
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.. versionadded:: 10Mar2021
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This is a wrapper around the functions :cpp:func:`lammps_plugin_count()`
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and :cpp:func:`lammps_plugin_name()` of the library interface.
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.. versionadded:: 10Mar2021
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:return: list of style/name pairs of loaded plugins
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:rtype: list
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"""
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@ -2024,11 +2025,11 @@ class lammps(object):
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def fix_external_get_force(self, fix_id):
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"""Get access to the array with per-atom forces of a fix external instance with a given fix ID.
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.. versionadded:: 28Jul2021
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This is a wrapper around the :cpp:func:`lammps_fix_external_get_force` function
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of the C-library interface.
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.. versionadded:: 28Jul2021
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:param fix_id: Fix-ID of a fix external instance
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:type: string
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:return: requested data
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@ -2043,11 +2044,11 @@ class lammps(object):
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def fix_external_set_energy_global(self, fix_id, eng):
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"""Set the global energy contribution for a fix external instance with the given ID.
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.. versionadded:: 28Jul2021
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This is a wrapper around the :cpp:func:`lammps_fix_external_set_energy_global` function
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of the C-library interface.
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.. versionadded:: 28Jul2021
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:param fix_id: Fix-ID of a fix external instance
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:type: string
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:param eng: potential energy value to be added by fix external
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@ -2062,11 +2063,11 @@ class lammps(object):
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def fix_external_set_virial_global(self, fix_id, virial):
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"""Set the global virial contribution for a fix external instance with the given ID.
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.. versionadded:: 28Jul2021
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This is a wrapper around the :cpp:func:`lammps_fix_external_set_virial_global` function
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of the C-library interface.
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.. versionadded:: 28Jul2021
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:param fix_id: Fix-ID of a fix external instance
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:type: string
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:param eng: list of 6 floating point numbers with the virial to be added by fix external
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@ -2082,11 +2083,11 @@ class lammps(object):
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def fix_external_set_energy_peratom(self, fix_id, eatom):
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"""Set the per-atom energy contribution for a fix external instance with the given ID.
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.. versionadded:: 28Jul2021
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This is a wrapper around the :cpp:func:`lammps_fix_external_set_energy_peratom` function
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of the C-library interface.
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.. versionadded:: 28Jul2021
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:param fix_id: Fix-ID of a fix external instance
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:type: string
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:param eatom: list of potential energy values for local atoms to be added by fix external
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@ -2105,11 +2106,11 @@ class lammps(object):
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def fix_external_set_virial_peratom(self, fix_id, vatom):
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"""Set the per-atom virial contribution for a fix external instance with the given ID.
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.. versionadded:: 28Jul2021
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This is a wrapper around the :cpp:func:`lammps_fix_external_set_virial_peratom` function
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of the C-library interface.
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.. versionadded:: 28Jul2021
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:param fix_id: Fix-ID of a fix external instance
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:type: string
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:param vatom: list of natoms lists with 6 floating point numbers to be added by fix external
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@ -2137,11 +2138,11 @@ class lammps(object):
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def fix_external_set_vector_length(self, fix_id, length):
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"""Set the vector length for a global vector stored with fix external for analysis
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.. versionadded:: 28Jul2021
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This is a wrapper around the :cpp:func:`lammps_fix_external_set_vector_length` function
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of the C-library interface.
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.. versionadded:: 28Jul2021
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:param fix_id: Fix-ID of a fix external instance
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:type: string
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:param length: length of the global vector
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@ -2155,11 +2156,11 @@ class lammps(object):
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def fix_external_set_vector(self, fix_id, idx, val):
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"""Store a global vector value for a fix external instance with the given ID.
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.. versionadded:: 28Jul2021
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This is a wrapper around the :cpp:func:`lammps_fix_external_set_vector` function
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of the C-library interface.
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.. versionadded:: 28Jul2021
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:param fix_id: Fix-ID of a fix external instance
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:type: string
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:param idx: 1-based index of the value in the global vector
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@ -262,12 +262,12 @@ class numpy_wrapper:
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def gather_bonds(self):
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"""Retrieve global list of bonds as NumPy array
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.. versionadded:: 28Jul2021
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This is a wrapper around :py:meth:`lammps.gather_bonds() <lammps.lammps.gather_bonds()>`
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It behaves the same as the original method, but returns a NumPy array instead
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of a ``ctypes`` list.
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.. versionadded:: 28Jul2021
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:return: the requested data as a 2d-integer numpy array
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:rtype: numpy.array(nbonds,3)
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"""
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@ -280,12 +280,12 @@ class numpy_wrapper:
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def gather_angles(self):
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""" Retrieve global list of angles as NumPy array
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.. versionadded:: 8Feb2023
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This is a wrapper around :py:meth:`lammps.gather_angles() <lammps.lammps.gather_angles()>`
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It behaves the same as the original method, but returns a NumPy array instead
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of a ``ctypes`` list.
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.. versionadded:: TBD
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:return: the requested data as a 2d-integer numpy array
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:rtype: numpy.array(nangles,4)
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"""
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@ -298,12 +298,12 @@ class numpy_wrapper:
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def gather_dihedrals(self):
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""" Retrieve global list of dihedrals as NumPy array
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.. versionadded:: 8Feb2023
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This is a wrapper around :py:meth:`lammps.gather_dihedrals() <lammps.lammps.gather_dihedrals()>`
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It behaves the same as the original method, but returns a NumPy array instead
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of a ``ctypes`` list.
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.. versionadded:: TBD
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:return: the requested data as a 2d-integer numpy array
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:rtype: numpy.array(ndihedrals,5)
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"""
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@ -316,12 +316,12 @@ class numpy_wrapper:
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def gather_impropers(self):
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""" Retrieve global list of impropers as NumPy array
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.. versionadded:: 8Feb2023
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This is a wrapper around :py:meth:`lammps.gather_impropers() <lammps.lammps.gather_impropers()>`
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It behaves the same as the original method, but returns a NumPy array instead
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of a ``ctypes`` list.
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.. versionadded:: TBD
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:return: the requested data as a 2d-integer numpy array
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:rtype: numpy.array(nimpropers,5)
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"""
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@ -334,13 +334,13 @@ class numpy_wrapper:
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def fix_external_get_force(self, fix_id):
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"""Get access to the array with per-atom forces of a fix external instance with a given fix ID.
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.. versionchanged:: 28Jul2021
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This function is a wrapper around the
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:py:meth:`lammps.fix_external_get_force() <lammps.lammps.fix_external_get_force()>`
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method. It behaves the same as the original method, but returns a NumPy array instead
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of a ``ctypes`` pointer.
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.. versionchanged:: 28Jul2021
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:param fix_id: Fix-ID of a fix external instance
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:type: string
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:return: requested data
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@ -356,13 +356,13 @@ class numpy_wrapper:
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def fix_external_set_energy_peratom(self, fix_id, eatom):
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"""Set the per-atom energy contribution for a fix external instance with the given ID.
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.. versionadded:: 28Jul2021
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This function is an alternative to
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:py:meth:`lammps.fix_external_set_energy_peratom() <lammps.lammps.fix_external_set_energy_peratom()>`
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method. It behaves the same as the original method, but accepts a NumPy array
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instead of a list as argument.
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.. versionadded:: 28Jul2021
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:param fix_id: Fix-ID of a fix external instance
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:type: string
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:param eatom: per-atom potential energy
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@ -383,13 +383,13 @@ class numpy_wrapper:
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def fix_external_set_virial_peratom(self, fix_id, vatom):
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"""Set the per-atom virial contribution for a fix external instance with the given ID.
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.. versionadded:: 28Jul2021
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This function is an alternative to
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:py:meth:`lammps.fix_external_set_virial_peratom() <lammps.lammps.fix_external_set_virial_peratom()>`
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method. It behaves the same as the original method, but accepts a NumPy array
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instead of a list as argument.
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.. versionadded:: 28Jul2021
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:param fix_id: Fix-ID of a fix external instance
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:type: string
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:param eatom: per-atom potential energy
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