git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@7088 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
@ -142,44 +142,49 @@ features that can be added in the manner just described:
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<A NAME = "mod_1"></A><H4>10.1 Atom styles
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<A NAME = "mod_1"></A><H4>10.1 Atom styles
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</H4>
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</H4>
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<P>Classes that define an atom style are derived from the Atom class.
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<P>Classes that define an atom style are derived from the AtomVec class
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The atom style determines what quantities are associated with an atom.
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and managed by the Atom class. The atom style determines what
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A new atom style can be created if one of the existing atom styles
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quantities are associated with an atom. A new atom style can be
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does not define all the arrays you need to store and communicate with
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created if one of the existing atom styles does not define all
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atoms.
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the arrays you need to store and communicate with atoms.
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</P>
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</P>
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<P>Atom_vec_atomic.cpp is a simple example of an atom style.
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<P>Atom_vec_atomic.cpp is a simple example of an atom style.
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</P>
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</P>
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<P>Here is a brief description of methods you define in your new derived
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<P>Here is a brief description of methods you define in your new derived
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class. See atom.h for details.
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class. See atom_vec.h for details.
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</P>
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</P>
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<DIV ALIGN=center><TABLE BORDER=1 >
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<DIV ALIGN=center><TABLE BORDER=1 >
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<TR><TD >grow</TD><TD > re-allocate atom arrays to longer lengths</TD></TR>
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<TR><TD >init</TD><TD > one time setup (optional)</TD></TR>
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<TR><TD >copy</TD><TD > copy info for one atom to another atom's array locations</TD></TR>
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<TR><TD >grow</TD><TD > re-allocate atom arrays to longer lengths (required)</TD></TR>
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<TR><TD >pack_comm</TD><TD > store an atom's info in a buffer communicated every timestep</TD></TR>
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<TR><TD >grow_reset</TD><TD > make array pointers in Atom and AtomVec classes consistent (required)</TD></TR>
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<TR><TD >pack_comm_vel</TD><TD > add velocity info to buffer</TD></TR>
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<TR><TD >copy</TD><TD > copy info for one atom to another atom's array locations (required)</TD></TR>
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<TR><TD >pack_comm_one</TD><TD > store extra info unique to this atom style</TD></TR>
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<TR><TD >pack_comm</TD><TD > store an atom's info in a buffer communicated every timestep (required)</TD></TR>
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<TR><TD >unpack_comm</TD><TD > retrieve an atom's info from the buffer</TD></TR>
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<TR><TD >pack_comm_vel</TD><TD > add velocity info to communication buffer (required)</TD></TR>
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<TR><TD >unpack_comm_vel</TD><TD > also retrieve velocity info</TD></TR>
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<TR><TD >pack_comm_hybrid</TD><TD > store extra info unique to this atom style (optional)</TD></TR>
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<TR><TD >unpack_comm_one</TD><TD > retreive extra info unique to this atom style</TD></TR>
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<TR><TD >unpack_comm</TD><TD > retrieve an atom's info from the buffer (required)</TD></TR>
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<TR><TD >pack_reverse</TD><TD > store an atom's info in a buffer communicating partial forces</TD></TR>
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<TR><TD >unpack_comm_vel</TD><TD > also retrieve velocity info (required)</TD></TR>
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<TR><TD >pack_reverse_one</TD><TD > store extra info unique to this atom style</TD></TR>
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<TR><TD >unpack_comm_hybrid</TD><TD > retreive extra info unique to this atom style (optional)</TD></TR>
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<TR><TD >unpack_reverse</TD><TD > retrieve an atom's info from the buffer</TD></TR>
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<TR><TD >pack_reverse</TD><TD > store an atom's info in a buffer communicating partial forces (required)</TD></TR>
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<TR><TD >unpack_reverse_one</TD><TD > retreive extra info unique to this atom style</TD></TR>
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<TR><TD >pack_reverse_hybrid</TD><TD > store extra info unique to this atom style (optional)</TD></TR>
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<TR><TD >pack_border</TD><TD > store an atom's info in a buffer communicated on neighbor re-builds</TD></TR>
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<TR><TD >unpack_reverse</TD><TD > retrieve an atom's info from the buffer (required)</TD></TR>
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<TR><TD >pack_border_vel</TD><TD > add velocity info to buffer</TD></TR>
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<TR><TD >unpack_reverse_hybrid</TD><TD > retreive extra info unique to this atom style (optional)</TD></TR>
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<TR><TD >pack_border_one</TD><TD > store extra info unique to this atom style</TD></TR>
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<TR><TD >pack_border</TD><TD > store an atom's info in a buffer communicated on neighbor re-builds (required)</TD></TR>
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<TR><TD >unpack_border</TD><TD > retrieve an atom's info from the buffer</TD></TR>
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<TR><TD >pack_border_vel</TD><TD > add velocity info to buffer (required)</TD></TR>
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<TR><TD >unpack_border_vel</TD><TD > also retrieve velocity info</TD></TR>
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<TR><TD >pack_border_hybrid</TD><TD > store extra info unique to this atom style (optional)</TD></TR>
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<TR><TD >unpack_border_one</TD><TD > retreive extra info unique to this atom style</TD></TR>
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<TR><TD >unpack_border</TD><TD > retrieve an atom's info from the buffer (required)</TD></TR>
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<TR><TD >pack_exchange</TD><TD > store all an atom's info to migrate to another processor</TD></TR>
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<TR><TD >unpack_border_vel</TD><TD > also retrieve velocity info (required)</TD></TR>
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<TR><TD >unpack_exchange</TD><TD > retrieve an atom's info from the buffer</TD></TR>
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<TR><TD >unpack_border_hybrid</TD><TD > retreive extra info unique to this atom style (optional)</TD></TR>
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<TR><TD >size_restart</TD><TD > number of restart quantities associated with proc's atoms</TD></TR>
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<TR><TD >pack_exchange</TD><TD > store all an atom's info to migrate to another processor (required)</TD></TR>
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<TR><TD >pack_restart</TD><TD > pack atom quantities into a buffer</TD></TR>
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<TR><TD >unpack_exchange</TD><TD > retrieve an atom's info from the buffer (required)</TD></TR>
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<TR><TD >unpack_restart</TD><TD > unpack atom quantities from a buffer</TD></TR>
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<TR><TD >size_restart</TD><TD > number of restart quantities associated with proc's atoms (required)</TD></TR>
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<TR><TD >create_atom</TD><TD > create an individual atom of this style</TD></TR>
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<TR><TD >pack_restart</TD><TD > pack atom quantities into a buffer (required)</TD></TR>
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<TR><TD >data_atom</TD><TD > parse an atom line from the data file</TD></TR>
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<TR><TD >unpack_restart</TD><TD > unpack atom quantities from a buffer (required)</TD></TR>
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<TR><TD >memory_usage</TD><TD > tally memory allocated by atom arrays
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<TR><TD >create_atom</TD><TD > create an individual atom of this style (required)</TD></TR>
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<TR><TD >data_atom</TD><TD > parse an atom line from the data file (required)</TD></TR>
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<TR><TD >data_atom_hybrid</TD><TD > parse additional atom info unique to this atom style (optional)</TD></TR>
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<TR><TD >data_vel</TD><TD > parse one line of velocity information from data file (optional)</TD></TR>
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<TR><TD >data_vel_hybrid</TD><TD > parse additional velocity data unique to this atom style (optional)</TD></TR>
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<TR><TD >memory_usage</TD><TD > tally memory allocated by atom arrays (required)
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</TD></TR></TABLE></DIV>
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</TD></TR></TABLE></DIV>
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<P>The constructor of the derived class sets values for several variables
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<P>The constructor of the derived class sets values for several variables
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@ -200,16 +205,21 @@ add new potentials to LAMMPS.
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the harmonic forms of the angle, dihedral, and improper style
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the harmonic forms of the angle, dihedral, and improper style
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commands.
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commands.
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</P>
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</P>
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<P>Here is a brief description of methods you define in your new derived
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<P>Here is a brief description of common methods you define in your
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bond class. See bond.h, angle.h, dihedral.h, and improper.h for
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new derived class. See bond.h, angle.h, dihedral.h, and improper.h
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details.
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for details and specific additional methods.
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</P>
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</P>
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<DIV ALIGN=center><TABLE BORDER=1 >
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<DIV ALIGN=center><TABLE BORDER=1 >
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<TR><TD >compute</TD><TD > compute the molecular interactions</TD></TR>
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<TR><TD >init</TD><TD > check if all coefficients are set, calls <I>init_style</I> (optional)</TD></TR>
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<TR><TD >coeff</TD><TD > set coefficients for one bond type</TD></TR>
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<TR><TD >init_style</TD><TD > check if style specific conditions are met (optional)</TD></TR>
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<TR><TD >equilibrium_distance</TD><TD > length of bond, used by SHAKE</TD></TR>
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<TR><TD >compute</TD><TD > compute the molecular interactions (required)</TD></TR>
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<TR><TD >write & read_restart</TD><TD > writes/reads coeffs to restart files</TD></TR>
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<TR><TD >settings</TD><TD > apply global settings for all types (optional)</TD></TR>
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<TR><TD >single</TD><TD > force and energy of a single bond
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<TR><TD >coeff</TD><TD > set coefficients for one type (required)</TD></TR>
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<TR><TD >equilibrium_distance</TD><TD > length of bond, used by SHAKE (required, bond only)</TD></TR>
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<TR><TD >equilibrium_angle</TD><TD > opening of angle, used by SHAKE (required, angle only)</TD></TR>
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<TR><TD >write & read_restart</TD><TD > writes/reads coeffs to restart files (required)</TD></TR>
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<TR><TD >single</TD><TD > force and energy of a single bond or angle (required, bond or angle only)</TD></TR>
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<TR><TD >memory_usage</TD><TD > tally memory allocated by the style (optional)
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</TD></TR></TABLE></DIV>
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</TD></TR></TABLE></DIV>
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<HR>
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<HR>
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@ -230,14 +240,21 @@ per-atom kinetic energy.
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class. See compute.h for details.
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class. See compute.h for details.
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</P>
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</P>
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<DIV ALIGN=center><TABLE BORDER=1 >
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<DIV ALIGN=center><TABLE BORDER=1 >
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<TR><TD >compute_scalar</TD><TD > compute a scalar quantity</TD></TR>
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<TR><TD >init</TD><TD > perform one time setup (required)</TD></TR>
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<TR><TD >compute_vector</TD><TD > compute a vector of quantities</TD></TR>
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<TR><TD >init_list</TD><TD > neighbor list setup, if needed (optional)</TD></TR>
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<TR><TD >compute_peratom</TD><TD > compute one or more quantities per atom</TD></TR>
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<TR><TD >compute_scalar</TD><TD > compute a scalar quantity (optional)</TD></TR>
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<TR><TD >pack_comm</TD><TD > pack a buffer with items to communicate</TD></TR>
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<TR><TD >compute_vector</TD><TD > compute a vector of quantities (optional)</TD></TR>
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<TR><TD >unpack_comm</TD><TD > unpack the buffer</TD></TR>
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<TR><TD >compute_peratom</TD><TD > compute one or more quantities per atom (optional)</TD></TR>
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<TR><TD >pack_reverse</TD><TD > pack a buffer with items to reverse communicate</TD></TR>
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<TR><TD >compute_local</TD><TD > compute one or more quantities per processor (optional)</TD></TR>
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<TR><TD >unpack_reverse</TD><TD > unpack the buffer</TD></TR>
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<TR><TD >pack_comm</TD><TD > pack a buffer with items to communicate (optional)</TD></TR>
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<TR><TD >memory_usage</TD><TD > tally memory usage
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<TR><TD >unpack_comm</TD><TD > unpack the buffer (optional)</TD></TR>
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<TR><TD >pack_reverse</TD><TD > pack a buffer with items to reverse communicate (optional)</TD></TR>
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<TR><TD >unpack_reverse</TD><TD > unpack the buffer (optional)</TD></TR>
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<TR><TD >remove_bias</TD><TD > remove velocity bias from one atom (optional)</TD></TR>
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<TR><TD >remove_bias_all</TD><TD > remove velocity bias from all atoms in group (optional)</TD></TR>
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<TR><TD >restore_bias</TD><TD > restore velocity bias for one atom after remove_bias (optional)</TD></TR>
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<TR><TD >restore_bias_all</TD><TD > same as before, but for all atoms in group (optional)</TD></TR>
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<TR><TD >memory_usage</TD><TD > tally memory usage (optional)
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</TD></TR></TABLE></DIV>
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</TD></TR></TABLE></DIV>
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<HR>
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<HR>
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@ -295,34 +312,59 @@ implement.
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derived class. See fix.h for details.
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derived class. See fix.h for details.
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</P>
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</P>
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<DIV ALIGN=center><TABLE BORDER=1 >
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<DIV ALIGN=center><TABLE BORDER=1 >
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<TR><TD >setmask</TD><TD > determines when the fix is called during the timestep</TD></TR>
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<TR><TD >setmask</TD><TD > determines when the fix is called during the timestep (required)</TD></TR>
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<TR><TD >init</TD><TD > initialization before a run</TD></TR>
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<TR><TD >init</TD><TD > initialization before a run (optional)</TD></TR>
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<TR><TD >setup</TD><TD > called immediately before the 1st timestep</TD></TR>
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<TR><TD >setup_pre_exchange</TD><TD > called before atom exchange in setup (optional)</TD></TR>
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<TR><TD >initial_integrate</TD><TD > called at very beginning of each timestep</TD></TR>
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<TR><TD >setup_pre_force</TD><TD > called before force computation in setup (optional)</TD></TR>
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<TR><TD >pre_exchange</TD><TD > called before atom exchange on re-neighboring steps</TD></TR>
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<TR><TD >setup</TD><TD > called immediately before the 1st timestep and after forces are computed (optional)</TD></TR>
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<TR><TD >pre_neighbor</TD><TD > called before neighbor list build</TD></TR>
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<TR><TD >min_setup_pre_force</TD><TD > like setup_pre_force, but for minimizations instead of MD runs (optional)</TD></TR>
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<TR><TD >post_force</TD><TD > called after pair & molecular forces are computed</TD></TR>
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<TR><TD >min_setup</TD><TD > like setup, but for minimizations instead of MD runs (optional)</TD></TR>
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<TR><TD >final_integrate</TD><TD > called at end of each timestep</TD></TR>
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<TR><TD >initial_integrate</TD><TD > called at very beginning of each timestep (optional)</TD></TR>
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<TR><TD >end_of_step</TD><TD > called at very end of timestep</TD></TR>
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<TR><TD >pre_exchange</TD><TD > called before atom exchange on re-neighboring steps (optional)</TD></TR>
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<TR><TD >write_restart</TD><TD > dumps fix info to restart file</TD></TR>
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<TR><TD >pre_neighbor</TD><TD > called before neighbor list build (optional)</TD></TR>
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<TR><TD >restart</TD><TD > uses info from restart file to re-initialize the fix</TD></TR>
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<TR><TD >pre_force</TD><TD > called after pair & molecular forces are computed (optional)</TD></TR>
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<TR><TD >grow_arrays</TD><TD > allocate memory for atom-based arrays used by fix</TD></TR>
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<TR><TD >post_force</TD><TD > called after pair & molecular forces are computed and communicated (optional)</TD></TR>
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<TR><TD >copy_arrays</TD><TD > copy atom info when an atom migrates to a new processor</TD></TR>
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<TR><TD >final_integrate</TD><TD > called at end of each timestep (optional)</TD></TR>
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<TR><TD >memory_usage</TD><TD > report memory used by fix</TD></TR>
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<TR><TD >end_of_step</TD><TD > called at very end of timestep (optional)</TD></TR>
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<TR><TD >pack_exchange</TD><TD > store atom's data in a buffer</TD></TR>
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<TR><TD >write_restart</TD><TD > dumps fix info to restart file (optional)</TD></TR>
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<TR><TD >unpack_exchange</TD><TD > retrieve atom's data from a buffer</TD></TR>
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<TR><TD >restart</TD><TD > uses info from restart file to re-initialize the fix (optional)</TD></TR>
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<TR><TD >pack_restart</TD><TD > store atom's data for writing to restart file</TD></TR>
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<TR><TD >grow_arrays</TD><TD > allocate memory for atom-based arrays used by fix (optional)</TD></TR>
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<TR><TD >unpack_restart</TD><TD > retrieve atom's data from a restart file buffer</TD></TR>
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<TR><TD >copy_arrays</TD><TD > copy atom info when an atom migrates to a new processor (optional)</TD></TR>
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<TR><TD >size_restart</TD><TD > size of atom's data</TD></TR>
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<TR><TD >pack_exchange</TD><TD > store atom's data in a buffer (optional)</TD></TR>
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<TR><TD >maxsize_restart</TD><TD > max size of atom's data</TD></TR>
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<TR><TD >unpack_exchange</TD><TD > retrieve atom's data from a buffer (optional)</TD></TR>
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<TR><TD >initial_integrate_respa</TD><TD > same as initial_integrate, but for rRESPA</TD></TR>
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<TR><TD >pack_restart</TD><TD > store atom's data for writing to restart file (optional)</TD></TR>
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<TR><TD >post_force_respa</TD><TD > same as post_force, but for rRESPA</TD></TR>
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<TR><TD >unpack_restart</TD><TD > retrieve atom's data from a restart file buffer (optional)</TD></TR>
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<TR><TD >final_integrate_respa</TD><TD > same as final_integrate, but for rRESPA</TD></TR>
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<TR><TD >size_restart</TD><TD > size of atom's data (optional)</TD></TR>
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<TR><TD >pack_comm</TD><TD > pack a buffer to communicate a per-atom quantity</TD></TR>
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<TR><TD >maxsize_restart</TD><TD > max size of atom's data (optional)</TD></TR>
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<TR><TD >unpack_comm</TD><TD > unpack a buffer to communicate a per-atom quantity</TD></TR>
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<TR><TD >setup_pre_force_respa</TD><TD > same as setup_pre_force, but for rRESPA (optional)</TD></TR>
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<TR><TD >pack_reverse_comm</TD><TD > pack a buffer to reverse communicate a per-atom quantity</TD></TR>
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<TR><TD >initial_integrate_respa</TD><TD > same as initial_integrate, but for rRESPA (optional)</TD></TR>
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<TR><TD >unpack_reverse_comm</TD><TD > unpack a buffer to reverse communicate a per-atom quantity</TD></TR>
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<TR><TD >post_integrate_respa</TD><TD > called after the first half integration step is done in rRESPA (optional)</TD></TR>
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<TR><TD >thermo</TD><TD > compute quantities for thermodynamic output
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<TR><TD >pre_force_respa</TD><TD > same as pre_force, but for rRESPA (optional)</TD></TR>
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<TR><TD >post_force_respa</TD><TD > same as post_force, but for rRESPA (optional)</TD></TR>
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<TR><TD >final_integrate_respa</TD><TD > same as final_integrate, but for rRESPA (optional)</TD></TR>
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<TR><TD >min_pre_force</TD><TD > called after pair & molecular forces are computed in minimizer (optional)</TD></TR>
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<TR><TD >min_post_force</TD><TD > called after pair & molecular forces are computed and communicated in minmizer (optional)</TD></TR>
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<TR><TD >min_store</TD><TD > store extra data for linesearch based minimization on a LIFO stack (optional)</TD></TR>
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<TR><TD >min_pushstore</TD><TD > push the minimization LIFO stack one element down (optional)</TD></TR>
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<TR><TD >min_popstore</TD><TD > pop the minimization LIFO stack one element up (optional)</TD></TR>
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<TR><TD >min_clearstore</TD><TD > clear minimization LIFO stack (optional)</TD></TR>
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<TR><TD >min_step</TD><TD > reset or move forward on line search minimization (optional)</TD></TR>
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<TR><TD >min_dof</TD><TD > report number of degrees of freedom <I>added</I> by this fix in minimization (optional)</TD></TR>
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<TR><TD >max_alpha</TD><TD > report maximum allowed step size during linesearch minimization (optional)</TD></TR>
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<TR><TD >pack_comm</TD><TD > pack a buffer to communicate a per-atom quantity (optional)</TD></TR>
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<TR><TD >unpack_comm</TD><TD > unpack a buffer to communicate a per-atom quantity (optional)</TD></TR>
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<TR><TD >pack_reverse_comm</TD><TD > pack a buffer to reverse communicate a per-atom quantity (optional)</TD></TR>
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<TR><TD >unpack_reverse_comm</TD><TD > unpack a buffer to reverse communicate a per-atom quantity (optional)</TD></TR>
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<TR><TD >dof</TD><TD > report number of degrees of freedom <I>removed</I> by this fix during MD (optional)</TD></TR>
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<TR><TD >compute_scalar</TD><TD > return a global scalar property that the fix computes (optional)</TD></TR>
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<TR><TD >compute_vector</TD><TD > return a component of a vector property that the fix computes (optional)</TD></TR>
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<TR><TD >compute_array</TD><TD > return a component of an array property that the fix computes (optional)</TD></TR>
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<TR><TD >deform</TD><TD > called when the box size is changed (optional)</TD></TR>
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<TR><TD >reset_target</TD><TD > called when a change of the target temperature is requested during a run (optional)</TD></TR>
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<TR><TD >reset_dt</TD><TD > is called when a change of the time step is requested during a run (optional)</TD></TR>
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<TR><TD >modify_param</TD><TD > called when a fix_modify request is executed (optional)</TD></TR>
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<TR><TD >memory_usage</TD><TD > report memory used by fix (optional)</TD></TR>
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<TR><TD >thermo</TD><TD > compute quantities for thermodynamic output (optional)
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</TD></TR></TABLE></DIV>
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</TD></TR></TABLE></DIV>
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<P>Typically, only a small fraction of these methods are defined for a
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<P>Typically, only a small fraction of these methods are defined for a
|
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|||||||
@ -140,43 +140,48 @@ features that can be added in the manner just described:
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|||||||
|
|
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10.1 Atom styles :link(mod_1),h4
|
10.1 Atom styles :link(mod_1),h4
|
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|
|
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Classes that define an atom style are derived from the Atom class.
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Classes that define an atom style are derived from the AtomVec class
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||||||
The atom style determines what quantities are associated with an atom.
|
and managed by the Atom class. The atom style determines what
|
||||||
A new atom style can be created if one of the existing atom styles
|
quantities are associated with an atom. A new atom style can be
|
||||||
does not define all the arrays you need to store and communicate with
|
created if one of the existing atom styles does not define all
|
||||||
atoms.
|
the arrays you need to store and communicate with atoms.
|
||||||
|
|
||||||
Atom_vec_atomic.cpp is a simple example of an atom style.
|
Atom_vec_atomic.cpp is a simple example of an atom style.
|
||||||
|
|
||||||
Here is a brief description of methods you define in your new derived
|
Here is a brief description of methods you define in your new derived
|
||||||
class. See atom.h for details.
|
class. See atom_vec.h for details.
|
||||||
|
|
||||||
grow: re-allocate atom arrays to longer lengths
|
init: one time setup (optional)
|
||||||
copy: copy info for one atom to another atom's array locations
|
grow: re-allocate atom arrays to longer lengths (required)
|
||||||
pack_comm: store an atom's info in a buffer communicated every timestep
|
grow_reset: make array pointers in Atom and AtomVec classes consistent (required)
|
||||||
pack_comm_vel: add velocity info to buffer
|
copy: copy info for one atom to another atom's array locations (required)
|
||||||
pack_comm_one: store extra info unique to this atom style
|
pack_comm: store an atom's info in a buffer communicated every timestep (required)
|
||||||
unpack_comm: retrieve an atom's info from the buffer
|
pack_comm_vel: add velocity info to communication buffer (required)
|
||||||
unpack_comm_vel: also retrieve velocity info
|
pack_comm_hybrid: store extra info unique to this atom style (optional)
|
||||||
unpack_comm_one: retreive extra info unique to this atom style
|
unpack_comm: retrieve an atom's info from the buffer (required)
|
||||||
pack_reverse: store an atom's info in a buffer communicating partial forces
|
unpack_comm_vel: also retrieve velocity info (required)
|
||||||
pack_reverse_one: store extra info unique to this atom style
|
unpack_comm_hybrid: retreive extra info unique to this atom style (optional)
|
||||||
unpack_reverse: retrieve an atom's info from the buffer
|
pack_reverse: store an atom's info in a buffer communicating partial forces (required)
|
||||||
unpack_reverse_one: retreive extra info unique to this atom style
|
pack_reverse_hybrid: store extra info unique to this atom style (optional)
|
||||||
pack_border: store an atom's info in a buffer communicated on neighbor re-builds
|
unpack_reverse: retrieve an atom's info from the buffer (required)
|
||||||
pack_border_vel: add velocity info to buffer
|
unpack_reverse_hybrid: retreive extra info unique to this atom style (optional)
|
||||||
pack_border_one: store extra info unique to this atom style
|
pack_border: store an atom's info in a buffer communicated on neighbor re-builds (required)
|
||||||
unpack_border: retrieve an atom's info from the buffer
|
pack_border_vel: add velocity info to buffer (required)
|
||||||
unpack_border_vel: also retrieve velocity info
|
pack_border_hybrid: store extra info unique to this atom style (optional)
|
||||||
unpack_border_one: retreive extra info unique to this atom style
|
unpack_border: retrieve an atom's info from the buffer (required)
|
||||||
pack_exchange: store all an atom's info to migrate to another processor
|
unpack_border_vel: also retrieve velocity info (required)
|
||||||
unpack_exchange: retrieve an atom's info from the buffer
|
unpack_border_hybrid: retreive extra info unique to this atom style (optional)
|
||||||
size_restart: number of restart quantities associated with proc's atoms
|
pack_exchange: store all an atom's info to migrate to another processor (required)
|
||||||
pack_restart: pack atom quantities into a buffer
|
unpack_exchange: retrieve an atom's info from the buffer (required)
|
||||||
unpack_restart: unpack atom quantities from a buffer
|
size_restart: number of restart quantities associated with proc's atoms (required)
|
||||||
create_atom: create an individual atom of this style
|
pack_restart: pack atom quantities into a buffer (required)
|
||||||
data_atom: parse an atom line from the data file
|
unpack_restart: unpack atom quantities from a buffer (required)
|
||||||
memory_usage: tally memory allocated by atom arrays :tb(s=:)
|
create_atom: create an individual atom of this style (required)
|
||||||
|
data_atom: parse an atom line from the data file (required)
|
||||||
|
data_atom_hybrid: parse additional atom info unique to this atom style (optional)
|
||||||
|
data_vel: parse one line of velocity information from data file (optional)
|
||||||
|
data_vel_hybrid: parse additional velocity data unique to this atom style (optional)
|
||||||
|
memory_usage: tally memory allocated by atom arrays (required) :tb(s=:)
|
||||||
|
|
||||||
The constructor of the derived class sets values for several variables
|
The constructor of the derived class sets values for several variables
|
||||||
that you must set when defining a new atom style, which are documented
|
that you must set when defining a new atom style, which are documented
|
||||||
@ -196,15 +201,20 @@ Bond_harmonic.cpp is the simplest example of a bond style. Ditto for
|
|||||||
the harmonic forms of the angle, dihedral, and improper style
|
the harmonic forms of the angle, dihedral, and improper style
|
||||||
commands.
|
commands.
|
||||||
|
|
||||||
Here is a brief description of methods you define in your new derived
|
Here is a brief description of common methods you define in your
|
||||||
bond class. See bond.h, angle.h, dihedral.h, and improper.h for
|
new derived class. See bond.h, angle.h, dihedral.h, and improper.h
|
||||||
details.
|
for details and specific additional methods.
|
||||||
|
|
||||||
compute: compute the molecular interactions
|
init: check if all coefficients are set, calls {init_style} (optional)
|
||||||
coeff: set coefficients for one bond type
|
init_style: check if style specific conditions are met (optional)
|
||||||
equilibrium_distance: length of bond, used by SHAKE
|
compute: compute the molecular interactions (required)
|
||||||
write & read_restart: writes/reads coeffs to restart files
|
settings: apply global settings for all types (optional)
|
||||||
single: force and energy of a single bond :tb(s=:)
|
coeff: set coefficients for one type (required)
|
||||||
|
equilibrium_distance: length of bond, used by SHAKE (required, bond only)
|
||||||
|
equilibrium_angle: opening of angle, used by SHAKE (required, angle only)
|
||||||
|
write & read_restart: writes/reads coeffs to restart files (required)
|
||||||
|
single: force and energy of a single bond or angle (required, bond or angle only)
|
||||||
|
memory_usage: tally memory allocated by the style (optional) :tb(s=:)
|
||||||
|
|
||||||
:line
|
:line
|
||||||
|
|
||||||
@ -223,14 +233,21 @@ per-atom kinetic energy.
|
|||||||
Here is a brief description of methods you define in your new derived
|
Here is a brief description of methods you define in your new derived
|
||||||
class. See compute.h for details.
|
class. See compute.h for details.
|
||||||
|
|
||||||
compute_scalar: compute a scalar quantity
|
init: perform one time setup (required)
|
||||||
compute_vector: compute a vector of quantities
|
init_list: neighbor list setup, if needed (optional)
|
||||||
compute_peratom: compute one or more quantities per atom
|
compute_scalar: compute a scalar quantity (optional)
|
||||||
pack_comm: pack a buffer with items to communicate
|
compute_vector: compute a vector of quantities (optional)
|
||||||
unpack_comm: unpack the buffer
|
compute_peratom: compute one or more quantities per atom (optional)
|
||||||
pack_reverse: pack a buffer with items to reverse communicate
|
compute_local: compute one or more quantities per processor (optional)
|
||||||
unpack_reverse: unpack the buffer
|
pack_comm: pack a buffer with items to communicate (optional)
|
||||||
memory_usage: tally memory usage :tb(s=:)
|
unpack_comm: unpack the buffer (optional)
|
||||||
|
pack_reverse: pack a buffer with items to reverse communicate (optional)
|
||||||
|
unpack_reverse: unpack the buffer (optional)
|
||||||
|
remove_bias: remove velocity bias from one atom (optional)
|
||||||
|
remove_bias_all: remove velocity bias from all atoms in group (optional)
|
||||||
|
restore_bias: restore velocity bias for one atom after remove_bias (optional)
|
||||||
|
restore_bias_all: same as before, but for all atoms in group (optional)
|
||||||
|
memory_usage: tally memory usage (optional) :tb(s=:)
|
||||||
|
|
||||||
:line
|
:line
|
||||||
|
|
||||||
@ -283,34 +300,59 @@ implement.
|
|||||||
Here is a brief description of methods you can define in your new
|
Here is a brief description of methods you can define in your new
|
||||||
derived class. See fix.h for details.
|
derived class. See fix.h for details.
|
||||||
|
|
||||||
setmask: determines when the fix is called during the timestep
|
setmask: determines when the fix is called during the timestep (required)
|
||||||
init: initialization before a run
|
init: initialization before a run (optional)
|
||||||
setup: called immediately before the 1st timestep
|
setup_pre_exchange: called before atom exchange in setup (optional)
|
||||||
initial_integrate: called at very beginning of each timestep
|
setup_pre_force: called before force computation in setup (optional)
|
||||||
pre_exchange: called before atom exchange on re-neighboring steps
|
setup: called immediately before the 1st timestep and after forces are computed (optional)
|
||||||
pre_neighbor: called before neighbor list build
|
min_setup_pre_force: like setup_pre_force, but for minimizations instead of MD runs (optional)
|
||||||
post_force: called after pair & molecular forces are computed
|
min_setup: like setup, but for minimizations instead of MD runs (optional)
|
||||||
final_integrate: called at end of each timestep
|
initial_integrate: called at very beginning of each timestep (optional)
|
||||||
end_of_step: called at very end of timestep
|
pre_exchange: called before atom exchange on re-neighboring steps (optional)
|
||||||
write_restart: dumps fix info to restart file
|
pre_neighbor: called before neighbor list build (optional)
|
||||||
restart: uses info from restart file to re-initialize the fix
|
pre_force: called after pair & molecular forces are computed (optional)
|
||||||
grow_arrays: allocate memory for atom-based arrays used by fix
|
post_force: called after pair & molecular forces are computed and communicated (optional)
|
||||||
copy_arrays: copy atom info when an atom migrates to a new processor
|
final_integrate: called at end of each timestep (optional)
|
||||||
memory_usage: report memory used by fix
|
end_of_step: called at very end of timestep (optional)
|
||||||
pack_exchange: store atom's data in a buffer
|
write_restart: dumps fix info to restart file (optional)
|
||||||
unpack_exchange: retrieve atom's data from a buffer
|
restart: uses info from restart file to re-initialize the fix (optional)
|
||||||
pack_restart: store atom's data for writing to restart file
|
grow_arrays: allocate memory for atom-based arrays used by fix (optional)
|
||||||
unpack_restart: retrieve atom's data from a restart file buffer
|
copy_arrays: copy atom info when an atom migrates to a new processor (optional)
|
||||||
size_restart: size of atom's data
|
pack_exchange: store atom's data in a buffer (optional)
|
||||||
maxsize_restart: max size of atom's data
|
unpack_exchange: retrieve atom's data from a buffer (optional)
|
||||||
initial_integrate_respa: same as initial_integrate, but for rRESPA
|
pack_restart: store atom's data for writing to restart file (optional)
|
||||||
post_force_respa: same as post_force, but for rRESPA
|
unpack_restart: retrieve atom's data from a restart file buffer (optional)
|
||||||
final_integrate_respa: same as final_integrate, but for rRESPA
|
size_restart: size of atom's data (optional)
|
||||||
pack_comm: pack a buffer to communicate a per-atom quantity
|
maxsize_restart: max size of atom's data (optional)
|
||||||
unpack_comm: unpack a buffer to communicate a per-atom quantity
|
setup_pre_force_respa: same as setup_pre_force, but for rRESPA (optional)
|
||||||
pack_reverse_comm: pack a buffer to reverse communicate a per-atom quantity
|
initial_integrate_respa: same as initial_integrate, but for rRESPA (optional)
|
||||||
unpack_reverse_comm: unpack a buffer to reverse communicate a per-atom quantity
|
post_integrate_respa: called after the first half integration step is done in rRESPA (optional)
|
||||||
thermo: compute quantities for thermodynamic output :tb(s=:)
|
pre_force_respa: same as pre_force, but for rRESPA (optional)
|
||||||
|
post_force_respa: same as post_force, but for rRESPA (optional)
|
||||||
|
final_integrate_respa: same as final_integrate, but for rRESPA (optional)
|
||||||
|
min_pre_force: called after pair & molecular forces are computed in minimizer (optional)
|
||||||
|
min_post_force: called after pair & molecular forces are computed and communicated in minmizer (optional)
|
||||||
|
min_store: store extra data for linesearch based minimization on a LIFO stack (optional)
|
||||||
|
min_pushstore: push the minimization LIFO stack one element down (optional)
|
||||||
|
min_popstore: pop the minimization LIFO stack one element up (optional)
|
||||||
|
min_clearstore: clear minimization LIFO stack (optional)
|
||||||
|
min_step: reset or move forward on line search minimization (optional)
|
||||||
|
min_dof: report number of degrees of freedom {added} by this fix in minimization (optional)
|
||||||
|
max_alpha: report maximum allowed step size during linesearch minimization (optional)
|
||||||
|
pack_comm: pack a buffer to communicate a per-atom quantity (optional)
|
||||||
|
unpack_comm: unpack a buffer to communicate a per-atom quantity (optional)
|
||||||
|
pack_reverse_comm: pack a buffer to reverse communicate a per-atom quantity (optional)
|
||||||
|
unpack_reverse_comm: unpack a buffer to reverse communicate a per-atom quantity (optional)
|
||||||
|
dof: report number of degrees of freedom {removed} by this fix during MD (optional)
|
||||||
|
compute_scalar: return a global scalar property that the fix computes (optional)
|
||||||
|
compute_vector: return a component of a vector property that the fix computes (optional)
|
||||||
|
compute_array: return a component of an array property that the fix computes (optional)
|
||||||
|
deform: called when the box size is changed (optional)
|
||||||
|
reset_target: called when a change of the target temperature is requested during a run (optional)
|
||||||
|
reset_dt: is called when a change of the time step is requested during a run (optional)
|
||||||
|
modify_param: called when a fix_modify request is executed (optional)
|
||||||
|
memory_usage: report memory used by fix (optional)
|
||||||
|
thermo: compute quantities for thermodynamic output (optional) :tb(s=:)
|
||||||
|
|
||||||
Typically, only a small fraction of these methods are defined for a
|
Typically, only a small fraction of these methods are defined for a
|
||||||
particular fix. Setmask is mandatory, as it determines when the fix
|
particular fix. Setmask is mandatory, as it determines when the fix
|
||||||
|
|||||||
Reference in New Issue
Block a user