add large nylon example for parallel validation, reformat doc page
This commit is contained in:
jrgissing
@ -39,7 +39,7 @@ react = mandatory argument indicating new reaction specification
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fraction = initiate reaction with this probability if otherwise eligible
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seed = random number seed (positive integer)
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{stabilize_steps} value = timesteps
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timesteps = number of timesteps to apply internally created nve/limit:pre
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timesteps = number of timesteps to apply internally created nve/limit :pre
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:ule
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[Examples:]
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@ -59,50 +59,152 @@ fix 6 nvt_grp nvt temp 300 300 100 # system-wide thermostat must be defined afte
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[Description:]
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Initiate complex covalent bonding (topology) changes. These topology changes will be referred to as "reactions" throughout this documentation. Topology changes are defined in pre- and post-reaction molecule templates and can include creation and deletion of bonds, angles, dihedrals, impropers, bond-types, angle-types, dihedral-types, atom-types, or atomic charges.
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Initiate complex covalent bonding (topology) changes. These topology
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changes will be referred to as "reactions" throughout this
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documentation. Topology changes are defined in pre- and post-reaction
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molecule templates and can include creation and deletion of bonds,
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angles, dihedrals, impropers, bond-types, angle-types, dihedral-types,
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atom-types, or atomic charges.
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Fix bond/react does not use quantum mechanical (eg. fix qmmm) or pairwise bond-order potential (eg. Tersoff or AIREBO) methods to determine bonding changes a priori. Rather, it uses a distance-based probabilistic criteria to effect predetermined topology changes in simulations using standard force fields.
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Fix bond/react does not use quantum mechanical (eg. fix qmmm) or
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pairwise bond-order potential (eg. Tersoff or AIREBO) methods to
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determine bonding changes a priori. Rather, it uses a distance-based
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probabilistic criteria to effect predetermined topology changes in
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simulations using standard force fields.
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This fix was created to facilitate the dynamic creation of polymeric, amorphous or highly-crosslinked systems. A suggested workflow for using this fix is: 1) identify a reaction to be simulated 2) build a molecule template of the reaction site before the reaction has occurred 3) build a molecule template of the reaction site after the reaction has occurred 4) create a map that relates the template-atom-IDs of each atom between pre- and post-reaction molecule templates 5) fill a simulation box with molecules and run a simulation with fix/bond react.
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This fix was created to facilitate the dynamic creation of polymeric,
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amorphous or highly-crosslinked systems. A suggested workflow for
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using this fix is: 1) identify a reaction to be simulated 2) build a
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molecule template of the reaction site before the reaction has
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occurred 3) build a molecule template of the reaction site after the
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reaction has occurred 4) create a map that relates the
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template-atom-IDs of each atom between pre- and post-reaction molecule
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templates 5) fill a simulation box with molecules and run a simulation
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with fix/bond react.
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Only one 'fix bond/react' command can be used at a time. Multiple reactions can be simultaneously applied by specifying multiple 'react' arguments to a single 'fix bond/react' command. This syntax is necessary because the ‘common keywords’ are applied to all reactions.
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Only one 'fix bond/react' command can be used at a time. Multiple
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reactions can be simultaneously applied by specifying multiple 'react'
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arguments to a single 'fix bond/react' command. This syntax is
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necessary because the ‘common keywords’ are applied to all reactions.
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The {stabilization} keyword enables reaction site stabilization. Reaction site stabilization is performed by including reacting atoms in an internally created fix "nve/limit"_fix_nve_limit.html time integrator for a set number of timesteps given by the {stabilize_steps} keyword. While reacting atoms are being time integrated by the internal nve/limit, they are prevented from being involved in any new reactions. The {xmax} value keyword should typically be set to the maximum distance that non-reacting atoms move during the simulation.
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The {stabilization} keyword enables reaction site stabilization.
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Reaction site stabilization is performed by including reacting atoms
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in an internally created fix "nve/limit"_fix_nve_limit.html time
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integrator for a set number of timesteps given by the
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{stabilize_steps} keyword. While reacting atoms are being time
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integrated by the internal nve/limit, they are prevented from being
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involved in any new reactions. The {xmax} value keyword should
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typically be set to the maximum distance that non-reacting atoms move
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during the simulation.
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The group-ID set using the {stabilization} keyword should be a previously unused group-ID. The fix bond/react command creates a "dynamic group"_group.html of this name that excludes reacting atoms. This dynamic group-ID should then be used by a subsequent system-wide time integrator, as shown in the second example above. It is necessary to place the time integration command after the fix bond/react command due to the internal dynamic grouping performed by fix bond/react.
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The group-ID set using the {stabilization} keyword should be a
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previously unused group-ID. The fix bond/react command creates a
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"dynamic group"_group.html of this name that excludes reacting atoms.
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This dynamic group-ID should then be used by a subsequent system-wide
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time integrator, as shown in the second example above. It is necessary
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to place the time integration command after the fix bond/react command
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due to the internal dynamic grouping performed by fix bond/react.
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The following comments pertain to each 'react' argument:
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A check for possible new reaction sites is performed every Nevery timesteps.
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A check for possible new reaction sites is performed every Nevery
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timesteps.
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Two conditions must be met for a reaction to occur. First a bonding atom pair must be identified. Second, the topology surrounding the bonding atom pair must match the topology of the pre-reaction template. If both these conditions are met, the reaction site is modified to match the post-reaction template.
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Two conditions must be met for a reaction to occur. First a bonding
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atom pair must be identified. Second, the topology surrounding the
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bonding atom pair must match the topology of the pre-reaction
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template. If both these conditions are met, the reaction site is
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modified to match the post-reaction template.
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A bonding atom pair will be identified if several conditions are met. First, a pair of atoms within the specified react-group-ID of type typei and typej must be within a distance Rmin of each other. The atom types typei and typej are specified in the pre- and post-reaction templates. The distance calculation uses the pair neighbor list, therefore bonded neighbor exclusions may prevent a reaction between 1st, 2nd or 3rd bonded neighbor atoms. If multiple bonding atom pairs are identified for an atom, the closest bonding atom partner is set as its "nearest" bonding partner. Then, if both an atomi and atomj have each other as their nearest bonding partners, these two atoms are identified as the bonding atom pair of the reaction site. Once this unique bonding atom pair is identified for each reaction, there could two or more reactions that involve a given atom on the same timestep. If this is the case, only one such reaction is permitted to occur. This reaction is chosen randomly from all potential reactions. This capability allows e.g. for different reaction pathways to proceed from identical reaction sites with user-specified probabilities.
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A bonding atom pair will be identified if several conditions are met.
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First, a pair of atoms within the specified react-group-ID of type
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typei and typej must be within a distance Rmin of each other. The atom
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types typei and typej are specified in the pre- and post-reaction
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templates. The distance calculation uses the pair neighbor list,
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therefore bonded neighbor exclusions may prevent a reaction between
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1st, 2nd or 3rd bonded neighbor atoms. If multiple bonding atom pairs
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are identified for an atom, the closest bonding atom partner is set as
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its "nearest" bonding partner. Then, if both an atomi and atomj have
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each other as their nearest bonding partners, these two atoms are
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identified as the bonding atom pair of the reaction site. Once this
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unique bonding atom pair is identified for each reaction, there could
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two or more reactions that involve a given atom on the same timestep.
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If this is the case, only one such reaction is permitted to occur.
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This reaction is chosen randomly from all potential reactions. This
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capability allows e.g. for different reaction pathways to proceed from
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identical reaction sites with user-specified probabilities.
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The pre-reacted molecule template is specified by a molecule command. This molecule template file contains a sample reaction site and its surrounding topology. As described below, the bonding atom pairs of the pre-reacted template are specified by atom ID in the map file. The pre-reacted molecule template should contain as few atoms as possible while still completely describing the topology of all atoms affected by the reaction. For example, if the force field contains dihedrals, the pre-reacted template should contain any atom within three bonds of reacting atoms.
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The pre-reacted molecule template is specified by a molecule command.
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This molecule template file contains a sample reaction site and its
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surrounding topology. As described below, the bonding atom pairs of
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the pre-reacted template are specified by atom ID in the map file. The
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pre-reacted molecule template should contain as few atoms as possible
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while still completely describing the topology of all atoms affected
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by the reaction. For example, if the force field contains dihedrals,
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the pre-reacted template should contain any atom within three bonds of
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reacting atoms.
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Some atoms in the pre-reacted template that are not reacting may have missing topology with respect to the simulation. For example, the pre-reacted template may contain an atom that would connect to the rest of a long polymer chain. These are referred to as edge atoms, and are also specified in the map file.
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Some atoms in the pre-reacted template that are not reacting may have
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missing topology with respect to the simulation. For example, the
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pre-reacted template may contain an atom that would connect to the
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rest of a long polymer chain. These are referred to as edge atoms, and
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are also specified in the map file.
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Note that some care must be taken when a building a molecule template for a given simulation. All atom types in the pre-reacted template must be the same as those of a potential reaction site in the simulation. A detailed discussion of matching molecule template atom types with the simulation is provided on the "molecule"_molecule.html command page.
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Note that some care must be taken when a building a molecule template
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for a given simulation. All atom types in the pre-reacted template
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must be the same as those of a potential reaction site in the
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simulation. A detailed discussion of matching molecule template atom
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types with the simulation is provided on the "molecule"_molecule.html
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command page.
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The post-reacted molecule template contains a sample of the reaction site and its surrounding topology after the reaction has occurred. It must contain the same number of atoms as the pre-reacted template. A one-to-one correspondence between the atom IDs in the pre- and post-reacted templates is specified in the map file as described below. Note that during a reaction, an atom, bond, etc. type may change to one that was previously not present in the simulation. These new types must also be defined during the setup of a given simulation. A discussion of correctly handling this is also provided on the "molecule"_molecule.html command page.
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The post-reacted molecule template contains a sample of the reaction
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site and its surrounding topology after the reaction has occurred. It
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must contain the same number of atoms as the pre-reacted template. A
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one-to-one correspondence between the atom IDs in the pre- and
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post-reacted templates is specified in the map file as described
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below. Note that during a reaction, an atom, bond, etc. type may
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change to one that was previously not present in the simulation. These
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new types must also be defined during the setup of a given simulation.
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A discussion of correctly handling this is also provided on the
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"molecule"_molecule.html command page.
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The map file is a text document with the following format:
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Format of the map file
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A map file has a header and a body. The header appears first. The first line of the header is always skipped; it typically contains a description of the file. Lines can have a trailing comment starting with '#' that is ignored. If the line is blank (only whitespace after comment is deleted), it is skipped. If the line contains a header keyword, the corresponding value(s) is read from the line. If it doesn’t contain a header keyword, the line begins the body of the file.
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A map file has a header and a body. The header appears first. The
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first line of the header is always skipped; it typically contains a
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description of the file. Lines can have a trailing comment starting
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with '#' that is ignored. If the line is blank (only whitespace after
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comment is deleted), it is skipped. If the line contains a header
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keyword, the corresponding value(s) is read from the line. If it
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doesn’t contain a header keyword, the line begins the body of the
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file.
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The header contains one mandatory keyword and one optional keyword. The mandatory keyword is 'equivalences' and the optional keyword is 'edgeIDs.' These specify the number of atoms in the pre- and post-reacted templates and the number of edge atoms in pre-reacted template, respectively.
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The header contains one mandatory keyword and one optional keyword.
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The mandatory keyword is 'equivalences' and the optional keyword is
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'edgeIDs.' These specify the number of atoms in the pre- and
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post-reacted templates and the number of edge atoms in pre-reacted
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template, respectively.
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The body contains two mandatory sections and one optional section. The first section begins with the keyword 'BondingIDs' and lists the atom IDs of the bonding atom pair in the pre-reacted molecule template. The second mandatory section begins with the keyword 'Equivalences' and lists a one-to-one correspondence between atom IDs of the pre- and post-reacted templates. The optional section begins with the keyword 'EdgeIDs' and list the atom IDs of edge atoms in the pre-reacted molecule template.
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The body contains two mandatory sections and one optional section. The
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first section begins with the keyword 'BondingIDs' and lists the atom
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IDs of the bonding atom pair in the pre-reacted molecule template. The
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second mandatory section begins with the keyword 'Equivalences' and
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lists a one-to-one correspondence between atom IDs of the pre- and
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post-reacted templates. The optional section begins with the keyword
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'EdgeIDs' and list the atom IDs of edge atoms in the pre-reacted
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molecule template.
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Format of the header of the map file
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These are the recognized header keywords. Header lines can come in any order. The value(s) are read from the beginning of the line. Thus the keyword 'equivalences' should be in a line like "25 equivalences."
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These are the recognized header keywords. Header lines can come in any
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order. The value(s) are read from the beginning of the line. Thus the
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keyword 'equivalences' should be in a line like "25 equivalences."
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equivalences = # of atoms in the pre- and post-reacted molecule templates
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edgeIDs = # of edge atoms in the pre-reacted molecule template
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equivalences = # of atoms in the pre- and post-reacted molecule
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templates edgeIDs = # of edge atoms in the pre-reacted molecule
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template
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The edgeIDs keyword is optional.
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@ -110,13 +212,19 @@ Format of the body of the map file
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These are the section keywords for the body of the file.
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BondingIDs, EdgeIDs = list of atom IDs of bonding and edge atoms in the pre-reacted molecule template
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BondingIDs, EdgeIDs = list of atom IDs of bonding and edge atoms in
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the pre-reacted molecule template
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Equivalences = a two column list where the first column is an atom ID of the pre-reacted
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molecule template, and the second column is the corresponding atom ID of the post-reacted
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molecule template
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Equivalences = a two column list where the first column is an atom ID
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of the pre-reacted molecule template, and the second column is the
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corresponding atom ID of the post-reacted molecule template
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The bondingIDs section will always contain two atom IDs, corresponding to the bonding atom pairs of the pre-reacted map file. The Equivalences section will contain as many rows as there are atoms in the pre- and post-reacted molecule templates. The edgeIDs section is optional, but would contain an atom ID for each edge atom in the pre-reacted molecule template.
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The bondingIDs section will always contain two atom IDs, corresponding
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to the bonding atom pairs of the pre-reacted map file. The
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Equivalences section will contain as many rows as there are atoms in
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the pre- and post-reacted molecule templates. The edgeIDs section is
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optional, but would contain an atom ID for each edge atom in the
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pre-reacted molecule template.
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A sample map file is given below:
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@ -128,13 +236,11 @@ this is a map file
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BondingIDs
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3
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5
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3 5
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EdgeIDs
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1
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7
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1 7
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Equivalences
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@ -147,54 +253,99 @@ Equivalences
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7 7
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---------------
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Once a reaction site has been successfully identified, data structures within LAMMPS that store bond topology are updated to reflect the post-reacted molecule template. All force fields with fixed bonds, angles, dihedrals or impropers are supported.
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Once a reaction site has been successfully identified, data structures
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within LAMMPS that store bond topology are updated to reflect the
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post-reacted molecule template. All force fields with fixed bonds,
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angles, dihedrals or impropers are supported.
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A few capabilities to note: 1) You may specify as many 'react' arguments as desired. For example, you could break down a complicated reaction mechanism into several reaction steps, each defined by a fix bond/react. 2) While typically a bond is formed between the bonding atom pairs specified in the pre-reacted molecule template, this is not required. 3) By reversing the order of the pre- and post-reacted molecule template in another fix bond/react command, you can allow for the possibility of one or more reverse reactions.
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A few capabilities to note: 1) You may specify as many 'react'
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arguments as desired. For example, you could break down a complicated
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reaction mechanism into several reaction steps, each defined by a fix
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bond/react. 2) While typically a bond is formed between the bonding
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atom pairs specified in the pre-reacted molecule template, this is not
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required. 3) By reversing the order of the pre- and post-reacted
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molecule template in another fix bond/react command, you can allow for
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the possibility of one or more reverse reactions.
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The optional keywords deal with the probability of a given reaction occurring as well as the stable equilibration of each reaction site as it occurs.
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The optional keywords deal with the probability of a given reaction
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occurring as well as the stable equilibration of each reaction site as
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it occurs.
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The {prob} keyword can affect whether an eligible reaction actually occurs. The fraction setting must be a value between 0.0 and 1.0. A uniform random number between 0.0 and 1.0 is generated and the eligible reaction only occurs if the random number is less than the fraction.
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The {prob} keyword can affect whether an eligible reaction actually
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occurs. The fraction setting must be a value between 0.0 and 1.0. A
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uniform random number between 0.0 and 1.0 is generated and the
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eligible reaction only occurs if the random number is less than the
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fraction.
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The {stabilize_steps} keyword allows for the specification of how many timesteps a reaction site is stabilized before being returned to the overall system thermostat.
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The {stabilize_steps} keyword allows for the specification of how many
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timesteps a reaction site is stabilized before being returned to the
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overall system thermostat.
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In order to produce the most physical behavior, this 'reaction site equilibration time' should be tuned to be as small as possible while retaining stability for a given system or reaction step. After a limited number of case studies, this number has been set to a default of 60 timesteps. Ideally, it should be individually tuned for each fix bond/react. Note that in some situations, decreasing rather than increasing this parameter will result in an increase in stability.
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In order to produce the most physical behavior, this 'reaction site
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equilibration time' should be tuned to be as small as possible while
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retaining stability for a given system or reaction step. After a
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limited number of case studies, this number has been set to a default
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of 60 timesteps. Ideally, it should be individually tuned for each fix
|
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bond/react. Note that in some situations, decreasing rather than
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increasing this parameter will result in an increase in stability.
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A few other considerations:
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It may be beneficial to ensure reacting atoms are at a certain temperature before being released to the overall thermostat. For this, you can use the internally-created dynamic group named "bond_react_MASTER_group." For example, adding the following command would thermostat the group of all atoms currently involved in a reaction:
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It may be beneficial to ensure reacting atoms are at a certain
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temperature before being released to the overall thermostat. For this,
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you can use the internally-created dynamic group named
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"bond_react_MASTER_group." For example, adding the following command
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would thermostat the group of all atoms currently involved in a
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reaction:
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fix 1 bond_react_MASTER_group temp/rescale 1 300 300 10 1
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NOTE: This command must be added after the fix bond/react command, and will apply to all reaction specifications.
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NOTE: This command must be added after the fix bond/react command, and
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will apply to all reaction specifications.
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Computationally, each timestep this fix operates, it loops over neighbor lists and computes distances between pairs of atoms in the list. It also communicates between neighboring processors to coordinate which bonds are created. All of these operations increase the cost of a timestep. Thus you should be cautious about invoking this fix too frequently.
|
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Computationally, each timestep this fix operates, it loops over
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neighbor lists and computes distances between pairs of atoms in the
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list. It also communicates between neighboring processors to
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coordinate which bonds are created. All of these operations increase
|
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the cost of a timestep. Thus you should be cautious about invoking
|
||||
this fix too frequently.
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You can dump out snapshots of the current bond topology via the dump local command.
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You can dump out snapshots of the current bond topology via the dump
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local command.
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:line
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[Restart, fix_modify, output, run start/stop, minimize info:]
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No information about this fix is written to "binary restart files"_restart.html. None of the "fix_modify"_fix_modify.html options are relevant to this fix.
|
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No information about this fix is written to "binary restart
|
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files"_restart.html. None of the "fix_modify"_fix_modify.html options
|
||||
are relevant to this fix.
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This fix computes one statistic for each 'react' argument that it stores in a global vector, of length 'number of react arguments', that can be accessed by various "output commands"_Section_howto.html#howto_15. The vector values calculated by this fix are "intensive".
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This fix computes one statistic for each 'react' argument that it
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stores in a global vector, of length 'number of react arguments', that
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can be accessed by various "output
|
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commands"_Section_howto.html#howto_15. The vector values calculated by
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this fix are "intensive".
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These is 1 quantity for each react argument:
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|
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(1) cumulative # of reactions occurred :ul
|
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No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy minimization"_minimize.html.
|
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No parameter of this fix can be used with the {start/stop} keywords of
|
||||
the "run"_run.html command. This fix is not invoked during "energy
|
||||
minimization"_minimize.html.
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[Restrictions:]
|
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|
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This fix is part of the MC package. It is only enabled if LAMMPS was built with that package. See the "Making LAMMPS"_Section_start.html#start_3 section for more info.
|
||||
This fix is part of the MC package. It is only enabled if LAMMPS was
|
||||
built with that package. See the "Making
|
||||
LAMMPS"_Section_start.html#start_3 section for more info.
|
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|
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[Related commands:]
|
||||
|
||||
"fix bond/create"_fix_bond_create.html,
|
||||
"fix bond/break"_fix_bond_break.html, "fix
|
||||
bond/swap"_fix_bond_swap.html, "dump local"_dump.html,
|
||||
"special_bonds"_special_bonds.html
|
||||
"fix bond/create"_fix_bond_create.html, "fix
|
||||
bond/break"_fix_bond_break.html, "fix bond/swap"_fix_bond_swap.html,
|
||||
"dump local"_dump.html, "special_bonds"_special_bonds.html
|
||||
|
||||
[Default:]
|
||||
|
||||
@ -202,5 +353,5 @@ The option defaults are stabilization = no, stabilize_steps = 60
|
||||
|
||||
:line
|
||||
|
||||
:link(Gissinger)
|
||||
[(Gissinger)] Gissinger, Jensen and Wise, Polymer, 128, 211 (2017).
|
||||
:link(Gissinger) [(Gissinger)] Gissinger, Jensen and Wise, Polymer,
|
||||
128, 211 (2017).
|
||||
|
||||
52
examples/bond_react/nylon,6-6_melt/infromdata.class2
Normal file
52
examples/bond_react/nylon,6-6_melt/infromdata.class2
Normal file
@ -0,0 +1,52 @@
|
||||
# 35,000 atom nylon melt example
|
||||
|
||||
units real
|
||||
|
||||
boundary p p p
|
||||
|
||||
atom_style full
|
||||
|
||||
log testing_log
|
||||
|
||||
kspace_style pppm 1.0e-2 # actually, this appears required to check 1-3 neighbors
|
||||
|
||||
pair_style lj/class2/coul/long 8.5
|
||||
|
||||
angle_style class2
|
||||
|
||||
bond_style class2
|
||||
|
||||
dihedral_style class2
|
||||
|
||||
improper_style class2
|
||||
|
||||
read_data large_nylon_melt.data
|
||||
|
||||
velocity all create 800.0 4928459 dist gaussian
|
||||
|
||||
molecule mol1 rxn1_stp1_unreacted.data_template
|
||||
molecule mol2 rxn1_stp1_reacted.data_template
|
||||
molecule mol3 rxn1_stp2_unreacted.data_template
|
||||
molecule mol4 rxn1_stp2_reacted.data_template
|
||||
|
||||
thermo 50
|
||||
|
||||
dump 1 all xyz 100 test_vis.xyz
|
||||
|
||||
fix myrxns all bond/react stabilization yes statted_grp .03 &
|
||||
react rxn1 all 1 2.9 mol1 mol2 rxn1_stp1_map &
|
||||
react rxn2 all 1 5 mol3 mol4 rxn1_stp2_map
|
||||
|
||||
# stable at 800K
|
||||
fix 1 statted_grp nvt temp 800 800 100
|
||||
|
||||
fix 4 bond_react_MASTER_group temp/rescale 1 800 800 10 1
|
||||
|
||||
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts
|
||||
|
||||
restart 100 restart1 restart2
|
||||
|
||||
run 200000
|
||||
|
||||
write_restart restart_longrun
|
||||
write_data restart_longrun.data
|
||||
278810
examples/bond_react/nylon,6-6_melt/large_nylon_melt.data
Normal file
278810
examples/bond_react/nylon,6-6_melt/large_nylon_melt.data
Normal file
File diff suppressed because it is too large
Load Diff
35
examples/bond_react/nylon,6-6_melt/rxn1_stp1_map
Normal file
35
examples/bond_react/nylon,6-6_melt/rxn1_stp1_map
Normal file
@ -0,0 +1,35 @@
|
||||
this is a nominal superimpose file
|
||||
|
||||
2 edgeIDs
|
||||
18 equivalences
|
||||
|
||||
BondingIDs
|
||||
|
||||
10
|
||||
1
|
||||
|
||||
EdgeIDs
|
||||
|
||||
16
|
||||
8
|
||||
|
||||
Equivalences
|
||||
|
||||
1 1
|
||||
2 2
|
||||
3 3
|
||||
4 4
|
||||
5 5
|
||||
6 6
|
||||
7 7
|
||||
8 8
|
||||
9 9
|
||||
10 10
|
||||
11 11
|
||||
12 12
|
||||
13 13
|
||||
14 14
|
||||
15 15
|
||||
16 16
|
||||
17 17
|
||||
18 18
|
||||
@ -0,0 +1,189 @@
|
||||
this is a molecule template for: initial nylon crosslink, post-reacting
|
||||
|
||||
18 atoms
|
||||
17 bonds
|
||||
31 angles
|
||||
39 dihedrals
|
||||
20 impropers
|
||||
|
||||
Types
|
||||
|
||||
1 9
|
||||
2 1
|
||||
3 1
|
||||
4 4
|
||||
5 4
|
||||
6 3
|
||||
7 3
|
||||
8 1
|
||||
9 1
|
||||
10 5
|
||||
11 8
|
||||
12 6
|
||||
13 3
|
||||
14 3
|
||||
15 7
|
||||
16 1
|
||||
17 3
|
||||
18 3
|
||||
|
||||
Charges
|
||||
|
||||
1 -0.300000
|
||||
2 0.000000
|
||||
3 0.000000
|
||||
4 0.000000
|
||||
5 0.000000
|
||||
6 0.000000
|
||||
7 0.000000
|
||||
8 0.000000
|
||||
9 0.000000
|
||||
10 0.300000
|
||||
11 0.000000
|
||||
12 0.000000
|
||||
13 0.000000
|
||||
14 0.000000
|
||||
15 0.000000
|
||||
16 0.000000
|
||||
17 0.000000
|
||||
18 0.000000
|
||||
|
||||
Coords
|
||||
|
||||
1 -5.522237 -0.752722 1.631158
|
||||
2 -5.170398 -0.545733 0.178130
|
||||
3 -6.469695 -0.553072 -0.648889
|
||||
4 -6.052076 -1.721152 1.744648
|
||||
5 -6.183059 0.071387 1.971497
|
||||
6 -4.489340 -1.389197 -0.173156
|
||||
7 -4.637591 0.453703 0.051252
|
||||
8 -5.618658 0.138919 4.386107
|
||||
9 -4.669492 -0.989819 3.943591
|
||||
10 -4.270194 -0.766405 2.474102
|
||||
11 -3.348470 -1.875393 2.024289
|
||||
12 -3.569794 0.564183 2.345995
|
||||
13 -5.201079 -1.993301 4.044219
|
||||
14 -3.736682 -0.984819 4.598305
|
||||
15 -4.255402 1.370923 2.679069
|
||||
16 -6.136394 -0.339866 -2.136775
|
||||
17 -6.996331 -1.555519 -0.517408
|
||||
18 -7.153308 0.284949 -0.289930
|
||||
|
||||
Bonds
|
||||
|
||||
1 9 1 2
|
||||
2 10 1 4
|
||||
3 10 1 5
|
||||
4 11 1 10
|
||||
5 1 2 3
|
||||
6 2 2 6
|
||||
7 2 2 7
|
||||
8 1 3 16
|
||||
9 2 3 17
|
||||
10 2 3 18
|
||||
11 1 8 9
|
||||
12 6 9 10
|
||||
13 2 9 13
|
||||
14 2 9 14
|
||||
15 7 10 11
|
||||
16 5 10 12
|
||||
17 8 12 15
|
||||
|
||||
Angles
|
||||
|
||||
1 14 2 1 4
|
||||
2 14 2 1 5
|
||||
3 15 2 1 10
|
||||
4 16 4 1 5
|
||||
5 17 4 1 10
|
||||
6 17 5 1 10
|
||||
7 18 1 2 3
|
||||
8 19 1 2 6
|
||||
9 19 1 2 7
|
||||
10 1 3 2 6
|
||||
11 1 3 2 7
|
||||
12 3 6 2 7
|
||||
13 2 2 3 16
|
||||
14 1 2 3 17
|
||||
15 1 2 3 18
|
||||
16 1 16 3 17
|
||||
17 1 16 3 18
|
||||
18 3 17 3 18
|
||||
19 12 8 9 10
|
||||
20 1 8 9 13
|
||||
21 1 8 9 14
|
||||
22 13 13 9 10
|
||||
23 13 14 9 10
|
||||
24 3 13 9 14
|
||||
25 10 9 10 11
|
||||
26 8 9 10 12
|
||||
27 20 1 10 9
|
||||
28 21 11 10 12
|
||||
29 22 1 10 11
|
||||
30 23 1 10 12
|
||||
31 11 10 12 15
|
||||
|
||||
Dihedrals
|
||||
|
||||
1 16 4 1 2 3
|
||||
2 17 4 1 2 6
|
||||
3 17 4 1 2 7
|
||||
4 16 5 1 2 3
|
||||
5 17 5 1 2 6
|
||||
6 17 5 1 2 7
|
||||
7 18 10 1 2 3
|
||||
8 19 10 1 2 6
|
||||
9 19 10 1 2 7
|
||||
10 20 2 1 10 9
|
||||
11 21 2 1 10 11
|
||||
12 22 2 1 10 12
|
||||
13 23 4 1 10 9
|
||||
14 24 4 1 10 11
|
||||
15 25 4 1 10 12
|
||||
16 23 5 1 10 9
|
||||
17 24 5 1 10 11
|
||||
18 25 5 1 10 12
|
||||
19 26 1 2 3 16
|
||||
20 27 1 2 3 17
|
||||
21 27 1 2 3 18
|
||||
22 4 16 3 2 6
|
||||
23 2 6 2 3 17
|
||||
24 2 6 2 3 18
|
||||
25 4 16 3 2 7
|
||||
26 2 7 2 3 17
|
||||
27 2 7 2 3 18
|
||||
28 14 8 9 10 11
|
||||
29 12 8 9 10 12
|
||||
30 28 8 9 10 1
|
||||
31 15 13 9 10 11
|
||||
32 13 13 9 10 12
|
||||
33 29 13 9 10 1
|
||||
34 15 14 9 10 11
|
||||
35 13 14 9 10 12
|
||||
36 29 14 9 10 1
|
||||
37 10 9 10 12 15
|
||||
38 11 11 10 12 15
|
||||
39 30 1 10 12 15
|
||||
|
||||
Impropers
|
||||
|
||||
1 1 2 1 4 5
|
||||
2 1 2 1 4 10
|
||||
3 1 2 1 5 10
|
||||
4 1 4 1 5 10
|
||||
5 1 1 2 3 6
|
||||
6 1 1 2 3 7
|
||||
7 1 1 2 6 7
|
||||
8 1 3 2 6 7
|
||||
9 1 2 3 16 17
|
||||
10 1 2 3 16 18
|
||||
11 1 2 3 17 18
|
||||
12 1 16 3 17 18
|
||||
13 1 8 9 13 10
|
||||
14 1 8 9 14 10
|
||||
15 1 8 9 13 14
|
||||
16 1 13 9 14 10
|
||||
17 1 9 10 11 12
|
||||
18 1 1 10 9 11
|
||||
19 1 1 10 9 12
|
||||
20 1 1 10 11 12
|
||||
@ -0,0 +1,160 @@
|
||||
this is a molecule template for: initial nylon crosslink, pre-reacting
|
||||
|
||||
18 atoms
|
||||
16 bonds
|
||||
25 angles
|
||||
23 dihedrals
|
||||
14 impropers
|
||||
|
||||
Types
|
||||
|
||||
1 2
|
||||
2 1
|
||||
3 1
|
||||
4 4
|
||||
5 4
|
||||
6 3
|
||||
7 3
|
||||
8 1
|
||||
9 1
|
||||
10 5
|
||||
11 8
|
||||
12 6
|
||||
13 3
|
||||
14 3
|
||||
15 7
|
||||
16 1
|
||||
17 3
|
||||
18 3
|
||||
|
||||
Charges
|
||||
|
||||
1 -0.300000
|
||||
2 0.000000
|
||||
3 0.000000
|
||||
4 0.000000
|
||||
5 0.000000
|
||||
6 0.000000
|
||||
7 0.000000
|
||||
8 0.000000
|
||||
9 0.000000
|
||||
10 0.300000
|
||||
11 0.000000
|
||||
12 0.000000
|
||||
13 0.000000
|
||||
14 0.000000
|
||||
15 0.000000
|
||||
16 0.000000
|
||||
17 0.000000
|
||||
18 0.000000
|
||||
|
||||
Coords
|
||||
|
||||
1 -4.922858 -0.946982 1.146055
|
||||
2 -5.047195 -0.935267 -0.358173
|
||||
3 -6.526281 -0.755366 -0.743523
|
||||
4 -5.282604 0.020447 1.552710
|
||||
5 -3.860697 -1.095850 1.428305
|
||||
6 -4.662382 -1.920900 -0.781524
|
||||
7 -4.433977 -0.072765 -0.784071
|
||||
8 -5.506279 0.202610 4.825816
|
||||
9 -4.449177 -0.844592 4.423366
|
||||
10 -4.103916 -0.749629 2.925195
|
||||
11 -3.376249 -1.886171 2.245643
|
||||
12 -4.493235 0.477214 2.137199
|
||||
13 -4.849053 -1.888877 4.663994
|
||||
14 -3.491823 -0.662913 5.018510
|
||||
15 -5.020777 1.189745 2.805427
|
||||
16 -3.964987 2.900602 -1.551341
|
||||
17 -4.460694 2.836102 0.668882
|
||||
18 -4.828494 3.219656 -0.122111
|
||||
|
||||
Bonds
|
||||
|
||||
1 12 1 2
|
||||
2 4 1 4
|
||||
3 4 1 5
|
||||
4 1 2 3
|
||||
5 2 2 6
|
||||
6 2 2 7
|
||||
7 1 3 16
|
||||
8 2 3 17
|
||||
9 2 3 18
|
||||
10 1 8 9
|
||||
11 6 9 10
|
||||
12 2 9 13
|
||||
13 2 9 14
|
||||
14 7 10 11
|
||||
15 5 10 12
|
||||
16 8 12 15
|
||||
|
||||
Angles
|
||||
|
||||
1 6 2 1 4
|
||||
2 6 2 1 5
|
||||
3 7 4 1 5
|
||||
4 24 1 2 3
|
||||
5 5 1 2 6
|
||||
6 5 1 2 7
|
||||
7 1 3 2 6
|
||||
8 1 3 2 7
|
||||
9 3 6 2 7
|
||||
10 2 2 3 16
|
||||
11 1 2 3 17
|
||||
12 1 2 3 18
|
||||
13 1 16 3 17
|
||||
14 1 16 3 18
|
||||
15 3 17 3 18
|
||||
16 12 8 9 10
|
||||
17 1 8 9 13
|
||||
18 1 8 9 14
|
||||
19 13 13 9 10
|
||||
20 13 14 9 10
|
||||
21 3 13 9 14
|
||||
22 10 9 10 11
|
||||
23 8 9 10 12
|
||||
24 21 11 10 12
|
||||
25 11 10 12 15
|
||||
|
||||
Dihedrals
|
||||
|
||||
1 31 4 1 2 3
|
||||
2 32 4 1 2 6
|
||||
3 32 4 1 2 7
|
||||
4 31 5 1 2 3
|
||||
5 32 5 1 2 6
|
||||
6 32 5 1 2 7
|
||||
7 33 1 2 3 16
|
||||
8 1 1 2 3 17
|
||||
9 1 1 2 3 18
|
||||
10 4 16 3 2 6
|
||||
11 2 6 2 3 17
|
||||
12 2 6 2 3 18
|
||||
13 4 16 3 2 7
|
||||
14 2 7 2 3 17
|
||||
15 2 7 2 3 18
|
||||
16 14 8 9 10 11
|
||||
17 12 8 9 10 12
|
||||
18 15 13 9 10 11
|
||||
19 13 13 9 10 12
|
||||
20 15 14 9 10 11
|
||||
21 13 14 9 10 12
|
||||
22 10 9 10 12 15
|
||||
23 11 11 10 12 15
|
||||
|
||||
Impropers
|
||||
|
||||
1 1 2 1 4 5
|
||||
2 9 9 10 11 12
|
||||
3 1 1 2 3 6
|
||||
4 1 1 2 3 7
|
||||
5 1 1 2 6 7
|
||||
6 1 3 2 6 7
|
||||
7 1 2 3 16 17
|
||||
8 1 2 3 16 18
|
||||
9 1 2 3 17 18
|
||||
10 1 16 3 17 18
|
||||
11 1 8 9 13 10
|
||||
12 1 8 9 14 10
|
||||
13 1 8 9 13 14
|
||||
14 1 13 9 14 10
|
||||
32
examples/bond_react/nylon,6-6_melt/rxn1_stp2_map
Normal file
32
examples/bond_react/nylon,6-6_melt/rxn1_stp2_map
Normal file
@ -0,0 +1,32 @@
|
||||
this is a nominal superimpose file
|
||||
|
||||
2 edgeIDs
|
||||
15 equivalences
|
||||
|
||||
BondingIDs
|
||||
|
||||
4
|
||||
12
|
||||
|
||||
EdgeIDs
|
||||
|
||||
8
|
||||
3
|
||||
|
||||
Equivalences
|
||||
|
||||
1 1
|
||||
2 2
|
||||
3 3
|
||||
4 4
|
||||
5 5
|
||||
6 6
|
||||
7 7
|
||||
8 8
|
||||
9 9
|
||||
10 10
|
||||
11 11
|
||||
12 12
|
||||
13 13
|
||||
14 14
|
||||
15 15
|
||||
@ -0,0 +1,131 @@
|
||||
this is a molecule template for: water condensation, post-reacting
|
||||
|
||||
15 atoms
|
||||
13 bonds
|
||||
19 angles
|
||||
16 dihedrals
|
||||
10 impropers
|
||||
|
||||
Types
|
||||
|
||||
1 9
|
||||
2 1
|
||||
3 1
|
||||
4 10
|
||||
5 4
|
||||
6 3
|
||||
7 3
|
||||
8 1
|
||||
9 1
|
||||
10 5
|
||||
11 8
|
||||
12 11
|
||||
13 3
|
||||
14 3
|
||||
15 10
|
||||
|
||||
Charges
|
||||
|
||||
1 -0.300000
|
||||
2 0.000000
|
||||
3 0.000000
|
||||
4 0.410000
|
||||
5 0.000000
|
||||
6 0.000000
|
||||
7 0.000000
|
||||
8 0.000000
|
||||
9 0.000000
|
||||
10 0.300000
|
||||
11 0.000000
|
||||
12 -0.820000
|
||||
13 0.000000
|
||||
14 0.000000
|
||||
15 0.410000
|
||||
|
||||
Coords
|
||||
|
||||
1 -4.856280 -1.050468 1.432625
|
||||
2 -5.047195 -0.935267 -0.358173
|
||||
3 -6.526281 -0.755366 -0.743523
|
||||
4 -5.282604 0.020447 1.552710
|
||||
5 -3.860697 -1.095850 1.428305
|
||||
6 -4.662382 -1.920900 -0.781524
|
||||
7 -4.433977 -0.072765 -0.784071
|
||||
8 -5.506279 0.202610 4.825816
|
||||
9 -4.449177 -0.844592 4.423366
|
||||
10 -4.103916 -0.749629 2.925195
|
||||
11 -3.376249 -1.886171 2.245643
|
||||
12 -4.493235 0.477214 2.137199
|
||||
13 -4.849053 -1.888877 4.663994
|
||||
14 -3.491823 -0.662913 5.018510
|
||||
15 -5.020777 1.189745 2.805427
|
||||
|
||||
Bonds
|
||||
|
||||
1 9 1 2
|
||||
2 10 1 5
|
||||
3 11 1 10
|
||||
4 1 2 3
|
||||
5 2 2 6
|
||||
6 2 2 7
|
||||
7 13 4 12
|
||||
8 1 8 9
|
||||
9 6 9 10
|
||||
10 2 9 13
|
||||
11 2 9 14
|
||||
12 7 10 11
|
||||
13 13 15 12
|
||||
|
||||
Angles
|
||||
|
||||
1 14 2 1 5
|
||||
2 15 2 1 10
|
||||
3 17 5 1 10
|
||||
4 18 1 2 3
|
||||
5 19 1 2 6
|
||||
6 19 1 2 7
|
||||
7 1 3 2 6
|
||||
8 1 3 2 7
|
||||
9 3 6 2 7
|
||||
10 12 8 9 10
|
||||
11 1 8 9 13
|
||||
12 1 8 9 14
|
||||
13 13 13 9 10
|
||||
14 13 14 9 10
|
||||
15 3 13 9 14
|
||||
16 10 9 10 11
|
||||
17 20 1 10 9
|
||||
18 22 1 10 11
|
||||
19 25 15 12 4
|
||||
|
||||
Dihedrals
|
||||
|
||||
1 16 5 1 2 3
|
||||
2 17 5 1 2 6
|
||||
3 17 5 1 2 7
|
||||
4 18 10 1 2 3
|
||||
5 19 10 1 2 6
|
||||
6 19 10 1 2 7
|
||||
7 20 2 1 10 9
|
||||
8 21 2 1 10 11
|
||||
9 23 5 1 10 9
|
||||
10 24 5 1 10 11
|
||||
11 14 8 9 10 11
|
||||
12 28 8 9 10 1
|
||||
13 15 13 9 10 11
|
||||
14 29 13 9 10 1
|
||||
15 15 14 9 10 11
|
||||
16 29 14 9 10 1
|
||||
|
||||
Impropers
|
||||
|
||||
1 10 2 1 5 10
|
||||
2 11 1 10 9 11
|
||||
3 1 1 2 3 6
|
||||
4 1 1 2 3 7
|
||||
5 1 1 2 6 7
|
||||
6 1 3 2 6 7
|
||||
7 1 8 9 13 10
|
||||
8 1 8 9 14 10
|
||||
9 1 8 9 13 14
|
||||
10 1 13 9 14 10
|
||||
@ -0,0 +1,158 @@
|
||||
this is a molecule template for: water condensation, pre-reacting
|
||||
|
||||
15 atoms
|
||||
14 bonds
|
||||
25 angles
|
||||
30 dihedrals
|
||||
16 impropers
|
||||
|
||||
Types
|
||||
|
||||
1 9
|
||||
2 1
|
||||
3 1
|
||||
4 4
|
||||
5 4
|
||||
6 3
|
||||
7 3
|
||||
8 1
|
||||
9 1
|
||||
10 5
|
||||
11 8
|
||||
12 6
|
||||
13 3
|
||||
14 3
|
||||
15 7
|
||||
|
||||
Charges
|
||||
|
||||
1 -0.300000
|
||||
2 0.000000
|
||||
3 0.000000
|
||||
4 0.000000
|
||||
5 0.000000
|
||||
6 0.000000
|
||||
7 0.000000
|
||||
8 0.000000
|
||||
9 0.000000
|
||||
10 0.300000
|
||||
11 0.000000
|
||||
12 0.000000
|
||||
13 0.000000
|
||||
14 0.000000
|
||||
15 0.000000
|
||||
|
||||
Coords
|
||||
|
||||
1 -4.922858 -0.946982 1.146055
|
||||
2 -5.047195 -0.935267 -0.358173
|
||||
3 -6.526281 -0.755366 -0.743523
|
||||
4 -5.282604 0.020447 1.552710
|
||||
5 -3.860697 -1.095850 1.428305
|
||||
6 -4.662382 -1.920900 -0.781524
|
||||
7 -4.433977 -0.072765 -0.784071
|
||||
8 -5.506279 0.202610 4.825816
|
||||
9 -4.449177 -0.844592 4.423366
|
||||
10 -4.103916 -0.749629 2.925195
|
||||
11 -3.376249 -1.886171 2.245643
|
||||
12 -4.493235 0.477214 2.137199
|
||||
13 -4.849053 -1.888877 4.663994
|
||||
14 -3.491823 -0.662913 5.018510
|
||||
15 -5.020777 1.189745 2.805427
|
||||
|
||||
Bonds
|
||||
|
||||
1 9 1 2
|
||||
2 10 1 4
|
||||
3 10 1 5
|
||||
4 11 1 10
|
||||
5 1 2 3
|
||||
6 2 2 6
|
||||
7 2 2 7
|
||||
8 1 8 9
|
||||
9 6 9 10
|
||||
10 2 9 13
|
||||
11 2 9 14
|
||||
12 7 10 11
|
||||
13 5 10 12
|
||||
14 8 12 15
|
||||
|
||||
Angles
|
||||
|
||||
1 14 2 1 4
|
||||
2 14 2 1 5
|
||||
3 15 2 1 10
|
||||
4 16 4 1 5
|
||||
5 17 4 1 10
|
||||
6 17 5 1 10
|
||||
7 18 1 2 3
|
||||
8 19 1 2 6
|
||||
9 19 1 2 7
|
||||
10 1 3 2 6
|
||||
11 1 3 2 7
|
||||
12 3 6 2 7
|
||||
13 12 8 9 10
|
||||
14 1 8 9 13
|
||||
15 1 8 9 14
|
||||
16 13 13 9 10
|
||||
17 13 14 9 10
|
||||
18 3 13 9 14
|
||||
19 10 9 10 11
|
||||
20 8 9 10 12
|
||||
21 20 1 10 9
|
||||
22 21 11 10 12
|
||||
23 22 1 10 11
|
||||
24 23 1 10 12
|
||||
25 11 10 12 15
|
||||
|
||||
Dihedrals
|
||||
|
||||
1 16 4 1 2 3
|
||||
2 17 4 1 2 6
|
||||
3 17 4 1 2 7
|
||||
4 16 5 1 2 3
|
||||
5 17 5 1 2 6
|
||||
6 17 5 1 2 7
|
||||
7 18 10 1 2 3
|
||||
8 19 10 1 2 6
|
||||
9 19 10 1 2 7
|
||||
10 20 2 1 10 9
|
||||
11 21 2 1 10 11
|
||||
12 22 2 1 10 12
|
||||
13 23 4 1 10 9
|
||||
14 24 4 1 10 11
|
||||
15 25 4 1 10 12
|
||||
16 23 5 1 10 9
|
||||
17 24 5 1 10 11
|
||||
18 25 5 1 10 12
|
||||
19 14 8 9 10 11
|
||||
20 12 8 9 10 12
|
||||
21 28 8 9 10 1
|
||||
22 15 13 9 10 11
|
||||
23 13 13 9 10 12
|
||||
24 29 13 9 10 1
|
||||
25 15 14 9 10 11
|
||||
26 13 14 9 10 12
|
||||
27 29 14 9 10 1
|
||||
28 10 9 10 12 15
|
||||
29 11 11 10 12 15
|
||||
30 30 1 10 12 15
|
||||
|
||||
Impropers
|
||||
|
||||
1 1 2 1 4 5
|
||||
2 1 2 1 4 10
|
||||
3 1 2 1 5 10
|
||||
4 1 4 1 5 10
|
||||
5 1 1 2 3 6
|
||||
6 1 1 2 3 7
|
||||
7 1 1 2 6 7
|
||||
8 1 3 2 6 7
|
||||
9 1 8 9 13 10
|
||||
10 1 8 9 14 10
|
||||
11 1 8 9 13 14
|
||||
12 1 13 9 14 10
|
||||
13 1 9 10 11 12
|
||||
14 1 1 10 9 11
|
||||
15 1 1 10 9 12
|
||||
16 1 1 10 11 12
|
||||
@ -1,4 +1,5 @@
|
||||
# Jake practice run
|
||||
# two monomer nylon example
|
||||
# reaction produces a condensed water molecule
|
||||
|
||||
units real
|
||||
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
this is a marvellous superimpose file
|
||||
this is a nominal superimpose file
|
||||
|
||||
2 edgeIDs
|
||||
18 equivalences
|
||||
|
||||
@ -1,10 +1,10 @@
|
||||
LAMMPS data file. msi2lmp v3.9.6 / 11 Sep 2014 / CGCMM for rxn1_stp1_reacted
|
||||
this is a molecule template for: initial nylon crosslink, post-reacting
|
||||
|
||||
18 atoms
|
||||
17 bonds
|
||||
31 angles
|
||||
39 dihedrals
|
||||
20 impropers
|
||||
18 atoms
|
||||
17 bonds
|
||||
31 angles
|
||||
39 dihedrals
|
||||
20 impropers
|
||||
|
||||
Types
|
||||
|
||||
|
||||
@ -1,10 +1,10 @@
|
||||
LAMMPS data file. msi2lmp v3.9.6 / 11 Sep 2014 / CGCMM for rxn1_stp1_unreacted
|
||||
this is a molecule template for: initial nylon crosslink, pre-reacting
|
||||
|
||||
18 atoms
|
||||
16 bonds
|
||||
25 angles
|
||||
23 dihedrals
|
||||
14 impropers
|
||||
18 atoms
|
||||
16 bonds
|
||||
25 angles
|
||||
23 dihedrals
|
||||
14 impropers
|
||||
|
||||
Types
|
||||
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
this is a marvellous superimpose file
|
||||
this is a nominal superimpose file
|
||||
|
||||
2 edgeIDs
|
||||
15 equivalences
|
||||
|
||||
@ -1,10 +1,10 @@
|
||||
LAMMPS data file. msi2lmp v3.9.6 / 11 Sep 2014 / CGCMM for rxn1_stp2_reacted
|
||||
this is a molecule template for: water condensation, post-reacting
|
||||
|
||||
15 atoms
|
||||
13 bonds
|
||||
19 angles
|
||||
16 dihedrals
|
||||
10 impropers
|
||||
15 atoms
|
||||
13 bonds
|
||||
19 angles
|
||||
16 dihedrals
|
||||
10 impropers
|
||||
|
||||
Types
|
||||
|
||||
|
||||
@ -1,10 +1,10 @@
|
||||
LAMMPS data file. msi2lmp v3.9.6 / 11 Sep 2014 / CGCMM for rxn1_stp2_unreacted
|
||||
this is a molecule template for: water condensation, pre-reacting
|
||||
|
||||
15 atoms
|
||||
14 bonds
|
||||
25 angles
|
||||
30 dihedrals
|
||||
16 impropers
|
||||
15 atoms
|
||||
14 bonds
|
||||
25 angles
|
||||
30 dihedrals
|
||||
16 impropers
|
||||
|
||||
Types
|
||||
|
||||
|
||||
@ -1,4 +1,4 @@
|
||||
LAMMPS data file via write_data, version 23 Jun 2017, timestep = 10013
|
||||
this is LAMMPS data file containing two nylon monomers
|
||||
|
||||
44 atoms
|
||||
11 atom types
|
||||
|
||||
Reference in New Issue
Block a user