From 5ca5395c1624777eecb8f5e8b654c2b3d11a444e Mon Sep 17 00:00:00 2001 From: sjplimp Date: Tue, 7 Jan 2014 18:29:14 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11151 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- doc/fix_pour.html | 26 ++++----- doc/fix_pour.txt | 26 ++++----- doc/molecule.html | 131 +++++++++++++++++++++++++++++++++++++++++----- doc/molecule.txt | 131 +++++++++++++++++++++++++++++++++++++++++----- 4 files changed, 264 insertions(+), 50 deletions(-) diff --git a/doc/fix_pour.html b/doc/fix_pour.html index 4ef1378d12..fc83cab0e4 100644 --- a/doc/fix_pour.html +++ b/doc/fix_pour.html @@ -131,18 +131,20 @@ many timesteps until the desired # of particles has been inserted.

All other keywords are optional with defaults as shown below.

The diam option is only used when inserting atoms and specifes the -diameters of inserted particles. For molecule insertion, the -diameters of individual atoms in the molecule can be specified in the -file read by the molecule command. There are 3 -styles: one, range, or poly. For one, all particles will have -diameter D. For range, the diameter of each particle will be -chosen randomly and uniformly between the specified Dlo and Dhi -bounds. For poly, a series of Npoly diameters is specified. For -each diameter a percentage value from 0.0 to 1.0 is also specified. -The Npoly percentages must sum to 1.0. For the example shown above -with "diam 2 0.7 0.4 1.5 0.6", all inserted particles will have a -diameter of 0.7 or 1.5. 40% of the particles will be small; 60% will -be large. +diameters of inserted particles. There are 3 styles: one, range, +or poly. For one, all particles will have diameter D. For +range, the diameter of each particle will be chosen randomly and +uniformly between the specified Dlo and Dhi bounds. For poly, a +series of Npoly diameters is specified. For each diameter a +percentage value from 0.0 to 1.0 is also specified. The Npoly +percentages must sum to 1.0. For the example shown above with "diam 2 +0.7 0.4 1.5 0.6", all inserted particles will have a diameter of 0.7 +or 1.5. 40% of the particles will be small; 60% will be large. +

+

Note that for molecule insertion, the diameters of individual atoms in +the molecule can be specified in the file read by the +molecule command. If not specified, the diameter of +each atom in the molecule has a default diameter of 1.0.

The dens and vel options enable inserted particles to have a range of densities or xy velocities. The specific values for a particular diff --git a/doc/fix_pour.txt b/doc/fix_pour.txt index 7dc49742dd..3d1cff35c4 100644 --- a/doc/fix_pour.txt +++ b/doc/fix_pour.txt @@ -120,18 +120,20 @@ many timesteps until the desired # of particles has been inserted. All other keywords are optional with defaults as shown below. The {diam} option is only used when inserting atoms and specifes the -diameters of inserted particles. For molecule insertion, the -diameters of individual atoms in the molecule can be specified in the -file read by the "molecule"_molecule.html command. There are 3 -styles: {one}, {range}, or {poly}. For {one}, all particles will have -diameter {D}. For {range}, the diameter of each particle will be -chosen randomly and uniformly between the specified {Dlo} and {Dhi} -bounds. For {poly}, a series of {Npoly} diameters is specified. For -each diameter a percentage value from 0.0 to 1.0 is also specified. -The {Npoly} percentages must sum to 1.0. For the example shown above -with "diam 2 0.7 0.4 1.5 0.6", all inserted particles will have a -diameter of 0.7 or 1.5. 40% of the particles will be small; 60% will -be large. +diameters of inserted particles. There are 3 styles: {one}, {range}, +or {poly}. For {one}, all particles will have diameter {D}. For +{range}, the diameter of each particle will be chosen randomly and +uniformly between the specified {Dlo} and {Dhi} bounds. For {poly}, a +series of {Npoly} diameters is specified. For each diameter a +percentage value from 0.0 to 1.0 is also specified. The {Npoly} +percentages must sum to 1.0. For the example shown above with "diam 2 +0.7 0.4 1.5 0.6", all inserted particles will have a diameter of 0.7 +or 1.5. 40% of the particles will be small; 60% will be large. + +Note that for molecule insertion, the diameters of individual atoms in +the molecule can be specified in the file read by the +"molecule"_molecule.html command. If not specified, the diameter of +each atom in the molecule has a default diameter of 1.0. The {dens} and {vel} options enable inserted particles to have a range of densities or xy velocities. The specific values for a particular diff --git a/doc/molecule.html b/doc/molecule.html index f2fc5f694b..0f73a4647a 100644 --- a/doc/molecule.html +++ b/doc/molecule.html @@ -27,10 +27,16 @@ molecule CO2 co2.txt

Define a molecule template that can be used as part of other LAMMPS commands, typically to define a collection of particles as a bonded -molecule or a rigid body. Commands that use molecule templates -include (or will include) fix deposit, fix -pour, and fix gcmc. +molecule or a rigid body. Commands that currently use molecule +templates (or will in the future) include:

+

The ID of a molecule template can only contain alphanumeric characters and underscores.

@@ -86,7 +92,8 @@ internally.

IMPORTANT NOTE: Whether a section is required depends on how the molecule template is used by other LAMMPS commands. For example, to @@ -104,10 +111,10 @@ templates for more details.

Each section is listed below in alphabetic order. The format of each section is described including the number of lines it must contain and rules (if any) for whether it can appear in the data file. In each -case the ID is ignored; it is simply included for readability as a -number from 1 to Nlines for the section, indicating which atom (or -bond, etc) the entry applies to. The lines are assumed to be listed -in order from 1 to Nlines. +case the ID is ignored; it is simply included for readability, and +should be a number from 1 to Nlines for the section, indicating which +atom (or bond, etc) the entry applies to. The lines are assumed to be +listed in order from 1 to Nlines, but LAMMPS does not check for this.

@@ -134,8 +141,8 @@ in order from 1 to Nlines.
  • q = charge on atom

    This section is only allowed for atom styles that -support charge. If not listed, the default charge on each atom in the -molecule is 0.0. +support charge. If this section is not included, the default charge +on each atom in the molecule is 0.0.

    @@ -159,9 +166,10 @@ not listed, the default diameter of each atom in the molecule is 1.0.

    This section is only allowed for atom styles that support per-atom mass, as opposed to per-type mass. See the -mass command for details. If not listed, the default mass -for each atom is derived from its volume (see Diameters section) and a -default density of 1.0, in units of mass/volume. +mass command for details. If this section is not +included, the default mass for each atom is derived from its volume +(see Diameters section) and a default density of 1.0, in +units of mass/volume.

    @@ -253,6 +261,103 @@ appears, the Special Bond Counts section must also appear. If this section is not specied, the atoms in the molecule will have no special bonds.

    +

    Shake Flags section: +

    + +

    This section is only needed when molecules created using the template +will be constrained by SHAKE via the "fix shake" command. The other +two Shake sections must also appear in the file, following this one. +

    +

    The meaning of the flag for each atom is as follows. See the fix +shake doc page for a further description of SHAKE +clusters. +

    + +

    Shake Atoms section: +

    + +

    This section is only needed when molecules created using the template +will be constrained by SHAKE via the "fix shake" command. The other +two Shake sections must also appear in the file. +

    +

    The a,b,c,d values are atom IDs (from 1 to Natoms) for all the atoms +in the SHAKE cluster that this atom belongs to. The number of values +that must appear is determined by the shake flag for the atom (see the +Shake Flags section above). All atoms in a particular cluster should +list their a,b,c,d values identically. +

    +

    If flag = 0, no a,b,c,d values are listed on the line, just the +(ignored) ID. +

    +

    If flag = 1, a,b,c are listed, where a = ID of central atom in the +angle, and b,c the other two atoms in the angle. +

    +

    If flag = 2, a,b are listed, where a = ID of atom in bond with the the +lowest ID, and b = ID of atom in bond with the highest ID. +

    +

    If flag = 3, a,b,c are listed, where a = ID of central atom, +and b,c = IDs of other two atoms bonded to the central atom. +

    +

    If flag = 4, a,b,c,d are listed, where a = ID of central atom, +and b,c,d = IDs of other three atoms bonded to the central atom. +

    +

    See the fix shake doc page for a further description +of SHAKE clusters. +

    +

    Shake Bond Types section: +

    + +

    This section is only needed when molecules created using the template +will be constrained by SHAKE via the "fix shake" command. The other +two Shake sections must also appear in the file. +

    +

    The a,b,c values are bond types (from 1 to Nbondtypes) for all bonds +in the SHAKE cluster that this atom belongs to. The number of values +that must appear is determined by the shake flag for the atom (see the +Shake Flags section above). All atoms in a particular cluster should +list their a,b,c values identically. +

    +

    If flag = 0, no a,b,c values are listed on the line, just the +(ignored) ID. +

    +

    If flag = 1, a,b,c are listed, where a = bondtype of the bond between +the central atom and the first non-central atom (value b in the Shake +Atoms section), b = bondtype of the bond between the central atom and +the 2nd non-central atom (value c in the Shake Atoms section), and c = +the angle type (1 to Nangletypes) of the angle between the 3 atoms. +

    +

    If flag = 2, only a is listed, where a = bondtype of the bond between +the 2 atoms in the cluster. +

    +

    If flag = 3, a,b are listed, where a = bondtype of the bond between +the central atom and the first non-central atom (value b in the Shake +Atoms section), and b = bondtype of the bond between the central atom +and the 2nd non-central atom (value c in the Shake Atoms section). +

    +

    If flag = 4, a,b,c are listed, where a = bondtype of the bond between +the central atom and the first non-central atom (value b in the Shake +Atoms section), b = bondtype of the bond between the central atom and +the 2nd non-central atom (value c in the Shake Atoms section), and c = +bondtype of the bond between the central atom and the 3rd non-central +atom (value d in the Shake Atoms section). +

    +

    See the fix shake doc page for a further description +of SHAKE clusters. +

    Restrictions: none diff --git a/doc/molecule.txt b/doc/molecule.txt index 7a609a7674..24871ec0dc 100644 --- a/doc/molecule.txt +++ b/doc/molecule.txt @@ -24,9 +24,15 @@ molecule CO2 co2.txt :pre Define a molecule template that can be used as part of other LAMMPS commands, typically to define a collection of particles as a bonded -molecule or a rigid body. Commands that use molecule templates -include (or will include) "fix deposit"_fix_deposit.html, "fix -pour"_fix_pour.html, and "fix gcmc"_fix_gcmc.html. +molecule or a rigid body. Commands that currently use molecule +templates (or will in the future) include: + +"fix deposit"_fix_deposit.html +"fix pour"_fix_pour.html +"fix rigid/small"_fix_rigid.html +"fix shake"_fix_shake.html +"fix gcmc"_fix_gcmc.html (not yet) +"create_atoms"_create_atoms.html (not yet) :ul The ID of a molecule template can only contain alphanumeric characters and underscores. @@ -83,7 +89,8 @@ These are the allowed section keywords for the body of the file. {Coords, Types, Charges, Diameters, Masses} = atom-property sections {Bonds, Angles, Dihedrals, Impropers} = molecular topology sections -{Special Bond Counts, Special Bonds} = special neighbor info :ul +{Special Bond Counts, Special Bonds} = special neighbor info +{Shake Flags, Shake Atoms, Shake Bond Types} = SHAKE info :ul IMPORTANT NOTE: Whether a section is required depends on how the molecule template is used by other LAMMPS commands. For example, to @@ -101,10 +108,10 @@ templates for more details. Each section is listed below in alphabetic order. The format of each section is described including the number of lines it must contain and rules (if any) for whether it can appear in the data file. In each -case the ID is ignored; it is simply included for readability as a -number from 1 to Nlines for the section, indicating which atom (or -bond, etc) the entry applies to. The lines are assumed to be listed -in order from 1 to Nlines. +case the ID is ignored; it is simply included for readability, and +should be a number from 1 to Nlines for the section, indicating which +atom (or bond, etc) the entry applies to. The lines are assumed to be +listed in order from 1 to Nlines, but LAMMPS does not check for this. :line @@ -131,8 +138,8 @@ line syntax: ID q q = charge on atom :ul This section is only allowed for "atom styles"_atom_style.html that -support charge. If not listed, the default charge on each atom in the -molecule is 0.0. +support charge. If this section is not included, the default charge +on each atom in the molecule is 0.0. :line @@ -156,9 +163,10 @@ mass = mass of atom :ul This section is only allowed for "atom styles"_atom_style.html that support per-atom mass, as opposed to per-type mass. See the -"mass"_mass.html command for details. If not listed, the default mass -for each atom is derived from its volume (see Diameters section) and a -default density of 1.0, in "units"_units.html of mass/volume. +"mass"_mass.html command for details. If this section is not +included, the default mass for each atom is derived from its volume +(see Diameters section) and a default density of 1.0, in +"units"_units.html of mass/volume. :line @@ -250,6 +258,103 @@ appears, the Special Bond Counts section must also appear. If this section is not specied, the atoms in the molecule will have no special bonds. +{Shake Flags} section: + +one line per atom +line syntax: ID flag +flag = 0,1,2,3,4 :ul + +This section is only needed when molecules created using the template +will be constrained by SHAKE via the "fix shake" command. The other +two Shake sections must also appear in the file, following this one. + +The meaning of the flag for each atom is as follows. See the "fix +shake"_fix_shake.html doc page for a further description of SHAKE +clusters. + +0 = not part of a SHAKE cluster +1 = part of a SHAKE angle cluster (two bonds and the angle they form) +2 = part of a 2-atom SHAKE cluster with a single bond +3 = part of a 3-atom SHAKE cluster with two bonds +4 = part of a 4-atom SHAKE cluster with three bonds :ul + +{Shake Atoms} section: + +one line per atom +line syntax: ID a b c d +a,b,c,d = IDs of atoms in cluster :ul + +This section is only needed when molecules created using the template +will be constrained by SHAKE via the "fix shake" command. The other +two Shake sections must also appear in the file. + +The a,b,c,d values are atom IDs (from 1 to Natoms) for all the atoms +in the SHAKE cluster that this atom belongs to. The number of values +that must appear is determined by the shake flag for the atom (see the +Shake Flags section above). All atoms in a particular cluster should +list their a,b,c,d values identically. + +If flag = 0, no a,b,c,d values are listed on the line, just the +(ignored) ID. + +If flag = 1, a,b,c are listed, where a = ID of central atom in the +angle, and b,c the other two atoms in the angle. + +If flag = 2, a,b are listed, where a = ID of atom in bond with the the +lowest ID, and b = ID of atom in bond with the highest ID. + +If flag = 3, a,b,c are listed, where a = ID of central atom, +and b,c = IDs of other two atoms bonded to the central atom. + +If flag = 4, a,b,c,d are listed, where a = ID of central atom, +and b,c,d = IDs of other three atoms bonded to the central atom. + +See the "fix shake"_fix_shake.html doc page for a further description +of SHAKE clusters. + +{Shake Bond Types} section: + +one line per atom +line syntax: ID a b c +a,b,c = bond types of bonds in cluster :ul + +This section is only needed when molecules created using the template +will be constrained by SHAKE via the "fix shake" command. The other +two Shake sections must also appear in the file. + +The a,b,c values are bond types (from 1 to Nbondtypes) for all bonds +in the SHAKE cluster that this atom belongs to. The number of values +that must appear is determined by the shake flag for the atom (see the +Shake Flags section above). All atoms in a particular cluster should +list their a,b,c values identically. + +If flag = 0, no a,b,c values are listed on the line, just the +(ignored) ID. + +If flag = 1, a,b,c are listed, where a = bondtype of the bond between +the central atom and the first non-central atom (value b in the Shake +Atoms section), b = bondtype of the bond between the central atom and +the 2nd non-central atom (value c in the Shake Atoms section), and c = +the angle type (1 to Nangletypes) of the angle between the 3 atoms. + +If flag = 2, only a is listed, where a = bondtype of the bond between +the 2 atoms in the cluster. + +If flag = 3, a,b are listed, where a = bondtype of the bond between +the central atom and the first non-central atom (value b in the Shake +Atoms section), and b = bondtype of the bond between the central atom +and the 2nd non-central atom (value c in the Shake Atoms section). + +If flag = 4, a,b,c are listed, where a = bondtype of the bond between +the central atom and the first non-central atom (value b in the Shake +Atoms section), b = bondtype of the bond between the central atom and +the 2nd non-central atom (value c in the Shake Atoms section), and c = +bondtype of the bond between the central atom and the 3rd non-central +atom (value d in the Shake Atoms section). + +See the "fix shake"_fix_shake.html doc page for a further description +of SHAKE clusters. + :line [Restrictions:] none