+ +
compute com/molecule command +
+Syntax: +
+compute ID group-ID com/molecule ++
- ID, group-ID are documented in compute command +
- com/molecule = style name of this compute command +
Examples: +
+compute 1 fluid com/molecule ++
Description: +
+Define a computation that calculates the center-of-mass of individual +molecules. The calculation includes all effects due to atoms passing +thru periodic boundaries. +
+The x,y,z coordinate of the center-of-mass for a particular molecule +is only computed if one or more of its atoms are in the specified +group. Normally all atoms in the molecule should be in the group, +however this is not required. LAMMPS will warn you if this is not the +case. Only atoms in the group contribute to the center-of-mass +calculation for the molecule. +
+Let Nmolecules be the number of molecules for which the center-of-mass +is calculated. If not all molecules have atoms in the group, then the +molecule with the lowest ID is the first of the Nmolecules. The next +lowest ID is the second, etc, up to Nmolecules. +
+IMPORTANT NOTE: The coordinates of an atom contribute to the +molecule's center-of-mass in "unwrapped" form, by using the image +flags associated with each atom. See the dump custom +command for a discussion of "unwrapped" coordinates. See the Atoms +section of the read_data command for a discussion of +image flags and how they are set for each atom. You can reset the +image flags (e.g. to 0) before invoking this compute by using the set +image command. +
+IMPORTANT NOTE: If an atom is part of a rigid body (see the fix +rigid command), it's periodic image flags are altered, +and its contribution to the center-of-mass may not reflect its true +contribution. See the fix rigid command for details. +Thus, to compute the center-of-mass of rigid bodies as they cross +periodic boundaries, you will need to post-process a dump +file containing coordinates of the atoms in the bodies. +
+Output info: +
+This compute calculates a global array with the number of rows = +Nmolecules and the number of columns = 3 for the x,y,z center-of-mass +coordinates of each molecule. These values can be accessed by any +command that uses global array values from a compute as input. See +this section for an overview of LAMMPS +output options. +
+The array values are "intensive", meaning they are independent of the +number of atoms in the simulation. +
+Restrictions: none +
+Related commands: +
+ +Default: none +
+ diff --git a/doc/compute_com_molecule.txt b/doc/compute_com_molecule.txt new file mode 100644 index 0000000000..034ea647c6 --- /dev/null +++ b/doc/compute_com_molecule.txt @@ -0,0 +1,75 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +compute com/molecule command :h3 + +[Syntax:] + +compute ID group-ID com/molecule :pre + +ID, group-ID are documented in "compute"_compute.html command +com/molecule = style name of this compute command :ul + +[Examples:] + +compute 1 fluid com/molecule :pre + +[Description:] + +Define a computation that calculates the center-of-mass of individual +molecules. The calculation includes all effects due to atoms passing +thru periodic boundaries. + +The x,y,z coordinate of the center-of-mass for a particular molecule +is only computed if one or more of its atoms are in the specified +group. Normally all atoms in the molecule should be in the group, +however this is not required. LAMMPS will warn you if this is not the +case. Only atoms in the group contribute to the center-of-mass +calculation for the molecule. + +Let Nmolecules be the number of molecules for which the center-of-mass +is calculated. If not all molecules have atoms in the group, then the +molecule with the lowest ID is the first of the Nmolecules. The next +lowest ID is the second, etc, up to Nmolecules. + +IMPORTANT NOTE: The coordinates of an atom contribute to the +molecule's center-of-mass in "unwrapped" form, by using the image +flags associated with each atom. See the "dump custom"_dump.html +command for a discussion of "unwrapped" coordinates. See the Atoms +section of the "read_data"_read_data.html command for a discussion of +image flags and how they are set for each atom. You can reset the +image flags (e.g. to 0) before invoking this compute by using the "set +image"_set.html command. + +IMPORTANT NOTE: If an atom is part of a rigid body (see the "fix +rigid"_fix_rigid.html command), it's periodic image flags are altered, +and its contribution to the center-of-mass may not reflect its true +contribution. See the "fix rigid"_fix_rigid.html command for details. +Thus, to compute the center-of-mass of rigid bodies as they cross +periodic boundaries, you will need to post-process a "dump +file"_dump.html containing coordinates of the atoms in the bodies. + +[Output info:] + +This compute calculates a global array with the number of rows = +Nmolecules and the number of columns = 3 for the x,y,z center-of-mass +coordinates of each molecule. These values can be accessed by any +command that uses global array values from a compute as input. See +"this section"_Section_howto.html#4_15 for an overview of LAMMPS +output options. + +The array values are "intensive", meaning they are independent of the +number of atoms in the simulation. + +[Restrictions:] none + +[Related commands:] + +"compute com"_compute_com.html + +[Default:] none diff --git a/doc/compute_gyration_molecule.html b/doc/compute_gyration_molecule.html new file mode 100644 index 0000000000..4fb804f87a --- /dev/null +++ b/doc/compute_gyration_molecule.html @@ -0,0 +1,78 @@ + ++ +
compute gyration/molecule command +
+Syntax: +
+compute ID group-ID gyration/molecule ++
- ID, group-ID are documented in compute command +
- gyration/molecule = style name of this compute command +
Examples: +
+compute 1 molecule gyration/molecule ++
Description: +
+Define a computation that calculates the radius of gyration Rg of +individual molecules. The calculation includes all effects due to +atoms passing thru periodic boundaries. +
+Rg is a measure of the size of a molecule, and is computed by this +formula +
+
+where M is the total mass of the molecule and Rcm is the center-of-mass +position of the molecule. +
+Rg for a particular molecule is only computed if one or more of its +atoms are in the specified group. Normally all atoms in the molecule +should be in the group, however this is not required. LAMMPS will +warn you if this is not the case. Only atoms in the group contribute +to the Rg calculation for the molecule. +
+Let Nmolecules be the number of molecules for which Rg is calculated. +If not all molecules have atoms in the group, then the molecule with +the lowest ID is the first of the Nmolecules. The next lowest ID is +the second, etc, up to Nmolecules. +
+IMPORTANT NOTE: The coordinates of an atom contribute to Rg in +"unwrapped" form, by using the image flags associated with each atom. +See the dump custom command for a discussion of +"unwrapped" coordinates. See the Atoms section of the +read_data command for a discussion of image flags and +how they are set for each atom. You can reset the image flags +(e.g. to 0) before invoking this compute by using the set +image command. +
+Output info: +
+This compute calculates a global vector of Rg values with the number +of elements = Nmolecules. These values can be used by any command +that uses a global vector values from a compute as input. See this +section for an overview of LAMMPS output +options. +
+The vector values calculated by this compute are "intensive", meaning +it is independent of the number of atoms in the simulation. +
+Restrictions: none +
+Related commands: none +
+ +Default: none +
+ diff --git a/doc/compute_gyration_molecule.txt b/doc/compute_gyration_molecule.txt new file mode 100644 index 0000000000..ef30b48b12 --- /dev/null +++ b/doc/compute_gyration_molecule.txt @@ -0,0 +1,73 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +compute gyration/molecule command :h3 + +[Syntax:] + +compute ID group-ID gyration/molecule :pre + +ID, group-ID are documented in "compute"_compute.html command +gyration/molecule = style name of this compute command :ul + +[Examples:] + +compute 1 molecule gyration/molecule :pre + +[Description:] + +Define a computation that calculates the radius of gyration Rg of +individual molecules. The calculation includes all effects due to +atoms passing thru periodic boundaries. + +Rg is a measure of the size of a molecule, and is computed by this +formula + +:c,image(Eqs/compute_gyration.jpg) + +where M is the total mass of the molecule and Rcm is the center-of-mass +position of the molecule. + +Rg for a particular molecule is only computed if one or more of its +atoms are in the specified group. Normally all atoms in the molecule +should be in the group, however this is not required. LAMMPS will +warn you if this is not the case. Only atoms in the group contribute +to the Rg calculation for the molecule. + +Let Nmolecules be the number of molecules for which Rg is calculated. +If not all molecules have atoms in the group, then the molecule with +the lowest ID is the first of the Nmolecules. The next lowest ID is +the second, etc, up to Nmolecules. + +IMPORTANT NOTE: The coordinates of an atom contribute to Rg in +"unwrapped" form, by using the image flags associated with each atom. +See the "dump custom"_dump.html command for a discussion of +"unwrapped" coordinates. See the Atoms section of the +"read_data"_read_data.html command for a discussion of image flags and +how they are set for each atom. You can reset the image flags +(e.g. to 0) before invoking this compute by using the "set +image"_set.html command. + +[Output info:] + +This compute calculates a global vector of Rg values with the number +of elements = Nmolecules. These values can be used by any command +that uses a global vector values from a compute as input. See "this +section"_Section_howto.html#4_15 for an overview of LAMMPS output +options. + +The vector values calculated by this compute are "intensive", meaning +it is independent of the number of atoms in the simulation. + +[Restrictions:] none + +[Related commands:] none + +"compute gyration"_compute_gyration.html + +[Default:] none diff --git a/doc/compute_msd_molecule.html b/doc/compute_msd_molecule.html new file mode 100644 index 0000000000..9c75944e14 --- /dev/null +++ b/doc/compute_msd_molecule.html @@ -0,0 +1,98 @@ + ++ +
compute msd/molecule command +
+Syntax: +
+compute ID group-ID msd/molecule ++
- ID, group-ID are documented in compute command +
- msd/molecule = style name of this compute command +
Examples: +
+compute 1 all msd/molecule ++
Description: +
+Define a computation that calculates the mean-squared displacement +(MSD) of individual molecules. The calculation includes all effects +due to atoms passing thru periodic boundaries. +
+Four quantites are calculated by this compute for each molecule. The +first 3 quantities are the squared dx,dy,dz displacements of the +center-of-mass. The 4th component is the total squared displacement, +i.e. (dx*dx + dy*dy + dz*dz) of the center-of-mass. +
+The slope of the mean-squared displacement (MSD) versus time is +proportional to the diffusion coefficient of the diffusing molecules. +
+The displacement of the center-of-mass of the molecule is from its +original center-of-mass position at the time the compute command was +issued. +
+The MSD for a particular molecule is only computed if one or more of +its atoms are in the specified group. Normally all atoms in the +molecule should be in the group, however this is not required. LAMMPS +will warn you if this is not the case. Only atoms in the group +contribute to the center-of-mass calculation for the molecule, which +is used to caculate its initial and current position. +
+Let Nmolecules be the number of molecules for which the MSD is +calculated. If not all molecules have atoms in the group, then the +molecule with the lowest ID is the first of the Nmolecules. The next +lowest ID is the second, etc, up to Nmolecules. +
+IMPORTANT NOTE: The initial coordinates of each molecule are stored in +"unwrapped" form, by using the image flags associated with each atom. +See the dump custom command for a discussion of +"unwrapped" coordinates. See the Atoms section of the +read_data command for a discussion of image flags and +how they are set for each atom. You can reset the image flags +(e.g. to 0) before invoking this compute by using the set +image command. +
+IMPORTANT NOTE: If an atom is part of a rigid body (see the fix +rigid command), it's periodic image flags are altered, +and its contribution to the MSD may not reflect its true contribution. +See the fix rigid command for details. Thus, to +compute the MSD of rigid bodies as they cross periodic boundaries, you +will need to post-process a dump file containing +coordinates of the atoms in the bodies. +
+IMPORTANT NOTE: Unlike the compute msd command, +this compute does not store the initial center-of-mass coorindates of +its molecules in a restart file. Thus you cannot continue the MSD per +molecule calculation when running from a restart +file. +
+Output info: +
+This compute calculates a global array with the number of rows = +Nmolecules and the number of columns = 4 for dx,dy,dz and the total +displacement. These values can be accessed by any command that uses +global array values from a compute as input. See this +section for an overview of LAMMPS output +options. +
+The array values are "intensive", meaning they are independent of the +number of atoms in the simulation. +
+Restrictions: none +
+Related commands: +
+ +Default: none +
+ diff --git a/doc/compute_msd_molecule.txt b/doc/compute_msd_molecule.txt new file mode 100644 index 0000000000..4869d8c5a7 --- /dev/null +++ b/doc/compute_msd_molecule.txt @@ -0,0 +1,93 @@ +"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c + +:link(lws,http://lammps.sandia.gov) +:link(ld,Manual.html) +:link(lc,Section_commands.html#comm) + +:line + +compute msd/molecule command :h3 + +[Syntax:] + +compute ID group-ID msd/molecule :pre + +ID, group-ID are documented in "compute"_compute.html command +msd/molecule = style name of this compute command :ul + +[Examples:] + +compute 1 all msd/molecule :pre + +[Description:] + +Define a computation that calculates the mean-squared displacement +(MSD) of individual molecules. The calculation includes all effects +due to atoms passing thru periodic boundaries. + +Four quantites are calculated by this compute for each molecule. The +first 3 quantities are the squared dx,dy,dz displacements of the +center-of-mass. The 4th component is the total squared displacement, +i.e. (dx*dx + dy*dy + dz*dz) of the center-of-mass. + +The slope of the mean-squared displacement (MSD) versus time is +proportional to the diffusion coefficient of the diffusing molecules. + +The displacement of the center-of-mass of the molecule is from its +original center-of-mass position at the time the compute command was +issued. + +The MSD for a particular molecule is only computed if one or more of +its atoms are in the specified group. Normally all atoms in the +molecule should be in the group, however this is not required. LAMMPS +will warn you if this is not the case. Only atoms in the group +contribute to the center-of-mass calculation for the molecule, which +is used to caculate its initial and current position. + +Let Nmolecules be the number of molecules for which the MSD is +calculated. If not all molecules have atoms in the group, then the +molecule with the lowest ID is the first of the Nmolecules. The next +lowest ID is the second, etc, up to Nmolecules. + +IMPORTANT NOTE: The initial coordinates of each molecule are stored in +"unwrapped" form, by using the image flags associated with each atom. +See the "dump custom"_dump.html command for a discussion of +"unwrapped" coordinates. See the Atoms section of the +"read_data"_read_data.html command for a discussion of image flags and +how they are set for each atom. You can reset the image flags +(e.g. to 0) before invoking this compute by using the "set +image"_set.html command. + +IMPORTANT NOTE: If an atom is part of a rigid body (see the "fix +rigid"_fix_rigid.html command), it's periodic image flags are altered, +and its contribution to the MSD may not reflect its true contribution. +See the "fix rigid"_fix_rigid.html command for details. Thus, to +compute the MSD of rigid bodies as they cross periodic boundaries, you +will need to post-process a "dump file"_dump.html containing +coordinates of the atoms in the bodies. + +IMPORTANT NOTE: Unlike the "compute msd"_compute_msd.html command, +this compute does not store the initial center-of-mass coorindates of +its molecules in a restart file. Thus you cannot continue the MSD per +molecule calculation when running from a "restart +file"_read_restart.html. + +[Output info:] + +This compute calculates a global array with the number of rows = +Nmolecules and the number of columns = 4 for dx,dy,dz and the total +displacement. These values can be accessed by any command that uses +global array values from a compute as input. See "this +section"_Section_howto.html#4_15 for an overview of LAMMPS output +options. + +The array values are "intensive", meaning they are independent of the +number of atoms in the simulation. + +[Restrictions:] none + +[Related commands:] + +"compute msd"_compute_msd.html + +[Default:] none