Examples:
-compute 1 all atom/molecule c_ke c_pe --
compute 1 top atom/molecule v_myFormula c_stress3 +compute 1 all atom/molecule c_ke c_pe +compute 1 top atom/molecule v_myFormula c_stress3Description:
@@ -54,13 +53,11 @@ they return. For example, if a compute is used as an input which generates a per-atom vector, it will generate values of 0.0 for atoms that are not in the group specified for that compute. -The ordering of per-molecule quantities produced by this compute are +
The ordering of per-molecule quantities produced by this compute is consistent with the ordering produced by other compute commands that -generate per-molecule datums. Let Nmolecules be the number of -molecules for which a result 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. +generate per-molecule datums. Conceptually, them molecule IDs will be +in ascending order for any molecule with one or more of its atoms in +the specified group.
If an input begins with "c_", a compute ID must follow which has been previously defined in the input script and which generates per-atom diff --git a/doc/compute_atom_molecute.txt b/doc/compute_atom_molecute.txt index c06bafebea..d348b82563 100644 --- a/doc/compute_atom_molecute.txt +++ b/doc/compute_atom_molecute.txt @@ -45,13 +45,11 @@ they return. For example, if a compute is used as an input which generates a per-atom vector, it will generate values of 0.0 for atoms that are not in the group specified for that compute. -The ordering of per-molecule quantities produced by this compute are +The ordering of per-molecule quantities produced by this compute is consistent with the ordering produced by other compute commands that -generate per-molecule datums. Let Nmolecules be the number of -molecules for which a result 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. +generate per-molecule datums. Conceptually, them molecule IDs will be +in ascending order for any molecule with one or more of its atoms in +the specified group. If an input begins with "c_", a compute ID must follow which has been previously defined in the input script and which generates per-atom diff --git a/doc/compute_com_molecule.html b/doc/compute_com_molecule.html index ee283c37bb..3f6ac13cb8 100644 --- a/doc/compute_com_molecule.html +++ b/doc/compute_com_molecule.html @@ -35,10 +35,11 @@ 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. +
The ordering of per-molecule quantities produced by this compute is +consistent with the ordering produced by other compute commands that +generate per-molecule datums. Conceptually, them molecule IDs will be +in ascending order for any molecule with one or more of its atoms in +the specified group.
IMPORTANT NOTE: The coordinates of an atom contribute to the molecule's center-of-mass in "unwrapped" form, by using the image diff --git a/doc/compute_com_molecule.txt b/doc/compute_com_molecule.txt index aa44a0e673..670c9117a8 100644 --- a/doc/compute_com_molecule.txt +++ b/doc/compute_com_molecule.txt @@ -32,10 +32,11 @@ 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. +The ordering of per-molecule quantities produced by this compute is +consistent with the ordering produced by other compute commands that +generate per-molecule datums. Conceptually, them molecule IDs will be +in ascending order for any molecule with one or more of its atoms in +the specified group. IMPORTANT NOTE: The coordinates of an atom contribute to the molecule's center-of-mass in "unwrapped" form, by using the image diff --git a/doc/compute_gyration_molecule.html b/doc/compute_gyration_molecule.html index 1ed23f540e..b8ad07e64c 100644 --- a/doc/compute_gyration_molecule.html +++ b/doc/compute_gyration_molecule.html @@ -43,10 +43,11 @@ 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. +
The ordering of per-molecule quantities produced by this compute is +consistent with the ordering produced by other compute commands that +generate per-molecule datums. Conceptually, them molecule IDs will be +in ascending order for any molecule with one or more of its atoms in +the specified group.
IMPORTANT NOTE: The coordinates of an atom contribute to Rg in "unwrapped" form, by using the image flags associated with each atom. diff --git a/doc/compute_gyration_molecule.txt b/doc/compute_gyration_molecule.txt index 98e6b22891..52abb883c5 100644 --- a/doc/compute_gyration_molecule.txt +++ b/doc/compute_gyration_molecule.txt @@ -40,10 +40,11 @@ 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. +The ordering of per-molecule quantities produced by this compute is +consistent with the ordering produced by other compute commands that +generate per-molecule datums. Conceptually, them molecule IDs will be +in ascending order for any molecule with one or more of its atoms in +the specified group. IMPORTANT NOTE: The coordinates of an atom contribute to Rg in "unwrapped" form, by using the image flags associated with each atom. diff --git a/doc/compute_msd_molecule.html b/doc/compute_msd_molecule.html index da0a0b716b..f00536e0d1 100644 --- a/doc/compute_msd_molecule.html +++ b/doc/compute_msd_molecule.html @@ -47,10 +47,11 @@ 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. +
The ordering of per-molecule quantities produced by this compute is +consistent with the ordering produced by other compute commands that +generate per-molecule datums. Conceptually, them molecule IDs will be +in ascending order for any molecule with one or more of its atoms in +the specified group.
IMPORTANT NOTE: The initial coordinates of each molecule are stored in "unwrapped" form, by using the image flags associated with each atom. diff --git a/doc/compute_msd_molecule.txt b/doc/compute_msd_molecule.txt index 14eecc9d94..d411a49d06 100644 --- a/doc/compute_msd_molecule.txt +++ b/doc/compute_msd_molecule.txt @@ -44,10 +44,11 @@ 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. +The ordering of per-molecule quantities produced by this compute is +consistent with the ordering produced by other compute commands that +generate per-molecule datums. Conceptually, them molecule IDs will be +in ascending order for any molecule with one or more of its atoms in +the specified group. IMPORTANT NOTE: The initial coordinates of each molecule are stored in "unwrapped" form, by using the image flags associated with each atom. diff --git a/doc/compute_property_molecule.html b/doc/compute_property_molecule.html index e3103abaff..fdb07af960 100644 --- a/doc/compute_property_molecule.html +++ b/doc/compute_property_molecule.html @@ -40,13 +40,16 @@ commands that generate per-molecule data, such as compute msd/molecule.
-The mol attribute generates a list of molecule IDs in ascending -order for any molecule with one or more of its atoms in the specified -group. This list and ordering of molecule IDs will be consistent with -the ordering produced by other compute commands that generate -per-molecule datums. Thus this attribute can be used to produce -molecule IDs as labels for those datums when they are output to a -file, e.g. by the fix ave/time command. +
The ordering of per-molecule quantities produced by this compute is +consistent with the ordering produced by other compute commands that +generate per-molecule datums. Conceptually, them molecule IDs will be +in ascending order for any molecule with one or more of its atoms in +the specified group. +
+The mol attribute is the molecule ID. This attribute can be used to +produce molecule IDs as labels for per-molecule datums generated by +other computes or fixes when they are output to a file, e.g. by the +fix ave/time command.
The count attribute is the number of atoms in the molecule.
diff --git a/doc/compute_property_molecule.txt b/doc/compute_property_molecule.txt index ebfcfab40f..540dab079c 100644 --- a/doc/compute_property_molecule.txt +++ b/doc/compute_property_molecule.txt @@ -33,13 +33,16 @@ commands that generate per-molecule data, such as "compute com/molecule"_compute_com_molecule.html and "compute msd/molecule"_compute_msd_molecule.html. -The {mol} attribute generates a list of molecule IDs in ascending -order for any molecule with one or more of its atoms in the specified -group. This list and ordering of molecule IDs will be consistent with -the ordering produced by other compute commands that generate -per-molecule datums. Thus this attribute can be used to produce -molecule IDs as labels for those datums when they are output to a -file, e.g. by the "fix ave/time"_fix_ave_time.html command. +The ordering of per-molecule quantities produced by this compute is +consistent with the ordering produced by other compute commands that +generate per-molecule datums. Conceptually, them molecule IDs will be +in ascending order for any molecule with one or more of its atoms in +the specified group. + +The {mol} attribute is the molecule ID. This attribute can be used to +produce molecule IDs as labels for per-molecule datums generated by +other computes or fixes when they are output to a file, e.g. by the +"fix ave/time"_fix_ave_time.html command. The {count} attribute is the number of atoms in the molecule.