Loading doc/compute_atom_molecute.html +61 −115 Original line number Diff line number Diff line Loading @@ -33,136 +33,82 @@ </UL> <P><B>Examples:</B> </P> <P>compute 1 all atom/molecule sum c_force compute 1 all reduce/region subbox sum c_force </P> <PRE>compute 1 all atom/molecule c_ke c_pe </PRE> <PRE>compute 1 top atom/molecule v_myFormula c_stress<B>3</B> </PRE> <P><B>Description:</B> </P> <P>Define a calculation that "reduces" one or more vector inputs into scalar values, one per listed input. The inputs can be per-atom or local quantities; they cannot be global quantities. Atom attributes are per-atom quantities, <A HREF = "compute.html">computes</A> and <A HREF = "fix.html">fixes</A> may generate any of the three kinds of quantities, and <A HREF = "variable.html">atom-style variables</A> generate per-atom quantities. See the <A HREF = "variable">variable</A> command and its special functions which can perform the same operations as the compute reduce command on global vectors. </P> <P>The reduction operation is specified by the <I>mode</I> setting. The <I>sum</I> option adds the values in the vector into a global total. The <I>min</I> or <I>max</I> options find the minimum or maximum value across all vector values. The <I>ave</I> setting adds the vector values into a global total, then divides by the number of values in the vector. </P> <P>Each listed input is operated on independently. For per-atom inputs, the group specified with this command means only atoms within the group contribute to the result. For per-atom inputs, if the compute reduce/region command is used, the atoms must also currently be within the region. Note that an input that produces per-atom quantities may define its own group which affects the quantities it returns. 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. </P> <P>Each listed input can be an atom attribute (position, velocity, force component) or can be the result of a <A HREF = "compute.html">compute</A> or <A HREF = "fix.html">fix</A> or the evaluation of an atom-style <A HREF = "variable.html">variable</A>. </P> <P>The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are self-explanatory. Note that other atom attributes can be used as inputs to this fix by using the <A HREF = "compute_property_atom.html">compute property/atom</A> command and then specifying an input value from that compute. </P> <P>If a value begins with "c_", a compute ID must follow which has been previously defined in the input script. Computes can generate per-atom or local quantities. See the individual <A HREF = "compute.html">compute</A> doc page for details. If no bracketed integer is appended, the vector calculated by the compute is used. If a bracketed interger is appended, the Ith column of the array calculated by the compute is used. Users can also write code for their own compute styles and <A HREF = "Section_modify.html">add them to LAMMPS</A>. </P> <P>If a value begins with "f_", a fix ID must follow which has been previously defined in the input script. Fixes can generate per-atom or local quantities. See the individual <A HREF = "fix.html">fix</A> doc page for details. Note that some fixes only produce their values on certain timesteps, which must be compatible with when compute reduce references the values, else an error results. If no bracketed integer is appended, the vector calculated by the fix is used. If a bracketed <P>Define a calculation that sums per-atom values on a per-molecule basis, one per listed input. The inputs can <A HREF = "compute.html">computes</A>, <A HREF = "fix.html">fixes</A>, or <A HREF = "variable.html">variables</A> that generate per-atom quantities. Note that attributes stored by atoms, such as mass or force, can also be summed on a per-molecule basis, by accessing these quantities via the <A HREF = "compute_property_atom.html">compute property/atom</A> command. </P> <P>Each listed input is operated on independently. Only atoms within the specified group contribute to the per-molecule sum. Note that compute or fix inputs define their own group which may affect the quantities 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. </P> <P>The ordering of per-molecule quantities produced by this compute are 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. </P> <P>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 quantities. See the individual <A HREF = "compute.html">compute</A> doc page for details. If no bracketed integer is appended, the vector calculated by the compute is used. If a bracketed interger is appended, the Ith column of the array calculated by the compute is used. Users can also write code for their own compute styles and <A HREF = "Section_modify.html">add them to LAMMPS</A>. </P> <P>If an input begins with "f_", a fix ID must follow which has been previously defined in the input script and which generates per-atom quantities. See the individual <A HREF = "fix.html">fix</A> doc page for details. Note that some fixes only produce their values on certain timesteps, which must be compatible with when compute atom/molecule references the values, else an error results. If no bracketed integer is appended, the vector calculated by the fix is used. If a bracketed integer is appended, the Ith column of the array calculated by the fix is used. Users can also write code for their own fix style and <A HREF = "Section_modify.html">add them to LAMMPS</A>. </P> <P>If a value begins with "v_", a variable name must follow which has <P>If an input begins with "v_", a variable name must follow which has been previously defined in the input script. It must be an <A HREF = "variable.html">atom-style variable</A>. Atom-style variables can reference thermodynamic keywords and various per-atom attributes, or invoke other computes, fixes, or variables when they are evaluated, so this is a very general means of generating per-atom quantities to reduce. </P> <HR> <P>If the <I>replace</I> keyword is used, two indices <I>vec1</I> and <I>vec2</I> are specified, where each index ranges from 1 to the # of input values. The replace keyword can only be used if the <I>mode</I> is <I>min</I> or <I>max</I>. It works as follows. A min/max is computed as usual on the <I>vec2</I> input vector. The index N of that value within <I>vec2</I> is also stored. Then, instead of performing a min/max on the <I>vec1</I> input vector, the stored index is used to select the Nth element of the <I>vec1</I> vector. </P> <P>Thus, for example, if you wish to use this compute to find the bond with maximum stretch, you can do it as follows: </P> <PRE>compute 1 all property/local batom1 batom2 compute 2 all bond/local dist compute 3 all reduce max c_1[1] c_1[2] c_2 replace 1 3 replace 2 3 thermo_style custom step temp c_3[1] c_3[2] c_3[3] </PRE> <P>The first two input values in the compute reduce command are vectors with the IDs of the 2 atoms in each bond, using the <A HREF = "compute_property_local.html">compute property/local</A> command. The last input value is bond distance, using the <A HREF = "compute_bond_local.html">compute bond/local</A> command. Instead of taking the max of the two atom ID vectors, which does not yield useful information in this context, the <I>replace</I> keywords will extract the atom IDs for the two atoms in the bond of maximum stretch. These atom IDs and the bond stretch will be printed with thermodynamic output. </P> <HR> <P>If a single input is specified this compute produces a global scalar value. If multiple inputs are specified, this compute produces a global vector of values, the length of which is equal to the number of inputs specified. </P> <P>As discussed below, for <I>sum</I> mode, the value(s) produced by this compute are all "extensive", meaning their value scales linearly with the number of atoms involved. If normalized values are desired, this compute can be accessed by the <A HREF = "thermo_style.html">thermo_style custom</A> command with <A HREF = "thermo_modify.html">thermo_modify norm yes</A> set as an option. Or it can be accessed by a <A HREF = "variable.html">variable</A> that divides by the appropriate atom count. this is a very general means of generating per-atom quantities to sum on a per-molecule basis. </P> <HR> <P><B>Output info:</B> </P> <P>This compute calculates a global scalar if a single input value is specified or a global vector of length N where N is the number of inputs, and which can be accessed by indices 1 to N. These values can be used by any command that uses global scalar or vector values from a compute as input. See <A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS output options. </P> <P>All the scalar or vector values calculated by this compute are "intensive", except when the <I>sum</I> mode is used on per-atom or local vectors, in which case the calculated values are "extensive". </P> <P>The scalar or vector values will be in whatever <A HREF = "units.html">units</A> the quantities being reduced are in. <P>This compute calculates a global vector or global array depending on the number of input values. The length of the vector or number of rows in the array is the number of molecules. If a single input is specified, a global vector is produced. If two or more inputs are specified, a global array is produced where the number of columns = the number of inputs. The vector or array can be accessed by any command that uses global values from a compute as input. See <A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS output options. </P> <P>All the vector or array values calculated by this compute are "extensive". </P> <P>The vector or array values will be in whatever <A HREF = "units.html">units</A> the input quantities are in. </P> <P><B>Restrictions:</B> none </P> Loading doc/compute_atom_molecute.txt +59 −114 Original line number Diff line number Diff line Loading @@ -25,136 +25,81 @@ input = c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l [Examples:] compute 1 all atom/molecule sum c_force compute 1 all reduce/region subbox sum c_force compute 1 all atom/molecule c_ke c_pe compute 1 top atom/molecule v_myFormula c_stress[3] :pre [Description:] Define a calculation that "reduces" one or more vector inputs into scalar values, one per listed input. The inputs can be per-atom or local quantities; they cannot be global quantities. Atom attributes are per-atom quantities, "computes"_compute.html and "fixes"_fix.html may generate any of the three kinds of quantities, and "atom-style variables"_variable.html generate per-atom quantities. See the "variable"_variable command and its special functions which can perform the same operations as the compute reduce command on global vectors. The reduction operation is specified by the {mode} setting. The {sum} option adds the values in the vector into a global total. The {min} or {max} options find the minimum or maximum value across all vector values. The {ave} setting adds the vector values into a global total, then divides by the number of values in the vector. Each listed input is operated on independently. For per-atom inputs, the group specified with this command means only atoms within the group contribute to the result. For per-atom inputs, if the compute reduce/region command is used, the atoms must also currently be within the region. Note that an input that produces per-atom quantities may define its own group which affects the quantities it returns. 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. Each listed input can be an atom attribute (position, velocity, force component) or can be the result of a "compute"_compute.html or "fix"_fix.html or the evaluation of an atom-style "variable"_variable.html. The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are self-explanatory. Note that other atom attributes can be used as inputs to this fix by using the "compute property/atom"_compute_property_atom.html command and then specifying an input value from that compute. If a value begins with "c_", a compute ID must follow which has been previously defined in the input script. Computes can generate per-atom or local quantities. See the individual "compute"_compute.html doc page for details. If no bracketed integer is appended, the vector calculated by the compute is used. If a bracketed interger is appended, the Ith column of the array calculated by the compute is used. Users can also write code for their own compute styles and "add them to LAMMPS"_Section_modify.html. If a value begins with "f_", a fix ID must follow which has been previously defined in the input script. Fixes can generate per-atom or local quantities. See the individual "fix"_fix.html doc page for details. Note that some fixes only produce their values on certain timesteps, which must be compatible with when compute reduce references the values, else an error results. If no bracketed integer is appended, the vector calculated by the fix is used. If a bracketed Define a calculation that sums per-atom values on a per-molecule basis, one per listed input. The inputs can "computes"_compute.html, "fixes"_fix.html, or "variables"_variable.html that generate per-atom quantities. Note that attributes stored by atoms, such as mass or force, can also be summed on a per-molecule basis, by accessing these quantities via the "compute property/atom"_compute_property_atom.html command. Each listed input is operated on independently. Only atoms within the specified group contribute to the per-molecule sum. Note that compute or fix inputs define their own group which may affect the quantities 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 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. 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 quantities. See the individual "compute"_compute.html doc page for details. If no bracketed integer is appended, the vector calculated by the compute is used. If a bracketed interger is appended, the Ith column of the array calculated by the compute is used. Users can also write code for their own compute styles and "add them to LAMMPS"_Section_modify.html. If an input begins with "f_", a fix ID must follow which has been previously defined in the input script and which generates per-atom quantities. See the individual "fix"_fix.html doc page for details. Note that some fixes only produce their values on certain timesteps, which must be compatible with when compute atom/molecule references the values, else an error results. If no bracketed integer is appended, the vector calculated by the fix is used. If a bracketed integer is appended, the Ith column of the array calculated by the fix is used. Users can also write code for their own fix style and "add them to LAMMPS"_Section_modify.html. If a value begins with "v_", a variable name must follow which has If an input begins with "v_", a variable name must follow which has been previously defined in the input script. It must be an "atom-style variable"_variable.html. Atom-style variables can reference thermodynamic keywords and various per-atom attributes, or invoke other computes, fixes, or variables when they are evaluated, so this is a very general means of generating per-atom quantities to reduce. :line If the {replace} keyword is used, two indices {vec1} and {vec2} are specified, where each index ranges from 1 to the # of input values. The replace keyword can only be used if the {mode} is {min} or {max}. It works as follows. A min/max is computed as usual on the {vec2} input vector. The index N of that value within {vec2} is also stored. Then, instead of performing a min/max on the {vec1} input vector, the stored index is used to select the Nth element of the {vec1} vector. Thus, for example, if you wish to use this compute to find the bond with maximum stretch, you can do it as follows: compute 1 all property/local batom1 batom2 compute 2 all bond/local dist compute 3 all reduce max c_1\[1\] c_1\[2\] c_2 replace 1 3 replace 2 3 thermo_style custom step temp c_3\[1\] c_3\[2\] c_3\[3\] :pre The first two input values in the compute reduce command are vectors with the IDs of the 2 atoms in each bond, using the "compute property/local"_compute_property_local.html command. The last input value is bond distance, using the "compute bond/local"_compute_bond_local.html command. Instead of taking the max of the two atom ID vectors, which does not yield useful information in this context, the {replace} keywords will extract the atom IDs for the two atoms in the bond of maximum stretch. These atom IDs and the bond stretch will be printed with thermodynamic output. :line If a single input is specified this compute produces a global scalar value. If multiple inputs are specified, this compute produces a global vector of values, the length of which is equal to the number of inputs specified. As discussed below, for {sum} mode, the value(s) produced by this compute are all "extensive", meaning their value scales linearly with the number of atoms involved. If normalized values are desired, this compute can be accessed by the "thermo_style custom"_thermo_style.html command with "thermo_modify norm yes"_thermo_modify.html set as an option. Or it can be accessed by a "variable"_variable.html that divides by the appropriate atom count. this is a very general means of generating per-atom quantities to sum on a per-molecule basis. :line [Output info:] This compute calculates a global scalar if a single input value is specified or a global vector of length N where N is the number of inputs, and which can be accessed by indices 1 to N. These values can be used by any command that uses global scalar or vector values from a compute as input. See "this section"_Section_howto.html#4_15 for an overview of LAMMPS output options. All the scalar or vector values calculated by this compute are "intensive", except when the {sum} mode is used on per-atom or local vectors, in which case the calculated values are "extensive". The scalar or vector values will be in whatever "units"_units.html the quantities being reduced are in. This compute calculates a global vector or global array depending on the number of input values. The length of the vector or number of rows in the array is the number of molecules. If a single input is specified, a global vector is produced. If two or more inputs are specified, a global array is produced where the number of columns = the number of inputs. The vector or array can be accessed by any command that uses global values from a compute as input. See "this section"_Section_howto.html#4_15 for an overview of LAMMPS output options. All the vector or array values calculated by this compute are "extensive". The vector or array values will be in whatever "units"_units.html the input quantities are in. [Restrictions:] none Loading Loading
doc/compute_atom_molecute.html +61 −115 Original line number Diff line number Diff line Loading @@ -33,136 +33,82 @@ </UL> <P><B>Examples:</B> </P> <P>compute 1 all atom/molecule sum c_force compute 1 all reduce/region subbox sum c_force </P> <PRE>compute 1 all atom/molecule c_ke c_pe </PRE> <PRE>compute 1 top atom/molecule v_myFormula c_stress<B>3</B> </PRE> <P><B>Description:</B> </P> <P>Define a calculation that "reduces" one or more vector inputs into scalar values, one per listed input. The inputs can be per-atom or local quantities; they cannot be global quantities. Atom attributes are per-atom quantities, <A HREF = "compute.html">computes</A> and <A HREF = "fix.html">fixes</A> may generate any of the three kinds of quantities, and <A HREF = "variable.html">atom-style variables</A> generate per-atom quantities. See the <A HREF = "variable">variable</A> command and its special functions which can perform the same operations as the compute reduce command on global vectors. </P> <P>The reduction operation is specified by the <I>mode</I> setting. The <I>sum</I> option adds the values in the vector into a global total. The <I>min</I> or <I>max</I> options find the minimum or maximum value across all vector values. The <I>ave</I> setting adds the vector values into a global total, then divides by the number of values in the vector. </P> <P>Each listed input is operated on independently. For per-atom inputs, the group specified with this command means only atoms within the group contribute to the result. For per-atom inputs, if the compute reduce/region command is used, the atoms must also currently be within the region. Note that an input that produces per-atom quantities may define its own group which affects the quantities it returns. 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. </P> <P>Each listed input can be an atom attribute (position, velocity, force component) or can be the result of a <A HREF = "compute.html">compute</A> or <A HREF = "fix.html">fix</A> or the evaluation of an atom-style <A HREF = "variable.html">variable</A>. </P> <P>The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are self-explanatory. Note that other atom attributes can be used as inputs to this fix by using the <A HREF = "compute_property_atom.html">compute property/atom</A> command and then specifying an input value from that compute. </P> <P>If a value begins with "c_", a compute ID must follow which has been previously defined in the input script. Computes can generate per-atom or local quantities. See the individual <A HREF = "compute.html">compute</A> doc page for details. If no bracketed integer is appended, the vector calculated by the compute is used. If a bracketed interger is appended, the Ith column of the array calculated by the compute is used. Users can also write code for their own compute styles and <A HREF = "Section_modify.html">add them to LAMMPS</A>. </P> <P>If a value begins with "f_", a fix ID must follow which has been previously defined in the input script. Fixes can generate per-atom or local quantities. See the individual <A HREF = "fix.html">fix</A> doc page for details. Note that some fixes only produce their values on certain timesteps, which must be compatible with when compute reduce references the values, else an error results. If no bracketed integer is appended, the vector calculated by the fix is used. If a bracketed <P>Define a calculation that sums per-atom values on a per-molecule basis, one per listed input. The inputs can <A HREF = "compute.html">computes</A>, <A HREF = "fix.html">fixes</A>, or <A HREF = "variable.html">variables</A> that generate per-atom quantities. Note that attributes stored by atoms, such as mass or force, can also be summed on a per-molecule basis, by accessing these quantities via the <A HREF = "compute_property_atom.html">compute property/atom</A> command. </P> <P>Each listed input is operated on independently. Only atoms within the specified group contribute to the per-molecule sum. Note that compute or fix inputs define their own group which may affect the quantities 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. </P> <P>The ordering of per-molecule quantities produced by this compute are 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. </P> <P>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 quantities. See the individual <A HREF = "compute.html">compute</A> doc page for details. If no bracketed integer is appended, the vector calculated by the compute is used. If a bracketed interger is appended, the Ith column of the array calculated by the compute is used. Users can also write code for their own compute styles and <A HREF = "Section_modify.html">add them to LAMMPS</A>. </P> <P>If an input begins with "f_", a fix ID must follow which has been previously defined in the input script and which generates per-atom quantities. See the individual <A HREF = "fix.html">fix</A> doc page for details. Note that some fixes only produce their values on certain timesteps, which must be compatible with when compute atom/molecule references the values, else an error results. If no bracketed integer is appended, the vector calculated by the fix is used. If a bracketed integer is appended, the Ith column of the array calculated by the fix is used. Users can also write code for their own fix style and <A HREF = "Section_modify.html">add them to LAMMPS</A>. </P> <P>If a value begins with "v_", a variable name must follow which has <P>If an input begins with "v_", a variable name must follow which has been previously defined in the input script. It must be an <A HREF = "variable.html">atom-style variable</A>. Atom-style variables can reference thermodynamic keywords and various per-atom attributes, or invoke other computes, fixes, or variables when they are evaluated, so this is a very general means of generating per-atom quantities to reduce. </P> <HR> <P>If the <I>replace</I> keyword is used, two indices <I>vec1</I> and <I>vec2</I> are specified, where each index ranges from 1 to the # of input values. The replace keyword can only be used if the <I>mode</I> is <I>min</I> or <I>max</I>. It works as follows. A min/max is computed as usual on the <I>vec2</I> input vector. The index N of that value within <I>vec2</I> is also stored. Then, instead of performing a min/max on the <I>vec1</I> input vector, the stored index is used to select the Nth element of the <I>vec1</I> vector. </P> <P>Thus, for example, if you wish to use this compute to find the bond with maximum stretch, you can do it as follows: </P> <PRE>compute 1 all property/local batom1 batom2 compute 2 all bond/local dist compute 3 all reduce max c_1[1] c_1[2] c_2 replace 1 3 replace 2 3 thermo_style custom step temp c_3[1] c_3[2] c_3[3] </PRE> <P>The first two input values in the compute reduce command are vectors with the IDs of the 2 atoms in each bond, using the <A HREF = "compute_property_local.html">compute property/local</A> command. The last input value is bond distance, using the <A HREF = "compute_bond_local.html">compute bond/local</A> command. Instead of taking the max of the two atom ID vectors, which does not yield useful information in this context, the <I>replace</I> keywords will extract the atom IDs for the two atoms in the bond of maximum stretch. These atom IDs and the bond stretch will be printed with thermodynamic output. </P> <HR> <P>If a single input is specified this compute produces a global scalar value. If multiple inputs are specified, this compute produces a global vector of values, the length of which is equal to the number of inputs specified. </P> <P>As discussed below, for <I>sum</I> mode, the value(s) produced by this compute are all "extensive", meaning their value scales linearly with the number of atoms involved. If normalized values are desired, this compute can be accessed by the <A HREF = "thermo_style.html">thermo_style custom</A> command with <A HREF = "thermo_modify.html">thermo_modify norm yes</A> set as an option. Or it can be accessed by a <A HREF = "variable.html">variable</A> that divides by the appropriate atom count. this is a very general means of generating per-atom quantities to sum on a per-molecule basis. </P> <HR> <P><B>Output info:</B> </P> <P>This compute calculates a global scalar if a single input value is specified or a global vector of length N where N is the number of inputs, and which can be accessed by indices 1 to N. These values can be used by any command that uses global scalar or vector values from a compute as input. See <A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS output options. </P> <P>All the scalar or vector values calculated by this compute are "intensive", except when the <I>sum</I> mode is used on per-atom or local vectors, in which case the calculated values are "extensive". </P> <P>The scalar or vector values will be in whatever <A HREF = "units.html">units</A> the quantities being reduced are in. <P>This compute calculates a global vector or global array depending on the number of input values. The length of the vector or number of rows in the array is the number of molecules. If a single input is specified, a global vector is produced. If two or more inputs are specified, a global array is produced where the number of columns = the number of inputs. The vector or array can be accessed by any command that uses global values from a compute as input. See <A HREF = "Section_howto.html#4_15">this section</A> for an overview of LAMMPS output options. </P> <P>All the vector or array values calculated by this compute are "extensive". </P> <P>The vector or array values will be in whatever <A HREF = "units.html">units</A> the input quantities are in. </P> <P><B>Restrictions:</B> none </P> Loading
doc/compute_atom_molecute.txt +59 −114 Original line number Diff line number Diff line Loading @@ -25,136 +25,81 @@ input = c_ID, c_ID\[N\], f_ID, f_ID\[N\], v_name :l [Examples:] compute 1 all atom/molecule sum c_force compute 1 all reduce/region subbox sum c_force compute 1 all atom/molecule c_ke c_pe compute 1 top atom/molecule v_myFormula c_stress[3] :pre [Description:] Define a calculation that "reduces" one or more vector inputs into scalar values, one per listed input. The inputs can be per-atom or local quantities; they cannot be global quantities. Atom attributes are per-atom quantities, "computes"_compute.html and "fixes"_fix.html may generate any of the three kinds of quantities, and "atom-style variables"_variable.html generate per-atom quantities. See the "variable"_variable command and its special functions which can perform the same operations as the compute reduce command on global vectors. The reduction operation is specified by the {mode} setting. The {sum} option adds the values in the vector into a global total. The {min} or {max} options find the minimum or maximum value across all vector values. The {ave} setting adds the vector values into a global total, then divides by the number of values in the vector. Each listed input is operated on independently. For per-atom inputs, the group specified with this command means only atoms within the group contribute to the result. For per-atom inputs, if the compute reduce/region command is used, the atoms must also currently be within the region. Note that an input that produces per-atom quantities may define its own group which affects the quantities it returns. 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. Each listed input can be an atom attribute (position, velocity, force component) or can be the result of a "compute"_compute.html or "fix"_fix.html or the evaluation of an atom-style "variable"_variable.html. The atom attribute values (x,y,z,vx,vy,vz,fx,fy,fz) are self-explanatory. Note that other atom attributes can be used as inputs to this fix by using the "compute property/atom"_compute_property_atom.html command and then specifying an input value from that compute. If a value begins with "c_", a compute ID must follow which has been previously defined in the input script. Computes can generate per-atom or local quantities. See the individual "compute"_compute.html doc page for details. If no bracketed integer is appended, the vector calculated by the compute is used. If a bracketed interger is appended, the Ith column of the array calculated by the compute is used. Users can also write code for their own compute styles and "add them to LAMMPS"_Section_modify.html. If a value begins with "f_", a fix ID must follow which has been previously defined in the input script. Fixes can generate per-atom or local quantities. See the individual "fix"_fix.html doc page for details. Note that some fixes only produce their values on certain timesteps, which must be compatible with when compute reduce references the values, else an error results. If no bracketed integer is appended, the vector calculated by the fix is used. If a bracketed Define a calculation that sums per-atom values on a per-molecule basis, one per listed input. The inputs can "computes"_compute.html, "fixes"_fix.html, or "variables"_variable.html that generate per-atom quantities. Note that attributes stored by atoms, such as mass or force, can also be summed on a per-molecule basis, by accessing these quantities via the "compute property/atom"_compute_property_atom.html command. Each listed input is operated on independently. Only atoms within the specified group contribute to the per-molecule sum. Note that compute or fix inputs define their own group which may affect the quantities 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 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. 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 quantities. See the individual "compute"_compute.html doc page for details. If no bracketed integer is appended, the vector calculated by the compute is used. If a bracketed interger is appended, the Ith column of the array calculated by the compute is used. Users can also write code for their own compute styles and "add them to LAMMPS"_Section_modify.html. If an input begins with "f_", a fix ID must follow which has been previously defined in the input script and which generates per-atom quantities. See the individual "fix"_fix.html doc page for details. Note that some fixes only produce their values on certain timesteps, which must be compatible with when compute atom/molecule references the values, else an error results. If no bracketed integer is appended, the vector calculated by the fix is used. If a bracketed integer is appended, the Ith column of the array calculated by the fix is used. Users can also write code for their own fix style and "add them to LAMMPS"_Section_modify.html. If a value begins with "v_", a variable name must follow which has If an input begins with "v_", a variable name must follow which has been previously defined in the input script. It must be an "atom-style variable"_variable.html. Atom-style variables can reference thermodynamic keywords and various per-atom attributes, or invoke other computes, fixes, or variables when they are evaluated, so this is a very general means of generating per-atom quantities to reduce. :line If the {replace} keyword is used, two indices {vec1} and {vec2} are specified, where each index ranges from 1 to the # of input values. The replace keyword can only be used if the {mode} is {min} or {max}. It works as follows. A min/max is computed as usual on the {vec2} input vector. The index N of that value within {vec2} is also stored. Then, instead of performing a min/max on the {vec1} input vector, the stored index is used to select the Nth element of the {vec1} vector. Thus, for example, if you wish to use this compute to find the bond with maximum stretch, you can do it as follows: compute 1 all property/local batom1 batom2 compute 2 all bond/local dist compute 3 all reduce max c_1\[1\] c_1\[2\] c_2 replace 1 3 replace 2 3 thermo_style custom step temp c_3\[1\] c_3\[2\] c_3\[3\] :pre The first two input values in the compute reduce command are vectors with the IDs of the 2 atoms in each bond, using the "compute property/local"_compute_property_local.html command. The last input value is bond distance, using the "compute bond/local"_compute_bond_local.html command. Instead of taking the max of the two atom ID vectors, which does not yield useful information in this context, the {replace} keywords will extract the atom IDs for the two atoms in the bond of maximum stretch. These atom IDs and the bond stretch will be printed with thermodynamic output. :line If a single input is specified this compute produces a global scalar value. If multiple inputs are specified, this compute produces a global vector of values, the length of which is equal to the number of inputs specified. As discussed below, for {sum} mode, the value(s) produced by this compute are all "extensive", meaning their value scales linearly with the number of atoms involved. If normalized values are desired, this compute can be accessed by the "thermo_style custom"_thermo_style.html command with "thermo_modify norm yes"_thermo_modify.html set as an option. Or it can be accessed by a "variable"_variable.html that divides by the appropriate atom count. this is a very general means of generating per-atom quantities to sum on a per-molecule basis. :line [Output info:] This compute calculates a global scalar if a single input value is specified or a global vector of length N where N is the number of inputs, and which can be accessed by indices 1 to N. These values can be used by any command that uses global scalar or vector values from a compute as input. See "this section"_Section_howto.html#4_15 for an overview of LAMMPS output options. All the scalar or vector values calculated by this compute are "intensive", except when the {sum} mode is used on per-atom or local vectors, in which case the calculated values are "extensive". The scalar or vector values will be in whatever "units"_units.html the quantities being reduced are in. This compute calculates a global vector or global array depending on the number of input values. The length of the vector or number of rows in the array is the number of molecules. If a single input is specified, a global vector is produced. If two or more inputs are specified, a global array is produced where the number of columns = the number of inputs. The vector or array can be accessed by any command that uses global values from a compute as input. See "this section"_Section_howto.html#4_15 for an overview of LAMMPS output options. All the vector or array values calculated by this compute are "extensive". The vector or array values will be in whatever "units"_units.html the input quantities are in. [Restrictions:] none Loading
