(1022815b) · Commits · 郑智淋 / lammps

doc/variable.html

+73 −57

Original line number	Diff line number	Diff line
		@@ -25,7 +25,7 @@
		<I>universe</I> args = one or more strings
		<I>uloop</I> args = N = integer size of loop
		<I>equal</I> or <I>atom</I> args = one formula containing numbers, thermo keywords, math operations, group functions, atom values and vectors, compute and fix references, other variables
		numbers = 0.0, -5.4, 2.8e-4, etc
		numbers = 0.0, 100, -5.4, 2.8e-4, etc
		thermo keywords = vol, ke, press, etc from <A HREF = "thermo_style.html">thermo_style</A>
		math operations = (), -x, x+y, x-y, x*y, x/y, x^y, sqrt(x), exp(x), ln(x)
		group functions = count(group), mass(group), charge(group),
		@@ -35,9 +35,9 @@
		vx[N], vy[N], vz[N], fx[N], fy[N], fz[N]
		atom vector = mass[], x[], y[], z[],
		vx[], vy[], vz[], fx[], fy[], fz[]
		compute references = c_ID, c_ID[N]
		fix references = f_ID, f_ID[N]
		other variables = v_abc, v_x, etc
		compute references = c_ID, c_ID[2], c_ID[N], c_ID[N][2], c_ID[], c_ID[][2]
		fix references = f_ID, f_ID[2], f_ID[N], f_ID[N][2], f_ID[], f_ID[][2]
		other variables = v_abc, v_abc[N], v_abc[]
		</PRE>

		</UL>
		@@ -210,24 +210,25 @@ operations, group functions, atom values, atom vectors, compute
		references, fix references, and references to other variables.
		</P>
		<DIV ALIGN=center><TABLE BORDER=1 >
		<TR><TD >Number</TD><TD > 0.2, 1.0e20, -15.4, etc</TD></TR>
		<TR><TD >Number</TD><TD > 0.2, 100, 1.0e20, -15.4, etc</TD></TR>
		<TR><TD >Thermo keywords</TD><TD > vol, pe, ebond, etc</TD></TR>
		<TR><TD >Math operations</TD><TD > (), -x, x+y, x-y, x*y, x/y, x^y, sqrt(x), exp(x), ln(x)</TD></TR>
		<TR><TD >Group functions</TD><TD > count(ID), mass(ID), charge(ID), xcm(ID,dim), vcm(ID,dim), fcm(ID,dim), bound(ID,dir), gyration(ID)</TD></TR>
		<TR><TD >Atom values</TD><TD > mass[N], x[N], y[N], z[N], vx[N], vy[N], vz[N], fx[N], fy[N], fz[N]</TD></TR>
		<TR><TD >Atom vectors</TD><TD > mass[], x[], y[], z[], vx[], vy[], vz[], fx[], fy[], fz[]</TD></TR>
		<TR><TD >Compute references</TD><TD > c_ID, c_ID[N]</TD></TR>
		<TR><TD >Fix references</TD><TD > f_ID, f_ID[N]</TD></TR>
		<TR><TD >Other variables</TD><TD > v_abc, v_x, etc
		<TR><TD >Compute references</TD><TD > c_ID, c_ID[2], c_ID[N], c_ID[N][2], c_ID[], c_ID[][2]</TD></TR>
		<TR><TD >Fix references</TD><TD > f_ID, f_ID[2], f_ID[N], f_ID[N][2], f_ID[], f_ID[][2]</TD></TR>
		<TR><TD >Other variables</TD><TD > v_abc, v_abc[N], v_abc[]
		</TD></TR></TABLE></DIV>

		<P>Note that a formula for equal-style variables cannot use any formula
		element that produces per-atom values. This includes atom vectors, a
		compute that produces per-atom values, a fix that produces per-atoms
		values, or an atom-style variable. A formula for an atom-style
		variables can use these elements, as well as elements that produce a
		global scalar or vector, e.g. a compute or fix that produces global
		quantities.
		<P>Note that formula elements that contain empty brackets, such as an
		atom vector, produce per-atom values. All other formula elements
		produce a global value.
		</P>
		<P>A formula for equal-style variables cannot use any formula element
		that produces per-atom values. A formula for an atom-style variable
		can use formula elements that produce either global values or per-atom
		values.
		</P>
		<P>The thermo keywords allowed in a formula are those defined by the
		"thermo_style custom" command. Since many thermodyanmic quantities
		@@ -262,50 +263,65 @@ gyration</A> command for a definition of the formula.
		desired atom-ID, e.g. x[243]., which means use the x coordinate of
		the atom with ID=243.
		</P>
		<P>Atom vectors take no argument. They generate one value per atom, so
		that a reference like x[] means the x-coord of each atom will be
		used when evaluating the variable.
		<P>Atom vectors use empty brackets, i.e. they take no argument. They
		generate one value per atom, so that a reference like x[] means the
		x-coord of each atom will be used when evaluating the variable.
		</P>
		<P>Compute references access global scalar or vector quantities or
		per-atom scalar or vector quantities calculated by a
		<P>Compute references access one or more quantities calculated by a
		<A HREF = "compute.html">compute</A>. The ID in the reference should be replaced by
		the actual ID of the compute defined elsewhere in the input script.
		See the <A HREF = "compute.html">compute</A> command for details. Any specific
		compute will either generate global or per-atom values, so there
		is no amiguity as to which is used.
		</P>
		<P>If <I>c_ID</I> is used as a keyword, then the scalar quantity calculated by
		the compute is used (global or per-atom). If <I>c_ID[N]</I> is used,
		then one component of the vector quantity calculated by the compute is
		used (global or per-atom). N should be an integer from 1-M, where M
		is the length of the vector calculated by the compute.
		</P>
		<P>Fix references access global scalar or vector quantities or per-atom
		scalar or vector quantities calculated by a <A HREF = "fix.html">fix</A>. The ID in
		the reference should be replaced by the actual ID of the fix defined
		elsewhere in the input script. See the doc pages for individual fixes
		to see which ones compute what kind of quantities. Any specific fix
		compute will either generate global or per-atom values, so there is no
		amiguity as to which is used. Some fixes only generate quantities on
		certain timesteps. If a variable attempts to access the fix on
		non-allowed timesteps, an error is generated. For example, the <A HREF = "fix_ave_time.html">fix
		ave/time</A> command may only generate averaged
		quantities every 100 steps. See the <A HREF = "fix.html">fix</A> command for
		details.
		</P>
		<P>If <I>f_ID</I> is used as a keyword, then the scalar quantity calculated by
		the fix is used (global or per-atom). If <I>f_ID[N]</I> is used, then
		one component of the vector quantity calculated by the fix is used
		(global or per-atom). N should be an integer from 1-M, where M is the
		length of the vector calculated by the fix.
		See the doc pages for individual computes to see which ones calculate
		global versus per-atom quantities. If the compute reference contains
		empty brackets, then per-atom values calculated by the compute are
		accessed. Otherwise a single value (global or per-atom) calculated by
		the compute is accessed.
		</P>
		<P>The different kinds of compute references are as follows. M is a
		positive integer <= the number of vector values calculated by the
		compute. N is a global atom ID (positive integer).
		</P>
		<DIV ALIGN=center><TABLE BORDER=1 >
		<TR><TD >c_ID</TD><TD > scalar value of a global compute</TD></TR>
		<TR><TD >c_ID[2]</TD><TD > vector component of a global compute</TD></TR>
		<TR><TD >c_ID[N]</TD><TD > single atom's scalar value of a per-atom compute</TD></TR>
		<TR><TD >c_ID[N][M]</TD><TD > single atom's vector component of a per-atom compute</TD></TR>
		<TR><TD >c_ID[]</TD><TD > per-atom scalar from a per-atom compute</TD></TR>
		<TR><TD >c_ID[][M]</TD><TD > per-atom vector component from a per-atom compute
		</TD></TR></TABLE></DIV>

		<P>Fix references access one or more quantities calculated by a
		<A HREF = "fix.html">fix</A>. The ID in the reference should be replaced by
		the actual ID of the fix defined elsewhere in the input script.
		See the doc pages for individual computes to see which ones calculate
		global versus per-atom quantities. If the compute reference contains
		empty brackets, then per-atom values calculated by the compute are
		accessed. Otherwise a single value (global or per-atom) calculated by
		the compute is accessed.
		</P>
		<P>Note that some fixes only generate quantities on certain timesteps.
		If a variable attempts to access the fix on non-allowed timesteps, an
		error is generated. For example, the <A HREF = "fix_ave_time.html">fix ave/time</A>
		command may only generate averaged quantities every 100 steps. See
		the doc pages for individual fix commands for details.
		</P>
		<P>The different kinds of fix references are exactly the same as the
		compute references listed in the above table, where "c_" is replaced
		by "f_", and the word "compute" is replaced by "fix".
		</P>
		<P>The current values of other variables can be accessed by prepending a
		"v_" to the variable name. This will cause that variable to be
		evaulated. Note that <I>equal</I> style variables generate single values
		and <I>atom</I> style variables generate one value per atom. Thus an
		atom-style variable cannot be referenced by the formula for an
		equal-style variable, but the converse is allowed.
		evaulated. Atom-style variables generate per-atom values; all other
		styles of variables generate a single scalar value.
		</P>
		<P>The different kinds of variable references are as follows. N is a
		global atom ID (positive integer).
		</P>
		<DIV ALIGN=center><TABLE BORDER=1 >
		<TR><TD >v_ID</TD><TD > scalar value of a non atom-style variable</TD></TR>
		<TR><TD >v_ID[N]</TD><TD > single atom's scalar value from an atom-style variable</TD></TR>
		<TR><TD >v_ID[]</TD><TD > per-atom value from an atom-style variable
		</TD></TR></TABLE></DIV>

		<P>IMPORTANT NOTE: If you define variables in circular manner like this:
		</P>
		<PRE>variable a equal v_b
		@@ -359,11 +375,11 @@ the first case, but would change dynamically for the second case.

		<P><B>Restrictions:</B>
		</P>
		<P>The use of atom values in <I>equal</I> or <I>atom</I> style variables requires
		the atom style to use a global mapping in order to look up the vector
		indices. By default, only atom styles with molecular information
		create global maps. The <A HREF = "atom_modify.html">atom_modify map</A> command
		can override the default.
		<P>Indexing any formula element by global atom ID, such as an atom value,
		requires the atom style to use a global mapping in order to look up
		the vector indices. By default, only atom styles with molecular
		information create global maps. The <A HREF = "atom_modify.html">atom_modify
		map</A> command can override the default.
		</P>
		<P>All <I>universe</I>- and <I>uloop</I>-style variables defined in an input script
		must have the same number of values.

doc/variable.txt

+70 −58

Original line number	Diff line number	Diff line
		@@ -20,7 +20,7 @@ style = {index} or {loop} or {world} or {universe} or {uloop} or {equal} or {ato
		{universe} args = one or more strings
		{uloop} args = N = integer size of loop
		{equal} or {atom} args = one formula containing numbers, thermo keywords, math operations, group functions, atom values and vectors, compute and fix references, other variables
		numbers = 0.0, -5.4, 2.8e-4, etc
		numbers = 0.0, 100, -5.4, 2.8e-4, etc
		thermo keywords = vol, ke, press, etc from "thermo_style"_thermo_style.html
		math operations = (), -x, x+y, x-y, x*y, x/y, x^y, sqrt(x), exp(x), ln(x)
		group functions = count(group), mass(group), charge(group),
		@@ -30,9 +30,9 @@ style = {index} or {loop} or {world} or {universe} or {uloop} or {equal} or {ato
		vx\[N\], vy\[N\], vz\[N\], fx\[N\], fy\[N\], fz\[N\]
		atom vector = mass\[\], x\[\], y\[\], z\[\],
		vx\[\], vy\[\], vz\[\], fx\[\], fy\[\], fz\[\]
		compute references = c_ID, c_ID\[N\]
		fix references = f_ID, f_ID\[N\]
		other variables = v_abc, v_x, etc :pre
		compute references = c_ID, c_ID\[2\], c_ID\[N\], c_ID\[N\]\[2\], c_ID\[\], c_ID\[\]\[2\]
		fix references = f_ID, f_ID\[2\], f_ID\[N\], f_ID\[N\]\[2\], f_ID\[\], f_ID\[\]\[2\]
		other variables = v_abc, v_abc\[N\], v_abc\[\] :pre
		:ule

		[Examples:]
		@@ -203,7 +203,7 @@ Specifically, an formula can contain numbers, thermo keywords, math
		operations, group functions, atom values, atom vectors, compute
		references, fix references, and references to other variables.

		Number: 0.2, 1.0e20, -15.4, etc
		Number: 0.2, 100, 1.0e20, -15.4, etc
		Thermo keywords: vol, pe, ebond, etc
		Math operations: (), -x, x+y, x-y, x*y, x/y, x^y, sqrt(x), exp(x), ln(x)
		Group functions: count(ID), mass(ID), charge(ID), xcm(ID,dim), \
		@@ -212,17 +212,18 @@ Atom values: mass\[N\], x\[N\], y\[N\], z\[N\], \
		vx\[N\], vy\[N\], vz\[N\], fx\[N\], fy\[N\], fz\[N\]
		Atom vectors: mass\[\], x\[\], y\[\], z\[\], \
		vx\[\], vy\[\], vz\[\], fx\[\], fy\[\], fz\[\]
		Compute references: c_ID, c_ID\[N\]
		Fix references: f_ID, f_ID\[N\]
		Other variables: v_abc, v_x, etc :tb(s=:)

		Note that a formula for equal-style variables cannot use any formula
		element that produces per-atom values. This includes atom vectors, a
		compute that produces per-atom values, a fix that produces per-atoms
		values, or an atom-style variable. A formula for an atom-style
		variables can use these elements, as well as elements that produce a
		global scalar or vector, e.g. a compute or fix that produces global
		quantities.
		Compute references: c_ID, c_ID\[2\], c_ID\[N\], c_ID\[N\]\[2\], c_ID\[\], c_ID\[\]\[2\]
		Fix references: f_ID, f_ID\[2\], f_ID\[N\], f_ID\[N\]\[2\], f_ID\[\], f_ID\[\]\[2\]
		Other variables: v_abc, v_abc\[N\], v_abc\[\] :tb(s=:)

		Note that formula elements that contain empty brackets, such as an
		atom vector, produce per-atom values. All other formula elements
		produce a global value.

		A formula for equal-style variables cannot use any formula element
		that produces per-atom values. A formula for an atom-style variable
		can use formula elements that produce either global values or per-atom
		values.

		The thermo keywords allowed in a formula are those defined by the
		"thermo_style custom" command. Since many thermodyanmic quantities
		@@ -257,49 +258,60 @@ Atom values take a single integer argument from 1-N, which is the
		desired atom-ID, e.g. x\[243\]., which means use the x coordinate of
		the atom with ID=243.

		Atom vectors take no argument. They generate one value per atom, so
		that a reference like x\[\] means the x-coord of each atom will be
		used when evaluating the variable.
		Atom vectors use empty brackets, i.e. they take no argument. They
		generate one value per atom, so that a reference like x\[\] means the
		x-coord of each atom will be used when evaluating the variable.

		Compute references access global scalar or vector quantities or
		per-atom scalar or vector quantities calculated by a
		Compute references access one or more quantities calculated by a
		"compute"_compute.html. The ID in the reference should be replaced by
		the actual ID of the compute defined elsewhere in the input script.
		See the "compute"_compute.html command for details. Any specific
		compute will either generate global or per-atom values, so there
		is no amiguity as to which is used.

		If {c_ID} is used as a keyword, then the scalar quantity calculated by
		the compute is used (global or per-atom). If {c_ID\[N\]} is used,
		then one component of the vector quantity calculated by the compute is
		used (global or per-atom). N should be an integer from 1-M, where M
		is the length of the vector calculated by the compute.

		Fix references access global scalar or vector quantities or per-atom
		scalar or vector quantities calculated by a "fix"_fix.html. The ID in
		the reference should be replaced by the actual ID of the fix defined
		elsewhere in the input script. See the doc pages for individual fixes
		to see which ones compute what kind of quantities. Any specific fix
		compute will either generate global or per-atom values, so there is no
		amiguity as to which is used. Some fixes only generate quantities on
		certain timesteps. If a variable attempts to access the fix on
		non-allowed timesteps, an error is generated. For example, the "fix
		ave/time"_fix_ave_time.html command may only generate averaged
		quantities every 100 steps. See the "fix"_fix.html command for
		details.

		If {f_ID} is used as a keyword, then the scalar quantity calculated by
		the fix is used (global or per-atom). If {f_ID\[N\]} is used, then
		one component of the vector quantity calculated by the fix is used
		(global or per-atom). N should be an integer from 1-M, where M is the
		length of the vector calculated by the fix.
		See the doc pages for individual computes to see which ones calculate
		global versus per-atom quantities. If the compute reference contains
		empty brackets, then per-atom values calculated by the compute are
		accessed. Otherwise a single value (global or per-atom) calculated by
		the compute is accessed.

		The different kinds of compute references are as follows. M is a
		positive integer <= the number of vector values calculated by the
		compute. N is a global atom ID (positive integer).

		c_ID: scalar value of a global compute
		c_ID\[2\]: vector component of a global compute
		c_ID\[N\]: single atom's scalar value of a per-atom compute
		c_ID\[N\]\[M\]: single atom's vector component of a per-atom compute
		c_ID\[\]: per-atom scalar from a per-atom compute
		c_ID\[\]\[M\]: per-atom vector component from a per-atom compute :tb(s=:)

		Fix references access one or more quantities calculated by a
		"fix"_fix.html. The ID in the reference should be replaced by
		the actual ID of the fix defined elsewhere in the input script.
		See the doc pages for individual computes to see which ones calculate
		global versus per-atom quantities. If the compute reference contains
		empty brackets, then per-atom values calculated by the compute are
		accessed. Otherwise a single value (global or per-atom) calculated by
		the compute is accessed.

		Note that some fixes only generate quantities on certain timesteps.
		If a variable attempts to access the fix on non-allowed timesteps, an
		error is generated. For example, the "fix ave/time"_fix_ave_time.html
		command may only generate averaged quantities every 100 steps. See
		the doc pages for individual fix commands for details.

		The different kinds of fix references are exactly the same as the
		compute references listed in the above table, where "c_" is replaced
		by "f_", and the word "compute" is replaced by "fix".

		The current values of other variables can be accessed by prepending a
		"v_" to the variable name. This will cause that variable to be
		evaulated. Note that {equal} style variables generate single values
		and {atom} style variables generate one value per atom. Thus an
		atom-style variable cannot be referenced by the formula for an
		equal-style variable, but the converse is allowed.
		evaulated. Atom-style variables generate per-atom values; all other
		styles of variables generate a single scalar value.

		The different kinds of variable references are as follows. N is a
		global atom ID (positive integer).

		v_ID: scalar value of a non atom-style variable
		v_ID\[N\]: single atom's scalar value from an atom-style variable
		v_ID\[\]: per-atom value from an atom-style variable :tb(s=:)

		IMPORTANT NOTE: If you define variables in circular manner like this:

		@@ -354,11 +366,11 @@ the first case, but would change dynamically for the second case.

		[Restrictions:]

		The use of atom values in {equal} or {atom} style variables requires
		the atom style to use a global mapping in order to look up the vector
		indices. By default, only atom styles with molecular information
		create global maps. The "atom_modify map"_atom_modify.html command
		can override the default.
		Indexing any formula element by global atom ID, such as an atom value,
		requires the atom style to use a global mapping in order to look up
		the vector indices. By default, only atom styles with molecular
		information create global maps. The "atom_modify
		map"_atom_modify.html command can override the default.

		All {universe}- and {uloop}-style variables defined in an input script
		must have the same number of values.

src/variable.cpp

+301 −159

File changed.

Preview size limit exceeded, changes collapsed.

src/variable.h

+2 −1

Original line number	Diff line number	Diff line
		@@ -60,7 +60,8 @@ class Variable : protected Pointers {
		int int_between_brackets(char *, int, int &, int);
		int math_function(char , char , Tree , Tree , int &, double *, int &);
		int group_function(char , char , Tree , Tree , int &, double *, int &);
		void atom_value(char , int, Tree , Tree , int &, double , int &);
		void peratom2global(int, char , double , int, int,
		Tree , Tree , int &, double *, int &);
		void atom_vector(char , Tree , Tree *, int &);
		};

Admin message