git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@5257 f3b2605a-c512-4ea7-a41b-209d697bcdaa

doc/Section_commands.html

@@ -114,11 +114,23 @@ underscores, or punctuation characters.
 line are arguments.
 </P>
 <P>(6) If you want text with spaces to be treated as a single argument,
-it can be enclosed in double quotes.  The quotes are removed when the
+it can be enclosed in either double or single quotes.  E.g.
-single argument is stored in its final form.  See the <A HREF = "dump_modify.html">dump modify
+</P>
-format</A> or <A HREF = "if.html">if</A> commands for examples.  A "#"
+<PRE>print "Volume = $v"
-or "$" character that is between double quotes will not be treated as
+print 'Volume = $v' 
-a comment indicator in (2) or substituted for as a variable in (3).
+</PRE>
+<P>The quotes are removed when the single argument is stored internally.
+See the <A HREF = "dump_modify.html">dump modify format</A> or <A HREF = "if.html">if</A> commands
+for examples.  A "#" or "$" character that is between quotes will not
+be treated as a comment indicator in (2) or substituted for as a
+variable in (3).
+</P>
+<P>IMPORTANT NOTE: If the argument is itself a command that requires a
+quoted argument (e.g. using a <A HREF = "print.html">print</A> command as part of an
+<A HREF = "if.html">if</A> or <A HREF = "run.html">run every</A> command), then the double and
+single quotes can be nested in the usual manner.  See the doc pages
+for those commands for examples.  Only one of level of nesting is
+allowed, but that should be sufficient for most use cases.
 </P>
 <HR>
 

doc/Section_commands.txt

@@ -111,11 +111,23 @@ underscores, or punctuation characters.
 line are arguments.
 
 (6) If you want text with spaces to be treated as a single argument,
-it can be enclosed in double quotes.  The quotes are removed when the
+it can be enclosed in either double or single quotes.  E.g.
-single argument is stored in its final form.  See the "dump modify
+
-format"_dump_modify.html or "if"_if.html commands for examples.  A "#"
+print "Volume = $v"
-or "$" character that is between double quotes will not be treated as
+print 'Volume = $v' :pre
-a comment indicator in (2) or substituted for as a variable in (3).
+
+The quotes are removed when the single argument is stored internally.
+See the "dump modify format"_dump_modify.html or "if"_if.html commands
+for examples.  A "#" or "$" character that is between quotes will not
+be treated as a comment indicator in (2) or substituted for as a
+variable in (3).
+
+IMPORTANT NOTE: If the argument is itself a command that requires a
+quoted argument (e.g. using a "print"_print.html command as part of an
+"if"_if.html or "run every"_run.html command), then the double and
+single quotes can be nested in the usual manner.  See the doc pages
+for those commands for examples.  Only one of level of nesting is
+allowed, but that should be sufficient for most use cases.
 
 :line
 

doc/angle_class2.html

@@ -20,6 +20,7 @@
 <PRE>angle_style class2
 angle_coeff * 75.0
 angle_coeff 1 bb 10.5872 1.0119 1.5228
+angle_coeff * ba 3.6551 24.895 1.0119 1.5228 
 </PRE>
 <P><B>Description:</B>
 </P>

doc/angle_class2.txt

@@ -16,7 +16,8 @@ angle_style class2 :pre
 
 angle_style class2
 angle_coeff * 75.0
-angle_coeff 1 bb 10.5872 1.0119 1.5228 :pre
+angle_coeff 1 bb 10.5872 1.0119 1.5228
+angle_coeff * ba 3.6551 24.895 1.0119 1.5228 :pre
 
 [Description:]
 

doc/dihedral_class2.html

@@ -19,6 +19,11 @@
 </P>
 <PRE>dihedral_style class2
 dihedral_coeff 1 100 75 100 70 80 60
+dihedral_coeff * mbt 3.5945 0.1704 -0.5490 1.5228 
+dihedral_coeff * ebt 0.3417 0.3264 -0.9036 0.1368 0.0 -0.8080 1.0119 1.1010
+dihedral_coeff 2 at 0.0 -0.1850 -0.7963 -2.0220 0.0 -0.3991 110.2453 105.1270 
+dihedral_coeff * aat -13.5271 110.2453 105.1270 
+dihedral_coeff * bb13 0.0 1.0119 1.1010 
 </PRE>
 <P><B>Description:</B>
 </P>

doc/dihedral_class2.txt

@@ -15,7 +15,12 @@ dihedral_style class2 :pre
 [Examples:]
 
 dihedral_style class2
-dihedral_coeff 1 100 75 100 70 80 60 :pre
+dihedral_coeff 1 100 75 100 70 80 60
+dihedral_coeff * mbt 3.5945 0.1704 -0.5490 1.5228 
+dihedral_coeff * ebt 0.3417 0.3264 -0.9036 0.1368 0.0 -0.8080 1.0119 1.1010
+dihedral_coeff 2 at 0.0 -0.1850 -0.7963 -2.0220 0.0 -0.3991 110.2453 105.1270 
+dihedral_coeff * aat -13.5271 110.2453 105.1270 
+dihedral_coeff * bb13 0.0 1.0119 1.1010 :pre
 
 [Description:]
 

doc/if.html

@@ -13,64 +13,81 @@
 </H3>
 <P><B>Syntax:</B>
 </P>
-<PRE>if value1 operator value2 then t1 t2 ... else e1 e2 ... 
+<PRE>if boolean then t1 t2 ... elif boolean f1 f2 ... elif boolean f1 f2 ... else e1 e2 ... 
 </PRE>
-<UL><LI>value1 = 1st value
+<UL><LI>boolean = a Boolean expression evaluated as TRUE or FALSE (see below)
-<LI>operator = "<" or "<=" or ">" or ">=" or "==" or "!="
-<LI>value2 = 2nd value
 <LI>then = required word
 <LI>t1,t2,...,tN = one or more LAMMPS commands to execute if condition is met, each enclosed in quotes
+<LI>elif = optional word, can appear multiple times
+<LI>f1,f2,...,fN = one or more LAMMPS commands to execute if elif condition is met, each enclosed in quotes (optional arguments)
 <LI>else = optional argument
-<LI>e1,e2,...,eN = one or more LAMMPS commands to execute if condition is not met, each enclosed in quotes (optional arguments) 
+<LI>e1,e2,...,eN = one or more LAMMPS commands to execute if no condition is met, each enclosed in quotes (optional arguments) 
 </UL>
 <P><B>Examples:</B>
 </P>
-<PRE>if ${steps} > 1000 then exit
+<PRE>if "${steps} > 1000" then exit
-if $x <= $y then "print X is smaller = $x" else "print Y is smaller = $y"
+if "$x <= $y" then "print X is smaller = $x" else "print Y is smaller = $y"
-if ${eng} > 0.0 then "timestep 0.005"
+if "(${eng} > 0.0) || ($n < 1000)" then &
-if ${eng} > ${eng_previous} then "jump file1" else "jump file2" 
+  "timestep 0.005" &
+elif $n<10000 &
+  "timestep 0.01" &
+else &
+  "timestep 0.02" &
+  "print 'Max step reached'"
+if "${eng} > ${eng_previous}" then "jump file1" else "jump file2" 
 </PRE>
 <P><B>Description:</B>
 </P>
 <P>This command provides an in-then-else capability within an input
-script.  Two values are numerically compared to each other and the
+script.  A Boolean expression is evaluted and the result is TRUE or
-result is TRUE or FALSE.  Note that as in the examples above, either
+FALSE.  Note that as in the examples above, the expression can contain
-of the two values can be variables, as defined by the
+variables, as defined by the <A HREF = "variable.html">variable</A> command, which
-<A HREF = "variable.html">variable</A> command, so that when the if command is
+will be evaluated as part of the expression.  Thus a user-defined
-executed, the variable(s) will be evaluated, which could calculate a
+formula that reflects the current state of the simulation can be used
-user-defined formula that reflects the current state of the
+to issue one or more new commands.
-simulation.
 </P>
-<P>If the result of the if test is TRUE, then one or more commands (t1,
+<P>If the result of the Boolean expression is TRUE, then one or more
-t2, ..., tN) are executed.  If the result of the if test is FALSE and
+commands (t1, t2, ..., tN) are executed.  If it is FALSE, then Boolean
-no optional "else" argument is included, then the if command does
+expressions associated with successive elif keywords are evaluated
-nothing.  If the result of the if test is FALSE and the optional
+until one is found to be true, in which case its commands (f1, f2,
-"else" argument is included, then one or more commands (e1,
+..., fN) are executed.  If no Boolean expression is TRUE, then the
-e2, ..., eN) are executed.
+commands associated witht the else keyword, namely (e1, e2, ..., eN),
+are executed.  The elif and else keywords and their associated
+commands are optional.  If they aren't specified and the initial
+Boolean expression is FALSE, then no commands are executed.
 </P>
-<P>Each then or else command (t1, e1, etc) can be any valid LAMMPS input
+<P>The allowed syntax for each Boolean expression is described below.
-script command.  Each command should be enclosed in quotes, so it will
+</P>
-be treated as a single argument, as in the examples above.
+<P>Each command (t1, f1, e1, etc) can be any valid LAMMPS input script
+command.  If the command is more than one word, it must enclosed in
+quotes, so it will be treated as a single argument, as in the examples
+above.
+</P>
+<P>IMPORTANT NOTE: If a command itself requires a quoted argument (e.g. a
+<A HREF = "print.html">print</A> command), then double and single quotes can be used
+and nested in the usual manner, as in the examples above and below.
+See <A HREF = "Section_commands.html#3_2">this section</A> of the manual for more
+details on using quotes in arguments.  Only one of level of nesting is
+allowed, but that should be sufficient for most use cases.
 </P>
 <P>Note that by using the line continuation character "&", the if command
-can be spread across many lines, though it is still a single
+can be spread across many lines, though it is still a single command:
-command:
 </P>
-<PRE>if $a < $b then &
+<PRE>if "$a < $b" then &
-  "print Minimum value = $a" &
+  "print 'Minimum value = $a'" &
   "run 1000" &
 else &      
-  "print Minimum value = $b" &
+  'print "Minimum value = $b"' &
   "minimize 0.001 0.001 1000 10000" 
 </PRE>
-<P>Note that if any executed comand is a bogus LAMMPS command, such as
+<P>Note that if one of the commands to execute is an invalid LAMMPS
-"exit" in the first example above, then executing the command will
+command, such as "exit" in the first example above, then executing the
-cause LAMMPS to halt.
+command will cause LAMMPS to halt.
 </P>
 <P>Note that by jumping to a label in the same input script, the if
 command can be used to break out of a loop.  See the <A HREF = "variable.html">variable
-delete</A> for info on how to delete the associated loop
+delete</A> command for info on how to delete the associated
-variable, so that it can be re-used later in the input script.
+loop variable, so that it can be re-used later in the input script.
 </P>
 <P>Here is an example of a double loop which uses the if and
 <A HREF = "jump.html">jump</A> commands to break out of the inner loop when a
@@ -82,7 +99,7 @@ variable    a loop 5
   variable  b loop 5
   print	    "A,B = $a,$b"
   run       10000
-  if	    $b > 2 then "jump in.script break"
+  if	    '$b > 2' then "print 'Jumping to another script'" "jump in.script break"
   next	    b
   jump	    in.script loopb
 label	    break
@@ -91,6 +108,52 @@ variable    b delete
 <PRE>next	    a
 jump	    in.script loopa 
 </PRE>
+<HR>
+
+<P>The Boolean expressions for the if and elif keywords have a C-like
+syntax.  Note that each expression is a single argument within the if
+command.  Thus if you want to include spaces in the expression for
+clarity, you must enclose the entire expression in quotes.
+</P>
+<P>An expression is built out of numbers
+</P>
+<PRE>0.2, 100, 1.0e20, -15.4, etc 
+</PRE>
+<P>and Boolean operators:
+</P>
+<PRE>A == B
+A != B
+A < B
+A <= B
+A > B
+A >= B
+A && B
+A || B 
+</PRE>
+<P>Each A and B is a number or a variable reference like $a or ${abc},
+or another Boolean expression.
+</P>
+<P>If a variable is used it must produce a number when evaluated and
+substituted for in the expression.
+</P>
+<P>Expressions are evaluated left to right and have the usual C-style
+precedence: the 4 relational operators "<", "<=", ">", and ">=" have
+the highest precedence; those 4 relational operators before the
+remaining two relational operators "==" and "!="; those two relational
+operators before the logical AND operator "&&"; and the AND operator
+"&&" before the logical OR operator "||".  Parenthesis can be used to
+group one or more portions of an expression and/or enforce a different
+order of evaluation than what would occur with the default precedence.
+</P>
+<P>The 6 relational operators return either a 1.0 or 0.0 depending on
+whether the relationship between x and y is true or false.  The
+logical AND operator will return 1.0 of both its arguments are
+non-zero, else return a 0.0.  The logical OR operator will return 1.0
+of either of its arguments is non-zero, else return a 0.0.
+</P>
+<P>The overall Boolean expression produces a TRUE result if the result is
+non-zero.  If the result is zero, the expression result is FALSE.
+</P>
 <P><B>Restrictions:</B> none
 </P>
 <P><B>Related commands:</B>

doc/if.txt

@@ -10,64 +10,81 @@ if command :h3
 
 [Syntax:]
 
-if value1 operator value2 then t1 t2 ... else e1 e2 ... :pre
+if boolean then t1 t2 ... elif boolean f1 f2 ... elif boolean f1 f2 ... else e1 e2 ... :pre
 
-value1 = 1st value
+boolean = a Boolean expression evaluated as TRUE or FALSE (see below)
-operator = "<" or "<=" or ">" or ">=" or "==" or "!="
-value2 = 2nd value
 then = required word
 t1,t2,...,tN = one or more LAMMPS commands to execute if condition is met, each enclosed in quotes
+elif = optional word, can appear multiple times
+f1,f2,...,fN = one or more LAMMPS commands to execute if elif condition is met, each enclosed in quotes (optional arguments)
 else = optional argument
-e1,e2,...,eN = one or more LAMMPS commands to execute if condition is not met, each enclosed in quotes (optional arguments) :ul
+e1,e2,...,eN = one or more LAMMPS commands to execute if no condition is met, each enclosed in quotes (optional arguments) :ul
 
 [Examples:]
 
-if $\{steps\} > 1000 then exit
+if "$\{steps\} > 1000" then exit
-if $x <= $y then "print X is smaller = $x" else "print Y is smaller = $y"
+if "$x <= $y" then "print X is smaller = $x" else "print Y is smaller = $y"
-if $\{eng\} > 0.0 then "timestep 0.005"
+if "($\{eng\} > 0.0) || ($n < 1000)" then &
-if $\{eng\} > $\{eng_previous\} then "jump file1" else "jump file2" :pre
+  "timestep 0.005" &
+elif $n<10000 &
+  "timestep 0.01" &
+else &
+  "timestep 0.02" &
+  "print 'Max step reached'"
+if "$\{eng\} > $\{eng_previous\}" then "jump file1" else "jump file2" :pre
 
 [Description:]
 
 This command provides an in-then-else capability within an input
-script.  Two values are numerically compared to each other and the
+script.  A Boolean expression is evaluted and the result is TRUE or
-result is TRUE or FALSE.  Note that as in the examples above, either
+FALSE.  Note that as in the examples above, the expression can contain
-of the two values can be variables, as defined by the
+variables, as defined by the "variable"_variable.html command, which
-"variable"_variable.html command, so that when the if command is
+will be evaluated as part of the expression.  Thus a user-defined
-executed, the variable(s) will be evaluated, which could calculate a
+formula that reflects the current state of the simulation can be used
-user-defined formula that reflects the current state of the
+to issue one or more new commands.
-simulation.
 
-If the result of the if test is TRUE, then one or more commands (t1,
+If the result of the Boolean expression is TRUE, then one or more
-t2, ..., tN) are executed.  If the result of the if test is FALSE and
+commands (t1, t2, ..., tN) are executed.  If it is FALSE, then Boolean
-no optional "else" argument is included, then the if command does
+expressions associated with successive elif keywords are evaluated
-nothing.  If the result of the if test is FALSE and the optional
+until one is found to be true, in which case its commands (f1, f2,
-"else" argument is included, then one or more commands (e1,
+..., fN) are executed.  If no Boolean expression is TRUE, then the
-e2, ..., eN) are executed.
+commands associated witht the else keyword, namely (e1, e2, ..., eN),
+are executed.  The elif and else keywords and their associated
+commands are optional.  If they aren't specified and the initial
+Boolean expression is FALSE, then no commands are executed.
 
-Each then or else command (t1, e1, etc) can be any valid LAMMPS input
+The syntax for Boolean expressions is described below.
-script command.  Each command should be enclosed in quotes, so it will
+
-be treated as a single argument, as in the examples above.
+Each command (t1, f1, e1, etc) can be any valid LAMMPS input script
+command.  If the command is more than one word, it must enclosed in
+quotes, so it will be treated as a single argument, as in the examples
+above.
+
+IMPORTANT NOTE: If a command itself requires a quoted argument (e.g. a
+"print"_print.html command), then double and single quotes can be used
+and nested in the usual manner, as in the examples above and below.
+See "this section"_Section_commands.html#3_2 of the manual for more
+details on using quotes in arguments.  Only one of level of nesting is
+allowed, but that should be sufficient for most use cases.
 
 Note that by using the line continuation character "&", the if command
-can be spread across many lines, though it is still a single
+can be spread across many lines, though it is still a single command:
-command:
 
-if $a < $b then &
+if "$a < $b" then &
-  "print Minimum value = $a" &
+  "print 'Minimum value = $a'" &
   "run 1000" &
 else &      
-  "print Minimum value = $b" &
+  'print "Minimum value = $b"' &
   "minimize 0.001 0.001 1000 10000" :pre
 
-Note that if any executed comand is a bogus LAMMPS command, such as
+Note that if one of the commands to execute is an invalid LAMMPS
-"exit" in the first example above, then executing the command will
+command, such as "exit" in the first example above, then executing the
-cause LAMMPS to halt.
+command will cause LAMMPS to halt.
 
 Note that by jumping to a label in the same input script, the if
 command can be used to break out of a loop.  See the "variable
-delete"_variable.html for info on how to delete the associated loop
+delete"_variable.html command for info on how to delete the associated
-variable, so that it can be re-used later in the input script.
+loop variable, so that it can be re-used later in the input script.
 
 Here is an example of a double loop which uses the if and
 "jump"_jump.html commands to break out of the inner loop when a
@@ -79,7 +96,7 @@ variable    a loop 5
   variable  b loop 5
   print	    "A,B = $a,$b"
   run       10000
-  if	    $b > 2 then "jump in.script break"
+  if	    '$b > 2' then "print 'Jumping to another script'" "jump in.script break"
   next	    b
   jump	    in.script loopb
 label	    break
@@ -87,6 +104,52 @@ variable    b delete :pre
 next	    a
 jump	    in.script loopa :pre
 
+:line
+
+The Boolean expressions for the if and elif keywords have a C-like
+syntax.  Note that each expression is a single argument within the if
+command.  Thus if you want to include spaces in the expression for
+clarity, you must enclose the entire expression in quotes.
+
+An expression is built out of numbers
+
+0.2, 100, 1.0e20, -15.4, etc :pre
+
+and Boolean operators:
+
+A == B
+A != B
+A < B
+A <= B
+A > B
+A >= B
+A && B
+A || B :pre
+
+Each A and B is a number or a variable reference like $a or $\{abc\},
+or another Boolean expression.
+
+If a variable is used it must produce a number when evaluated and
+substituted for in the expression.
+
+Expressions are evaluated left to right and have the usual C-style
+precedence: the 4 relational operators "<", "<=", ">", and ">=" have
+the highest precedence; those 4 relational operators before the
+remaining two relational operators "==" and "!="; those two relational
+operators before the logical AND operator "&&"; and the AND operator
+"&&" before the logical OR operator "||".  Parenthesis can be used to
+group one or more portions of an expression and/or enforce a different
+order of evaluation than what would occur with the default precedence.
+
+The 6 relational operators return either a 1.0 or 0.0 depending on
+whether the relationship between x and y is true or false.  The
+logical AND operator will return 1.0 if both its arguments are
+non-zero, else return a 0.0.  The logical OR operator will return 1.0
+if either of its arguments is non-zero, else return a 0.0.
+
+The overall Boolean expression produces a TRUE result if the result is
+non-zero.  If the result is zero, the expression result is FALSE.
+
 [Restrictions:] none
 
 [Related commands:]

doc/improper_class2.html

@@ -19,6 +19,7 @@
 </P>
 <PRE>improper_style class2
 improper_coeff 1 100.0 0
+improper_coeff * aa 0.0 0.0 0.0 115.06 130.01 115.06 
 </PRE>
 <P><B>Description:</B>
 </P>

doc/improper_class2.txt

@@ -15,7 +15,8 @@ improper_style class2 :pre
 [Examples:]
 
 improper_style class2
-improper_coeff 1 100.0 0 :pre
+improper_coeff 1 100.0 0
+improper_coeff * aa 0.0 0.0 0.0 115.06 130.01 115.06 :pre
 
 [Description:]
 

doc/print.html

@@ -13,23 +13,23 @@
 </H3>
 <P><B>Syntax:</B>
 </P>
-<PRE>print str1 str2 ... 
+<PRE>print str 
 </PRE>
-<UL><LI>str1,str2,...,strN = one or more text strings to print, which may contain variables 
+<UL><LI>str1 = text string to print, which may contain variables 
 </UL>
 <P><B>Examples:</B>
 </P>
-<PRE>print Done with equilibration
+<PRE>print "Done with equilibration"
-print The system volume is now $v
+print Vol=$v
 print "The system volume is now $v" 
 </PRE>
 <P><B>Description:</B>
 </P>
-<P>Print one or more text strings to the screen and logfile.  The
+<P>Print a text string to the screen and logfile.  One line of output is
-individual text strings are effectively concatenated into a single
+generated.  If the string has white space in it (spaces, tabs, etc),
-string, and one line of output is generated.  Thus the 2nd and 3rd
+then you must enclose it in single or double quotes so that it is
-examples above are equivalent.  If variables are included in any of
+treated as a single argument.  If variables are included in the
-the strings, they will be evaluated and their current values printed.
+string, they will be evaluated and their current values printed.
 </P>
 <P>If you want the print command to be executed multiple times (with
 changing variable values), there are 3 options.  First, consider using

doc/print.txt

@@ -10,23 +10,23 @@ print command :h3
 
 [Syntax:]
 
-print str1 str2 ... :pre
+print str :pre
 
-str1,str2,...,strN = one or more text strings to print, which may contain variables :ul
+str1 = text string to print, which may contain variables :ul
 
 [Examples:]
 
-print Done with equilibration
+print "Done with equilibration"
-print The system volume is now $v
+print Vol=$v
 print "The system volume is now $v" :pre
 
 [Description:]
 
-Print one or more text strings to the screen and logfile.  The
+Print a text string to the screen and logfile.  One line of output is
-individual text strings are effectively concatenated into a single
+generated.  If the string has white space in it (spaces, tabs, etc),
-string, and one line of output is generated.  Thus the 2nd and 3rd
+then you must enclose it in single or double quotes so that it is
-examples above are equivalent.  If variables are included in any of
+treated as a single argument.  If variables are included in the
-the strings, they will be evaluated and their current values printed.
+string, they will be evaluated and their current values printed.
 
 If you want the print command to be executed multiple times (with
 changing variable values), there are 3 options.  First, consider using

doc/run.html

@@ -41,7 +41,7 @@
 run 1000000 upto
 run 100 start 0 stop 1000
 run 1000 pre no post yes
-run 100000 start 0 stop 1000000 every 1000 "print Protein Rg = $r"
+run 100000 start 0 stop 1000000 every 1000 "print 'Protein Rg = $r'"
 run 100000 every 1000 NULL 
 </PRE>
 <P><B>Description:</B>
@@ -120,7 +120,10 @@ number of arguments.  Each of the trailing arguments is a single
 LAMMPS command, and each command should be enclosed in quotes, so that
 the entire command will be treated as a single argument.  This will
 also prevent any variables in the command from being evaluated until
-it is executed multiple times during the run.
+it is executed multiple times during the run.  Note that if a command
+itself needs one of its arguments quoted (e.g. the <A HREF = "print.html">print</A>
+command), then you can use a combination of single and double quotes,
+as in the example above.
 </P>
 <P>The <I>every</I> keyword is a means to avoid listing a long series of runs
 and interleaving commands in your input script.  For example, a
@@ -161,10 +164,10 @@ command can be spread across many lines, though it is still a single
 command:
 </P>
 <PRE>run 100000 every 1000 &
-  "print Minimum value = $a" &
+  "print 'Minimum value = $a'" &
-  "print Maximum value = $b" &
+  "print 'Maximum value = $b'" &
-  "print Temp = $c" &
+  "print 'Temp = $c'" &
-  "print Press = $d" 
+  "print 'Press = $d'" 
 </PRE>
 <P>If the <I>pre</I> and <I>post</I> options are set to "no" when used with the
 <I>every</I> keyword, then the 1st run will do the full setup and the last

doc/run.txt

@@ -34,7 +34,7 @@ run 10000
 run 1000000 upto
 run 100 start 0 stop 1000
 run 1000 pre no post yes
-run 100000 start 0 stop 1000000 every 1000 "print Protein Rg = $r"
+run 100000 start 0 stop 1000000 every 1000 "print 'Protein Rg = $r'"
 run 100000 every 1000 NULL :pre
 
 [Description:]
@@ -113,7 +113,10 @@ number of arguments.  Each of the trailing arguments is a single
 LAMMPS command, and each command should be enclosed in quotes, so that
 the entire command will be treated as a single argument.  This will
 also prevent any variables in the command from being evaluated until
-it is executed multiple times during the run.
+it is executed multiple times during the run.  Note that if a command
+itself needs one of its arguments quoted (e.g. the "print"_print.html
+command), then you can use a combination of single and double quotes,
+as in the example above.
 
 The {every} keyword is a means to avoid listing a long series of runs
 and interleaving commands in your input script.  For example, a
@@ -154,10 +157,10 @@ command can be spread across many lines, though it is still a single
 command:
 
 run 100000 every 1000 &
-  "print Minimum value = $a" &
+  "print 'Minimum value = $a'" &
-  "print Maximum value = $b" &
+  "print 'Maximum value = $b'" &
-  "print Temp = $c" &
+  "print 'Temp = $c'" &
-  "print Press = $d" :pre
+  "print 'Press = $d'" :pre
 
 If the {pre} and {post} options are set to "no" when used with the
 {every} keyword, then the 1st run will do the full setup and the last

doc/variable.html

@@ -332,9 +332,9 @@ relational operators "<", "<=", ">", and ">="; those 4 relational
 operators before the remaining two relational operators "==" and "!=";
 those two relational operators before the logical AND operator "&&";
 and the AND operator "&&" before the logical OR operator "||".
-Parenthesis can be used to group one or more portions of a formula and
+Parenthesis can be used to group one or more portions of a formula
-enforce a different order of evaluation than what would occur with the
+and/or enforce a different order of evaluation than what would occur
-default precedence.
+with the default precedence.
 </P>
 <P>The 6 relational operators return either a 1.0 or 0.0 depending on
 whether the relationship between x and y is true or false.  For

doc/variable.txt

@@ -331,17 +331,17 @@ relational operators "<", "<=", ">", and ">="; those 4 relational
 operators before the remaining two relational operators "==" and "!=";
 those two relational operators before the logical AND operator "&&";
 and the AND operator "&&" before the logical OR operator "||".
-Parenthesis can be used to group one or more portions of a formula and
+Parenthesis can be used to group one or more portions of a formula
-enforce a different order of evaluation than what would occur with the
+and/or enforce a different order of evaluation than what would occur
-default precedence.
+with the default precedence.
 
 The 6 relational operators return either a 1.0 or 0.0 depending on
 whether the relationship between x and y is true or false.  For
 example the expression x<10.0 in an atom-style variable formula will
 return 1.0 for all atoms whose x-coordinate is less than 10.0, and 0.0
-for the others.  The logical AND operator will return 1.0 of both its
+for the others.  The logical AND operator will return 1.0 if both its
 arguments are non-zero, else return a 0.0.  The logical OR operator
-will return 1.0 of either of its arguments is non-zero, else return a
+will return 1.0 if either of its arguments is non-zero, else return a
 0.0.  These relational and logical operators can be used as a masking
 or selection operation in a formula.  For example, the number of atoms
 whose properties satifsy one or more criteria could be calculated by