Document that atan2 can be used in custom expressions

docs-source/usersguide/theory.rst

@@ -1209,7 +1209,7 @@ The following operators are supported: + (add), - (subtract), * (multiply), /
 (divide), and ^ (power).  Parentheses “(“ and “)” may be used for grouping.
 
 The following standard functions are supported: sqrt, exp, log, sin, cos, sec,
-csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs,
+csc, tan, cot, asin, acos, atan, atan2, sinh, cosh, tanh, erf, erfc, min, max, abs,
 floor, ceil, step, delta, select. step(x) = 0 if x < 0, 1 otherwise.
 delta(x) = 1 if x is 0, 0 otherwise.  select(x,y,z) = z if x = 0, y otherwise.
 Some custom forces allow additional functions to be defined from tabulated values.

openmmapi/include/openmm/CustomAngleForce.h

@@ -69,7 +69,7 @@ namespace OpenMM {
  * computed.  You can then query its value in a Context by calling getState() on it.
  *
  * Expressions may involve the operators + (add), - (subtract), * (multiply), / (divide), and ^ (power), and the following
- * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta, select.  All trigonometric functions
+ * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, atan2, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta, select.  All trigonometric functions
  * are defined in radians, and log is the natural logarithm.  step(x) = 0 if x is less than 0, 1 otherwise.  delta(x) = 1 if x is 0, 0 otherwise.
  * select(x,y,z) = z if x = 0, y otherwise.
  */

openmmapi/include/openmm/CustomBondForce.h

@@ -69,7 +69,7 @@ namespace OpenMM {
  * computed.  You can then query its value in a Context by calling getState() on it.
  *
  * Expressions may involve the operators + (add), - (subtract), * (multiply), / (divide), and ^ (power), and the following
- * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta, select.  All trigonometric functions
+ * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, atan2, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta, select.  All trigonometric functions
  * are defined in radians, and log is the natural logarithm.  step(x) = 0 if x is less than 0, 1 otherwise.  delta(x) = 1 if x is 0, 0 otherwise.
  * select(x,y,z) = z if x = 0, y otherwise.
  */

openmmapi/include/openmm/CustomCVForce.h

@@ -63,7 +63,7 @@ namespace OpenMM {
  * computed.  You can then query its value in a Context by calling getState() on it.
  *
  * Expressions may involve the operators + (add), - (subtract), * (multiply), / (divide), and ^ (power), and the following
- * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta, select.  All trigonometric functions
+ * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, atan2, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta, select.  All trigonometric functions
  * are defined in radians, and log is the natural logarithm.  step(x) = 0 if x is less than 0, 1 otherwise.  delta(x) = 1 if x is 0, 0 otherwise.
  * select(x,y,z) = z if x = 0, y otherwise.
  *

openmmapi/include/openmm/CustomCentroidBondForce.h

@@ -104,7 +104,7 @@ namespace OpenMM {
  * computed.  You can then query its value in a Context by calling getState() on it.
  *
  * Expressions may involve the operators + (add), - (subtract), * (multiply), / (divide), and ^ (power), and the following
- * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta, select.  All trigonometric functions
+ * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, atan2, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta, select.  All trigonometric functions
  * are defined in radians, and log is the natural logarithm.  step(x) = 0 if x is less than 0, 1 otherwise.  delta(x) = 1 if x is 0, 0 otherwise.
  * select(x,y,z) = z if x = 0, y otherwise.
  *

openmmapi/include/openmm/CustomCompoundBondForce.h

@@ -93,7 +93,7 @@ namespace OpenMM {
  * computed.  You can then query its value in a Context by calling getState() on it.
  *
  * Expressions may involve the operators + (add), - (subtract), * (multiply), / (divide), and ^ (power), and the following
- * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta, select.  All trigonometric functions
+ * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, atan2, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta, select.  All trigonometric functions
  * are defined in radians, and log is the natural logarithm.  step(x) = 0 if x is less than 0, 1 otherwise.  delta(x) = 1 if x is 0, 0 otherwise.
  * select(x,y,z) = z if x = 0, y otherwise.
  *

openmmapi/include/openmm/CustomExternalForce.h

@@ -76,7 +76,7 @@ namespace OpenMM {
  * <tt>CustomExternalForce* force = new CustomExternalForce("k*periodicdistance(x, y, z, x0, y0, z0)^2");</tt>
  *
  * Expressions may involve the operators + (add), - (subtract), * (multiply), / (divide), and ^ (power), and the following
- * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta, select.  All trigonometric functions
+ * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, atan2, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta, select.  All trigonometric functions
  * are defined in radians, and log is the natural logarithm.  step(x) = 0 if x is less than 0, 1 otherwise.  delta(x) = 1 if x is 0, 0 otherwise.
  * select(x,y,z) = z if x = 0, y otherwise.
  */

openmmapi/include/openmm/CustomGBForce.h

@@ -133,7 +133,7 @@ namespace OpenMM {
  * computed.  You can then query its value in a Context by calling getState() on it.
  *
  * Expressions may involve the operators + (add), - (subtract), * (multiply), / (divide), and ^ (power), and the following
- * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta, select.  All trigonometric functions
+ * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, atan2, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta, select.  All trigonometric functions
  * are defined in radians, and log is the natural logarithm.  step(x) = 0 if x is less than 0, 1 otherwise.  delta(x) = 1 if x is 0, 0 otherwise.
  * select(x,y,z) = z if x = 0, y otherwise.  In expressions for particle pair calculations, the names of per-particle parameters and computed values
  * have the suffix "1" or "2" appended to them to indicate the values for the two interacting particles.  As seen in the above example,

openmmapi/include/openmm/CustomHbondForce.h

@@ -89,7 +89,7 @@ namespace OpenMM {
  * </pre></tt>
  *
  * Expressions may involve the operators + (add), - (subtract), * (multiply), / (divide), and ^ (power), and the following
- * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta, select.  All trigonometric functions
+ * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, atan2, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta, select.  All trigonometric functions
  * are defined in radians, and log is the natural logarithm.  step(x) = 0 if x is less than 0, 1 otherwise.  delta(x) = 1 if x is 0, 0 otherwise.
  * select(x,y,z) = z if x = 0, y otherwise.
  *

openmmapi/include/openmm/CustomIntegrator.h

@@ -254,7 +254,7 @@ namespace OpenMM {
  * the force from a single force group, or a random number.
  *
  * Expressions may involve the operators + (add), - (subtract), * (multiply), / (divide), and ^ (power), and the following
- * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta, select.  All trigonometric functions
+ * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, atan2, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta, select.  All trigonometric functions
  * are defined in radians, and log is the natural logarithm.  step(x) = 0 if x is less than 0, 1 otherwise.  delta(x) = 1 if x is 0, 0 otherwise.
  * select(x,y,z) = z if x = 0, y otherwise.  An expression may also involve intermediate quantities that are defined following the main expression, using ";" as a separator.
  * 

openmmapi/include/openmm/CustomManyParticleForce.h

@@ -149,7 +149,7 @@ namespace OpenMM {
  * still only be evaluated once for each triplet, so it must still be symmetric with respect to p2 and p3.
  *
  * Expressions may involve the operators + (add), - (subtract), * (multiply), / (divide), and ^ (power), and the following
- * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta, select.  All trigonometric functions
+ * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, atan2, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta, select.  All trigonometric functions
  * are defined in radians, and log is the natural logarithm.  step(x) = 0 if x is less than 0, 1 otherwise.  delta(x) = 1 if x is 0, 0 otherwise.
  * select(x,y,z) = z if x = 0, y otherwise.  The names of per-particle parameters have the suffix "1", "2", etc. appended to them to indicate the values for
  * the multiple interacting particles. For example, if you define a per-particle parameter called "charge", then the variable "charge2" is the charge of particle p2.

openmmapi/include/openmm/CustomNonbondedForce.h

@@ -124,7 +124,7 @@ namespace OpenMM {
  * computed.  You can then query its value in a Context by calling getState() on it.
  *
  * Expressions may involve the operators + (add), - (subtract), * (multiply), / (divide), and ^ (power), and the following
- * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta, select.  All trigonometric functions
+ * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, atan2, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta, select.  All trigonometric functions
  * are defined in radians, and log is the natural logarithm.  step(x) = 0 if x is less than 0, 1 otherwise.  delta(x) = 1 if x is 0, 0 otherwise.
  * select(x,y,z) = z if x = 0, y otherwise.  The names of per-particle parameters have the suffix "1" or "2" appended to them to indicate the values for the
  * two interacting particles.  As seen in the above example, the expression may also involve intermediate quantities that are defined following the main expression,

openmmapi/include/openmm/CustomTorsionForce.h

@@ -74,7 +74,7 @@ namespace OpenMM {
  * computed.  You can then query its value in a Context by calling getState() on it.
  *
  * Expressions may involve the operators + (add), - (subtract), * (multiply), / (divide), and ^ (power), and the following
- * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta, select.  All trigonometric functions
+ * functions: sqrt, exp, log, sin, cos, sec, csc, tan, cot, asin, acos, atan, atan2, sinh, cosh, tanh, erf, erfc, min, max, abs, floor, ceil, step, delta, select.  All trigonometric functions
  * are defined in radians, and log is the natural logarithm.  step(x) = 0 if x is less than 0, 1 otherwise.  delta(x) = 1 if x is 0, 0 otherwise.
  * select(x,y,z) = z if x = 0, y otherwise.
  */