where Ei is the improper term and Eaa is an angle-angle term. The chi -used in Ei is an average over 3 possible chi orientations. The -subscripts on the various theta's refer to different combinations of -atoms i,j,k,l used to form the angle; theta1, theta2, theta3 are the -equilibrium positions of those angles. +
where Ei is the improper term and Eaa is an angle-angle term. The 3 X +terms used in Ei are an average over the 3 out-of-plane angles. +
+The 4 atoms in an improper quadruplet (listed in the data file read by +the read_data command) are ordered I,J,K,L. X_IJKL +refers to the angle between the plane of I,J,K and the plane of J,K,L, +and the bond JK lies in both planes. Similarly for X_KJLI and X_LJIK. +Note that atom J appears in the common bonds (JI, JK, JL) of all 3 X +terms. Thus J (the 2nd atom in the quadruplet) is the atom of +symmetry in the 3 X angles. +
+The subscripts on the various theta's refer to different combinations +of 3 atoms (I,J,K,L) used to form a particular angle. E.g. Theta_IJL +is the angle formed by atoms I,J,L with J in the middle. Theta1, +theta2, theta3 are the equilibrium positions of those angles. Again, +atom J (the 2nd atom in the quadruplet) is the atom of symmetry in the +theta angles, since it is always the center atom. +
+Note that defining 4 atoms to interact in this way, does not mean that +bonds necessarily exist between I-J, J-K, or K-L, as they would in a +linear dihedral.
See (Sun) for a description of the COMPASS class2 force field.
diff -Naur lammps-30Jun07/doc/improper_class2.txt lammps-1Jul07/doc/improper_class2.txt --- lammps-30Jun07/doc/improper_class2.txt 2007-06-25 18:03:39.000000000 -0600 +++ lammps-1Jul07/doc/improper_class2.txt 2007-06-28 09:25:31.000000000 -0600 @@ -23,11 +23,27 @@ :c,image(Eqs/improper_class2.jpg) -where Ei is the improper term and Eaa is an angle-angle term. The chi -used in Ei is an average over 3 possible chi orientations. The -subscripts on the various theta's refer to different combinations of -atoms i,j,k,l used to form the angle; theta1, theta2, theta3 are the -equilibrium positions of those angles. +where Ei is the improper term and Eaa is an angle-angle term. The 3 X +terms used in Ei are an average over the 3 out-of-plane angles. + +The 4 atoms in an improper quadruplet (listed in the data file read by +the "read_data"_read_data.html command) are ordered I,J,K,L. X_IJKL +refers to the angle between the plane of I,J,K and the plane of J,K,L, +and the bond JK lies in both planes. Similarly for X_KJLI and X_LJIK. +Note that atom J appears in the common bonds (JI, JK, JL) of all 3 X +terms. Thus J (the 2nd atom in the quadruplet) is the atom of +symmetry in the 3 X angles. + +The subscripts on the various theta's refer to different combinations +of 3 atoms (I,J,K,L) used to form a particular angle. E.g. Theta_IJL +is the angle formed by atoms I,J,L with J in the middle. Theta1, +theta2, theta3 are the equilibrium positions of those angles. Again, +atom J (the 2nd atom in the quadruplet) is the atom of symmetry in the +theta angles, since it is always the center atom. + +Note that defining 4 atoms to interact in this way, does not mean that +bonds necessarily exist between I-J, J-K, or K-L, as they would in a +linear dihedral. See "(Sun)"_#Sun for a description of the COMPASS class2 force field. diff -Naur lammps-30Jun07/doc/improper_cvff.html lammps-1Jul07/doc/improper_cvff.html --- lammps-30Jun07/doc/improper_cvff.html 2007-06-25 08:36:36.000000000 -0600 +++ lammps-1Jul07/doc/improper_cvff.html 2007-06-28 09:07:55.000000000 -0600 @@ -28,10 +28,25 @@where phi is the Wilson out-of-plane angle.
-The following coefficients must be defined for each improper type via the -improper_coeff command as in the example above, or in -the data file or restart files read by the read_data -or read_restart commands: +
If the 4 atoms in an improper quadruplet (listed in the data file read +by the read_data command) are ordered I,J,K,L then +the Wilson angle is between the plane of I,J,K and the plane of J,K,L. +This is essentially a dihedral angle, which is why the formula for +this improper style is the same as for dihedral_style +harmonic. Alternatively, you can think of +atoms J,K,L as being in a plane, and atom I above the plane, and the +Wilson angle as a measure of how far out-of-plane I is with respect to +the other 3 atoms. +
+Note that defining 4 atoms to interact in this way, does not mean that +bonds necessarily exist between I-J, J-K, or K-L, as they would in a +linear dihedral. +
+The following coefficients must be defined for each improper type via +the improper_coeff command as in the example +above, or in the data file or restart files read by the +read_data or read_restart +commands:
where X is the improper angle, X0 is its equilibrium value, and K is a prefactor. Note that the usual 1/2 factor is included in K.
+If the 4 atoms in an improper quadruplet (listed in the data file read +by the read_data command) are ordered I,J,K,L then X +is the angle between the plane of I,J,K and the plane of J,K,L. +Alternatively, you can think of atoms J,K,L as being in a plane, and +atom I above the plane, and X as a measure of how far out-of-plane I +is with respect to the other 3 atoms. +
+Note that defining 4 atoms to interact in this way, does not mean that +bonds necessarily exist between I-J, J-K, or K-L, as they would in a +linear dihedral. +
The following coefficients must be defined for each improper type via the improper_coeff command as in the example above, or in the data file or restart files read by the read_data diff -Naur lammps-30Jun07/doc/improper_harmonic.txt lammps-1Jul07/doc/improper_harmonic.txt --- lammps-30Jun07/doc/improper_harmonic.txt 2007-06-25 18:03:39.000000000 -0600 +++ lammps-1Jul07/doc/improper_harmonic.txt 2007-06-28 09:07:55.000000000 -0600 @@ -26,6 +26,17 @@ where X is the improper angle, X0 is its equilibrium value, and K is a prefactor. Note that the usual 1/2 factor is included in K. +If the 4 atoms in an improper quadruplet (listed in the data file read +by the "read_data"_read_data.html command) are ordered I,J,K,L then X +is the angle between the plane of I,J,K and the plane of J,K,L. +Alternatively, you can think of atoms J,K,L as being in a plane, and +atom I above the plane, and X as a measure of how far out-of-plane I +is with respect to the other 3 atoms. + +Note that defining 4 atoms to interact in this way, does not mean that +bonds necessarily exist between I-J, J-K, or K-L, as they would in a +linear dihedral. + The following coefficients must be defined for each improper type via the "improper_coeff"_improper_coeff.html command as in the example above, or in the data file or restart files read by the "read_data"_read_data.html diff -Naur lammps-30Jun07/doc/improper_style.html lammps-1Jul07/doc/improper_style.html --- lammps-30Jun07/doc/improper_style.html 2007-06-25 08:36:36.000000000 -0600 +++ lammps-1Jul07/doc/improper_style.html 2007-06-28 09:07:55.000000000 -0600 @@ -29,7 +29,10 @@ between quadruplets of atoms, which remain in force for the duration of the simulation. The list of improper quadruplets is read in by a read_data or read_restart command -from a data or restart file. +from a data or restart file. Note that the ordering of the 4 atoms in +an improper quadruplet determines the the definition of the improper +angle used in the formula for each style. See the doc pages of +individual styles for details.
Hybrid models where impropers are computed using different improper potentials can be setup using the hybrid improper style. @@ -50,7 +53,7 @@
IMPORTANT NOTE: When both an improper and pair style is defined, the special_bonds command often needs to be used to turn off (or weight) the pairwise interaction that would otherwise -exist between 4 bonded atoms. +exist between a group of 4 bonded atoms.