Merge branch 'master' into collected-small-fixes

*Bond/react: A deleted atom cannot remain bonded to an atom that is not deleted*

   Self-explanatory.

*Bond/react: First neighbors of chiral atoms must be of mutually different types*

   Self-explanatory.

*Bond/react: Chiral atoms must have exactly four first neighbors*

   Self-explanatory.

*Bond/react: Molecule template 'Coords' section required for chiralIDs keyword*

   The coordinates of atoms in the pre-reacted template are used to determine

   chirality.

*Bond/react special bond generation overflow*

   The number of special bonds per-atom created by a reaction exceeds the

   system setting. See the read\_data or create\_box command for how to

The map file is a text document with the following format:

A map file has a header and a body. The header of map file the

contains one mandatory keyword and four optional keywords. The

contains one mandatory keyword and five optional keywords. The

mandatory keyword is 'equivalences':

   N *edgeIDs* = # of edge atoms N in the pre-reacted molecule template

   N *deleteIDs* = # of atoms N that are specified for deletion

   N *chiralIDs* = # of specified chiral centers N

   N *customIDs* = # of atoms N that are specified for a custom update

   N *constraints* = # of specified reaction constraints N

The body of the map file contains two mandatory sections and four

The body of the map file contains two mandatory sections and five

optional sections. The first mandatory section begins with the keyword

'BondingIDs' and lists the atom IDs of the bonding atom pair in the

pre-reacted molecule template. The second mandatory section begins

'EdgeIDs' and lists the atom IDs of edge atoms in the pre-reacted

molecule template. The second optional section begins with the keyword

'DeleteIDs' and lists the atom IDs of pre-reaction template atoms to

delete. The third optional section begins with the keyword 'Custom

delete. The third optional section begins with the keyword 'ChiralIDs'

lists the atom IDs of chiral atoms whose handedness should be

enforced. The fourth optional section begins with the keyword 'Custom

Edges' and allows for forcing the update of a specific atom's atomic

charge. The first column is the ID of an atom near the edge of the

pre-reacted molecule template, and the value of the second column is

either 'none' or 'charges.' Further details are provided in the

discussion of the 'update\_edges' keyword. The fourth optional section

discussion of the 'update\_edges' keyword. The fifth optional section

begins with the keyword 'Constraints' and lists additional criteria

that must be satisfied in order for the reaction to occur. Currently,

there are three types of constraints available, as discussed below.

----------

The handedness of atoms that are chiral centers can be enforced by

listing their IDs in the ChiralIDs section. A chiral atom must be

bonded to four atoms with mutually different atom types. This feature

uses the coordinates and types of the involved atoms in the

pre-reaction template to determine handedness. Three atoms bonded to

the chiral center are arbitrarily chosen, to define an oriented plane,

and the relative position of the fourth bonded atom determines the

chiral center's handedness.

Any number of additional constraints may be specified in the

Constraints section of the map file. The constraint of type 'distance'

has syntax as follows:

   Cmin(I,J,K) = Cmin screening parameter when I-J pair is screened

                 by K (I<=J); default = 2.0

   lattce(I,J) = lattice structure of I-J reference structure:

                   dia = diamond (interlaced fcc for alloy)

                   fcc = face centered cubic

                   bcc = body centered cubic

                   hcp = hexagonal close-packed

                   dim = dimer

                   dia = diamond (interlaced fcc for alloy)

                   dia3= diamond structure with primary 1NN and secondary 3NN interation

                   b1  = rock salt (NaCl structure)

                   hcp = hexagonal close-packed

                   c11 = MoSi2 structure

                   l12 = Cu3Au structure (lower case L, followed by 12)

                   b2  = CsCl structure (interpenetrating simple cubic)

                   ch4 = methane-like structure, only for binary system

                   lin = linear structure (180 degree angle)

                   zig = zigzag structure with a uniform angle

                   tri = H2O-like structure that has an angle

   nn2(I,J)    = turn on second-nearest neighbor MEAM formulation for

                 I-J pair (see for example :ref:`(Lee) <Lee>`).

                   0 = second-nearest neighbor formulation off

   zbl(I,J)    = blend the MEAM I-J pair potential with the ZBL potential for small

                 atom separations :ref:`(ZBL) <ZBL>`

                   default = 1

   theta(I,J)  = angle between three atoms in line, zigzag, and trimer reference structures in degrees

                   default = 180

   gsmooth_factor  = factor determining the length of the G-function smoothing

                     region; only significant for ibar=0 or ibar=4.

                         99.0 = short smoothing region, sharp step

lat      = lattice structure of reference configuration

z        = number of nearest neighbors in the reference structure

             This field is only read for compatibility, the correct

             value is inferred from the lattice structure

ielement = atomic number

atwt     = atomic weight

alat     = lattice constant of reference structure

gpu_SYSINC =

gpu_SYSLIB =  -lcudart -lcuda

gpu_SYSPATH = -L$(CUDA_HOME)/lib64

gpu_SYSPATH = -L$(CUDA_HOME)/lib64 -L$(CUDA_HOME)/lib64/stubs