Correction in improper type assignment (only in direct order)

.hooks/pre-commit

@@ -1,14 +1,11 @@
 #!/bin/bash
 date=$(LANG=en_US date +"%d %b %Y")
 
-line="'27s/.*/call writeln( \"Playmol ($date)\" )/'"
+line="'27s/.*/call writeln( \"Playmol (Version: $date)\" )/'"
 eval "sed -i $line ./src/playmol.f90"
 git add ./src/playmol.f90
 
 line="'3s/.*/PROJECT_BRIEF = \"(Version: $date)\"/'"
 eval "sed -i $line ./docs/Doxyfile"
 git add ./docs/Doxyfile
 
-make -C ./docs &> /dev/null
-git add ./docs/html/*
-

docs/Doxyfile

@@ -1,6 +1,6 @@
 DOXYFILE_ENCODING      = UTF-8
 PROJECT_NAME           = "Playmol"
-PROJECT_BRIEF = "(Version: 23 Aug 2017)"
+PROJECT_BRIEF = "(Version: 09 Sep 2017)"
 PROJECT_LOGO           = playmol_logo.gif
 OUTPUT_DIRECTORY       = .
 OUTPUT_DIRECTORY       = 

docs/commands.md

@@ -394,31 +394,25 @@ comment tags (#). When a [LAMMPS data file] is generated using the command [writ
 of _attribute-list_ is assumed to be the parameters of the [LAMMPS bond style] associated with the
 bond type in question.
 
-Bond types are considered as __identical__ if they are defined by the same identifiers _type-1_ and
-_type-2_, in either order. Playmol accepts definitions of identical bond types, which are applied
-simultaneously to every defined bond that fits into such identifiers. This is useful, for instance,
-when the stretching potential model is a sum of instances of a given [LAMMPS bond style], each one
-with a distinct set of parameter values.
-
-Bond types are considered as __ambiguous__ if, despite not being identical, they can fit to the
-same defined bond due to the presence of wildcard characters. Playmol accepts definitions of
-ambiguous bond types (or ambiguous sets of identical bond types), provided that they do not have
-the same number of wildcard-containing identifiers. If a detected bond fits to multiple ambiguous
-bond types (or sets thereof), Playmol will only apply the one (type or set) with the least number
-of wildcard-containing identifiers.
+Playmol is able to resolve __ambiguities__ in definitions of bond types. When several ambiguous
+bond types fit to a defined [bond] or [extra] bond, Playmol will classify them according to the
+number _N_ of wildcard-containing identifiers (_N_ = 0, 1, or 2). Then, it will simultaneously
+assign to the bond all those types with the smallest found value of _N_. Multiple assignments are
+useful, for instance, when the stretching potential model is a sum of instances of a given
+[LAMMPS bond style], each one with a distinct set of parameter values.
 
 **Examples**:
 
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-bond_type	CH* CH* 95.877 1.54
+bond_type	CH* CH* harmonic 95.877 1.54
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 In the example above, the given attributes will be associated with every bond involving atoms whose
 types have identifiers starting with _CH_.
 
 **See also**:
 
-[atom_type], [bond], [write], [prefix/suffix]
+[atom_type], [bond], [write], [prefix/suffix], [extra]
 
 ----------------------------------------------------------------------------------------------------
 <a name="angle_type"></a>
@@ -462,23 +456,17 @@ the moment a new angle is detected, then Playmol will ignore such angle and prod
 message. Besides the automatic detection, an angle can also be explicitly created using the [extra]
 command.
 
-Angle types are considered as __identical__ if they are defined by the same sequence of identifiers
-_type-1_, _type-2_, and _type-3_, in either the direct or the reverse order. Playmol accepts
-definitions of identical angle types, which are applied simultaneously to every detected angle that
-fits into such sequence. This is useful, for instance, when the bending potential model is a sum of
-instances of a given [LAMMPS angle style], each one with a distinct set of parameter values.
-
-Angle types are considered as __ambiguous__ if, despite not being identical, they can fit to the
-same detected angle due to the presence of wildcard characters. Playmol accepts definitions of
-ambiguous angle types (or ambiguous sets of identical angle types), provided that they do not have
-the same number of wildcard-containing identifiers. If a detected angle fits to multiple ambiguous
-angle types (or sets thereof), Playmol will only apply the one (type or set) with the least number
-of wildcard-containing identifiers.
+Playmol is able to resolve __ambiguities__ in definitions of angle types. When several ambiguous
+angle types fit to a detected angle or defined [extra] angle, Playmol will classify them according
+to the number _N_ of wildcard-containing identifiers (_N_ = 0, 1, 2, or 3). Then, it will
+simultaneously assign to the angle all those types with the smallest found value of _N_. Multiple
+assignments are useful, for instance, when the bending potential model is a sum of instances of
+a given [LAMMPS angle style], each one with a distinct set of parameter values.
 
 **Examples**:
 
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-angle_type	CH3 CH2 CH2 62.0965 114
+angle_type	CH3 CH2 CH2 harmonic 62.0965 114
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 In the example above, the given attributes will be associated with every detected or specified angle
@@ -509,7 +497,7 @@ the types of the four atoms involved.
 
 The parameters _type-1_, _type-2_, _type-3_, and _type-4_ are identifiers of previously defined atom
 types. The order of such identifiers is relevant in the case of dihedral types, that is, if the same
-identifiers are disposed in the inverse order, they will denote a different dihedral type. Wildcard
+identifiers are disposed in the inverse order, they will denote different dihedral types. Wildcard
 characters (? and *) can be used to refer to multiple atom types. If a type-related [prefix/suffix]
 has been previously activated, then each actual atom type identifier will contain such prefix and/or
 suffix added to _type-x_.
@@ -532,23 +520,33 @@ does not exist at the moment a new dihedral is detected, then Playmol will ignor
 produce a warning message. Besides the automatic detection, a dihedral can also be explicitly
 created using the [extra] command.
 
-Dihedral types are considered as __identical__ if they are defined by the same sequence of
-identifiers _type-1_, _type-2_, _type-3_, and _type-4_. Playmol accepts definitions of identical
-dihedral types, which are applied simultaneously to every detected dihedral that fits into such
-sequence. This is useful, for instance, when the torsional potential model is a sum of instances
-of a given [LAMMPS dihedral style], each one with a distinct set of parameter values.
-
-Dihedral types are considered as __ambiguous__ if, despite not being identical, they can fit to the
-same detected dihedral due to the presence of wildcard characters. Playmol accepts definitions of
-ambiguous dihedral types (or ambiguous sets of identical dihedral types), provided that they do not
-have the same number of wildcard-containing identifiers. If a detected dihedral fits to multiple
-ambiguous dihedral types (or sets thereof), Playmol will only apply the one (type or set) with the
-least number of wildcard-containing identifiers.
+Playmol is able to resolve __ambiguities__ in definitions of dihedral types. When several ambiguous
+dihedral types fit to a detected dihedral or defined [extra] dihedral, Playmol will classify them
+according to the number _N_ of wildcard-containing identifiers (_N_ = 0, 1, 2, 3, or 4). Then, it
+will simultaneously assign to the dihedral all those types with the smallest found value of _N_.
+Multiple assignments are useful, for instance, when the torsional potential model is a sum of
+instances of a given [LAMMPS dihedral style], each one with a distinct set of parameter values.
+
+__NOTE__: Because the direction of identifiers is relevant in the definition of a dihedral type, a
+__direction conflict__ might occur when multiple dihedral types are simultaneously assigned to a
+detected or defined dihedral. Such a conflict takes place when all the following three conditions
+are met:
+
+1. Some types fit to the dihedral exclusively in the direct order;
+2. Some types fit exclusively in the reverse order;
+3. Some other types can fit in either the direct or reverse order.
+
+Combinations of conditions (1) and (3) are okay. Playmol automatically solves a combination of (2)
+and (3) by flipping the new dihedral before inclusion. It also solves automatically a combination
+of (1) and (2) by including a flipped dihedral in addition to the original one. However, Playmol
+will only throw a warning message when faced with a combination of all three conditions. In this
+case, the user can try to solve the conflict by manually flipping the dihedral types that cause
+condition (2), for instance.
 
 **Examples**:
 
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-dihedral_type	CH3 CH2 CH2 CH2 1.41095 -0.27100 3.14484 0
+dihedral_type	CH3 CH2 CH2 CH2 opls 1.41095 -0.27100 3.14484 0
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 In the example above, the given attributes will be associated with every detected or specified
@@ -579,7 +577,7 @@ the types of the four atoms involved.
 
 The parameters _type-1_, _type-2_, _type-3_, and _type-4_ are identifiers of previously defined atom
 types. The order of such identifiers is relevant in the case of improper types, that is, if the same
-identifiers are disposed in the inverse order, they will denote a different improper type. Wildcard
+identifiers are disposed in the inverse order, they will denote different improper types. Wildcard
 characters (? and *) can be used to refer to multiple atom types. If a type-related [prefix/suffix]
 has been previously activated, then each actual atom type identifier will contain such prefix and/or
 suffix added to _type-x_.
@@ -600,32 +598,29 @@ defined. This is so because there are distinct possible definitions of improper
 must be manually created by using the [improper] command, which requires the previous definition of
 a fitting improper type.
 
-Improper types are considered as __identical__ if they are defined by the same sequence of
-identifiers _type-1_, _type-2_, _type-3_, and _type-4_. Playmol accepts definitions of identical
-improper types, which are applied simultaneously to every defined improper that fits into such
-sequence. This is useful, for instance, when the improper potential model is a sum of instances
-of a given [LAMMPS improper style], each one with a distinct set of parameter values.
+Playmol is able to resolve __ambiguities__ in definitions of improper types. When several ambiguous
+improper types fit to a defined improper, Playmol will classify them according to the number _N_
+of wildcard-containing identifiers (_N_ = 0, 1, 2, 3, or 4). Then, it will simultaneously assign
+to the improper all those types with the smallest found value of _N_. Multiple assignments are
+useful, for instance, when the torsional potential model is a sum of instances of a given
+[LAMMPS improper style], each one with a distinct set of parameter values.
 
-Improper types are considered as __ambiguous__ if, despite not being identical, they can fit to the
-same defined improper due to the presence of wildcard characters. Playmol accepts definitions of
-ambiguous improper types (or ambiguous sets of identical improper types), provided that they do not
-have the same number of wildcard-containing identifiers. If a defined improper fits to multiple
-ambiguous improper types (or sets thereof), Playmol will only apply the one (type or set) with the
-least number of wildcard-containing identifiers.
+__NOTE__: Improper types are only assigned to an [improper] if they match the atom types of the
+improper atoms in the exact order they are defined.
 
 **Examples**:
 
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-improper_type	CH3 CH2 CH2 CH2 1.41095 -0.27100 3.14484 0
+improper_type	 c2 c2 na c3 	cvff 1.1 -1 2
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 In the example above, the given attributes will be associated with every detected or specified
-improper that involves four consecutive atoms whose type identifiers are _CH3_ _CH2_ _CH2_ _CH2_,
-in this specific order.
+improper that involves four atoms whose type identifiers are _c2_ _c2_ _na_ _c3_, in this specific
+order.
 
 **See also**:
 
-[atom_type], [improper], [write], [prefix/suffix]
+[atom_type], [improper], [write], [prefix/suffix], [extra]
 
 ----------------------------------------------------------------------------------------------------
 <a name="atom"></a>
@@ -936,7 +931,7 @@ or
 **Description**:
 
 This command creates an extra structure (bond, angle, dihedral) involving the specified atoms. In
-the case of an extra angle or extra dihedral, all specified atoms must  belong to the same molecule.
+the case of an extra angle or extra dihedral, all specified atoms must belong to the same molecule.
 
 The parameter _atom-x_ is the identifier of a previously created atom. A unique identifier must be
 provided, with no use of wildcard characters (* or ?). A corresponding structure type (that is,

examples/linear-hydrocarbons/linear-hydrocarbons.mol

@@ -2,7 +2,7 @@ define N     as 5
 define FF    as nerd
 define seed  as 3467
 define nmols as 500
-define rho   as 0.6 # g/cm³
+define rho   as 0.3 # g/cm³
 define temp  as 180 # K
 
 mass CH4 16.04242 # Da

examples/linear-hydrocarbons/nerd.mol

@@ -21,6 +21,8 @@ endif
 atom_type       CH4     lj/cut {148.0*$kB} 3.730 $cutoff # TraPPE parameters
 
 bond_type     CH? CH?         harmonic {96500*$kB/2} $L
-angle_type    CH? CH? CH?     harmonic {62500*$kB/2} $theta
+#angle_type    CH? CH? CH?     harmonic {62500*$kB/2} $theta
+dihedral_type CH3 CH2 CH2 CH? opls {355.04*2*$kB} {-68.19*2*$kB} {701.32*2*$kB} 0.0
+dihedral_type CH? CH2 CH2 CH3 opls {355.04*2*$kB} {-68.19*2*$kB} {701.32*2*$kB} 0.0
 dihedral_type CH? CH2 CH2 CH? opls {355.04*2*$kB} {-68.19*2*$kB} {701.32*2*$kB} 0.0
 

src/mGlobal.f90

@@ -23,7 +23,11 @@ module mGlobal
 
 integer,      parameter :: rb = 8      !< Default number of bytes for real numbers
 integer,      parameter :: sl = 256    !< Default character string length
-character(3), parameter :: csl = "256" !< String with default character string length
+character(*), parameter :: csl = "256" !< String with default character string length
+
+character(*), parameter :: yellow = achar(27)//"[1;93m", &
+                           red = achar(27)//"[1;91m",    &
+                           decolor = achar(27)//"[0m"
 
 integer :: stdout = 6                  !< Standard output unit
 integer :: logunit = 0                 !< Output unit for logging
@@ -123,7 +127,7 @@ subroutine warning( msg, msg1, msg2, msg3, msg4, msg5, msg6, msg7, msg8, msg9 )
     if (present(msg7)) wmsg = trim(wmsg)//" "//trim(msg7)
     if (present(msg8)) wmsg = trim(wmsg)//" "//trim(msg8)
     if (present(msg9)) wmsg = trim(wmsg)//" "//trim(msg9)
-    write(stdout,'(A)') achar(27)//"[1;93mWARNING: "//trim(wmsg)//achar(27)//"[0m"
+    write(stdout,'(A)') yellow//"WARNING: "//trim(wmsg)//decolor
     if (logunit /= 0) write(logunit,'(A)') "WARNING: "//trim(wmsg)
     last_warning % msg = wmsg
   end subroutine warning
@@ -135,8 +139,8 @@ subroutine reprint_warnings
     ptr => first_warning
     if (associated(ptr)) then
       call writeln()
-      write(stdout,'(A)') achar(27)//"[1;93m*** SUMMARY OF WARNINGS ***"//achar(27)//"[0m"
-      if (logunit /= 0) write(logunit,'("********** SUMMARY OF WARNINGS **********")')
+      write(stdout,'(A)') yellow//"******** SUMMARY OF WARNINGS ********"//decolor
+      if (logunit /= 0) write(logunit,'("******** SUMMARY OF WARNINGS ********")')
     end if
     do while (associated(ptr))
       call writeln( ">", ptr % msg )
@@ -160,7 +164,7 @@ subroutine error( msg, msg1, msg2, msg3, msg4, msg5, msg6, msg7, msg8, msg9 )
     if (present(msg7)) emsg = trim(emsg)//" "//trim(msg7)
     if (present(msg8)) emsg = trim(emsg)//" "//trim(msg8)
     if (present(msg9)) emsg = trim(emsg)//" "//trim(msg9)
-    write(stdout,'(A)') achar(27)//"[1;91mERROR"//achar(27)//"[0m: "//trim(emsg)
+    write(stdout,'(A)') red//"ERROR"//decolor//": "//trim(emsg)
     if (logunit /= 0) write(logunit,'(A)') "ERROR: "//trim(emsg)
     stop
   end subroutine error

src/mPlaymol.f90

@@ -62,8 +62,8 @@ module mPlaymol
   type(StrucList) :: bond_list           = StrucList( "bond", 2 )
   type(StrucList) :: link_list           = StrucList( "virtual link", 2 )
   type(StrucList) :: angle_list          = StrucList( "angle", 3 )
-  type(StrucList) :: dihedral_list       = StrucList( "dihedral", 4, reversible = .false. )
-  type(StrucList) :: improper_list       = StrucList( "improper", 4, reversible = .false. )
+  type(StrucList) :: dihedral_list       = StrucList( "dihedral", 4, .false., .true. )
+  type(StrucList) :: improper_list       = StrucList( "improper", 4, .false. )
   type(StrucList) :: body_list           = StrucList( "rigid body" )
   type(StrucList) :: atom_bodies         = StrucList( "atom body" )
   type(StrucList) :: mixing_rule_list    = StrucList( "mixing rule", 2 )
@@ -982,7 +982,7 @@ subroutine tPlaymol_analyze_struct( me, structure, permol, total, type_map, list
         if (ptr % usable) then
           do i = 1, list%count
             associate (s => structure(i))
-              if (list%reversible) then
+              if (list%bothways) then
                 match = ptr % match_id( s%atom_types )
               else
                 match = all(match_str( ptr%id, s%atom_types ))
@@ -1008,7 +1008,7 @@ subroutine tPlaymol_analyze_struct( me, structure, permol, total, type_map, list
             if (any(s%wildcards /= s%wildcards(1))) then
               valid = s%wildcards == minval(s%wildcards)
               call warning( "ambiguity resolved for", list%name, join(s%atoms), &
-                            "( types", join(s%atom_types), ")" )
+                            "( atom types", join(s%atom_types), ")" )
               aux = pack(s%itype,valid)
               ptr => typelist % first
               do itype = 1, typelist % count