Input, Output, and Notation

Notation Used in this Manual

The input for critic2 is free-format and case-insensitive. Lines preceded by # are treated as comments. The input syntax is keyword-driven: the first word in any (non-blank) input line determines the task to be carried out.

In this manual, keywords are written in CAPS. Input variables are denoted using a suffix to indicate their type: a real number (.r), an integer (.i) or a string (.s). Almost anywhere that a number is expected, it is possible to use an arithmetic expression. If an arithmetic expression is required (and not merely optional), then it should be given in either double or single quotes are used (for instance, “$1+$2”). When several alternative keywords are possible, the or symbol (|) is used. Square brackets ([]) denote optional keywords and curly braces ({}) are used for grouping.

Some of the sections in the rest of this manual contain a subsection describing additional options. These provide some independent keywords that control the behavior of critic2 and are meant to be used either before or after the keywords in the section in which they appear. For instance, NOSYMM can be used before CRYSTAL to deactivate the automatic calculation of the crystal symmetry:

NOSYMM
CRYSTAL benzene.cif

Hence, NOSYMM appears in this manual as an additional option to CRYSTAL.

The critic2 output is mostly self-explanatory, although there are a number of key concepts that need to be understood. In the case of crystals, the crystal motif is represented in critic2 by two lists of atoms. The non-equivalent atom list contains the atoms in the asymmetric unit, that is, the minimal list of atoms that generate all the atomic positions in the crystal by symmetry. The cell atom list, equivalently called the complete atom list, contains all atoms in the unit cell. The non-equivalent atom list reproduces the complete atom list by applying all symmetry operations (other than pure lattice translations) known to critic2.

The atoms in each of those two lists are numbered. The integer identifier for an atom in the non-equivalent atom list is symbolized in this manual as nat.i. The integer identifier for an atom in the complete atom list is at.i. The syntax.txt file contains a summary of all available keywords and follows the same notation. The distinction between atoms from the complete list and from the non-equivalent list is irrelevant in the case of molecules, because symmetry is not used (hence both lists are the same).

In exact parallel to the atomic lists, critic2 also maintains a list of non-equivalent critical points (CP) and a complete (or cell) list of critical points found for a given scalar field. The CPs in the non-equivalent list reproduce all the CPs in the complete list by symmetry, and both lists are the exact same in molecules because symmetry is not used. The keyword definitions use ncp.i for the integer indices in the non-equivalent CP list, and cp.i for the integer identifiers in the complete CP list.

In critic2 atoms are considered critical points always (this may change at some point). Therefore, the non-equivalent (complete) atom list is a subset of the non-equivalent (complete) CP list. Critic2 makes sure that the integer identifier for all atoms in the atom lists are the same as in the corresponding CP lists. For instance, if an atom has index nat.i = 2 and at.i = 5, then necessarily ncp.i = 2 and cp.i = 5, regardless of how many additional critical points have been found for this system.

In most critic2 keywords, atoms can be selected by their atomic symbol (at.s in the syntax definitions), in which case the keyword applies to all atoms with the same atomic number unless otherwise stated. Atoms can also be selected by an integer identifier from the non-equivalent atom list (nat.i in the definitions) in those cases in which symmetry makes it irrelevant which of the symmetry-equivalent atoms in the cell are used. For example, the non-equivalent atom identifier can be used to instruct critic2 to calculate the charge of a certain atom, since all symmetry-equivalent atoms have the same charge.

Some additional notation and terms that are used in the manual:

  • By scalar field or field we mean a numerical or analytical representation of a function that associates a scalar value to every point in space. Often, this function is the electron density, for which special techniques are provided (for instance, core augmentation in the case of valence densities, see ZPSP.. However, critic2 can deal with any scalar field, and examples other than the density are the ELF, the Laplacian, etc.

  • The promolecular density is the scalar field built by using the sum of the in-vacuo atomic densities. This object comes up in a number of contexts. For instance, NCIPLOT and HIRSHFELD use it. The promolecular density does not require any input from the user other than the crystal or molecular structure, and is always available under field identifier $0 (or $rho0).

  • We denote by <root> the root of the input file, i.e., the name of the file minus its extension. If no input file is known (for instance, because critic2 is being run interactively), then the root defaults to “stdin”. The default root can be changed with the keyword ROOT.

  • The critical points of a field can be classified by their rank (r) and signature (s). The rank is the number of non-zero eigenvalues of the Hessian. In the vast majority of cases, r is

    1. The signature is the number of positive eigenvalues minus the number of negative eigenvalues. s = -3 is a maximum, s = -1 is a first-order saddle point, s = +1 is a second-order saddle point and s = 3 is a minimum. These four types of critical points receive special names: nuclear CP, bond CP, ring CP, and cage CP, respectively. The abbreviations ncp, bcp, rcp, and ccp are also used throughout the manual and in the output. Note that a maximum is always a “nuclear critical point” even though it may not be associated to any nucleus.

Input and Output Units

The default input and output units in critic2 are bohr for crystals (if the structure is loaded using the CRYSTAL keyword) and angstrom for molecules (if the MOLECULE keyword is used). In the particular case of molecules, the origin is also placed at the same point as in the structure provided by the user.

This default behavior can be changed with the UNITS keyword:

UNITS {BOHR|AU|A.U.|ANG|ANGSTROM}

This command changes the units of all distances in input and output to either bohr or angstrom.

Simple Input and Output for a Crystal

As an example, let us consider an input for the conventional cell of the fluorite (CaF2) crystal. Fluorite is cubic with space group Fm-3m. Ca forms a face-centerd cubic lattice and F occupies all the tetrahedral voids. The input is:

CRYSTAL
 SPG F m -3 m
 CELL 5.463 5.463 5.463 90 90 90 ang
 Ca 0   0   0
 F  1/4 1/4 1/4
ENDCRYSTAL

When this structure is read, the non-equivalent atom list contains two atoms: Ca at (0,0,0) with multiplicity 4 and F at (1/4,1/4,1/4) with multiplicity 8. The cell atom list contains twelve atoms: four Ca atoms at (0,0,0), (1/2,1/2,0), etc. and eight F atoms at (1/4,1/4,1/4), (3/4,1/4,1/4), etc.

The output for this example follows. First, the output gives the header with some information about the system, the version (the commit number), and the location of the relevant library and density files:

                  _   _     _          ___
                 (_) | |   (_)        |__ \
     ___   _ __   _  | |_   _    ___     ) |
    / __| | '__| | | | __| | |  / __|   / /
   | (__  | |    | | | |_  | | | (__   / /_
    \___| |_|    |_|  \__| |_|  \___| |____|

* CRITIC2: analysis of real-space scalar fields in solids
           and molecules.
  (c) 1996-2015 A. Otero-de-la-Roza, A. Martin-Pendas, V. Lua~na
  Distributed under GNU GPL v.3 (see COPYING for details)
  Bugs, requests, and rants: alberto@fluor.quimica.uniovi.es
  If you find this software useful, please cite:
  AOR, Comput. Phys. Commun. 185 (2014) 1007-1018.
  AOR, Comput. Phys. Commun. 180 (2009) 157-166.

+ critic2, commit e7c2707
 compile host: Linux puck 4.2.0-1-amd64 #1 SMP Debian
 compile date: Wed Oct 21 18:39:47 PDT 2015
    using f77: ifort -g
          f90: ifort -g -FR -fopenmp
      ldflags:
       debug?: no
 compiled dat: /usr/local/share/critic2
      datadir: /home/alberto/git/critic2/dat
     dic file: /home/alberto/git/critic2/dat/cif_core.dic
...was found?:  T

CRITIC2--2015/10/21, 23:08:09.362

After the CRYSTAL keyword is read, critic2 first lists the basic information about the crystal (note that the input lines read are copied to the output preceded by the “%%” prefix). The output starts with the cell parameters and the number of atoms in the crystal motif:

%% CRYSTAL
%% SPG f m -3 m
%% CELL 5.463 5.463 5.463 90 90 90 ANG
%% NEQ 0 0 0 ca
%% NEQ 1/4 1/4 1/4 f
%% ENDCRYSTAL
* Crystal structure
  From: <input>
  Lattice parameters (bohr): 10.323574  10.323574  10.323574
  Lattice parameters (ang): 5.463000  5.463000  5.463000
  Lattice angles (degrees): 90.000  90.000  90.000
  Empirical formula: 
    ca(1) f(2) 
  Number of non-equivalent atoms in the unit cell: 2
  Number of atoms in the unit cell: 12
  Number of atomic species: 2
  Number of electrons (with zero atomic charge): 152

Next is the list of atomic species. Internally, critic2 keeps a list of all the types of atoms present in the crystal or molecule. Normally, each atomic species corresponds to a different element but in some cases, for instance magnetic systems, it may be useful to differentiate between two different atomic types with the same atomic number.

+ List of atomic species: 
# spc  Z   name    Q   ZPSP
   1  20    ca     0.0  -- 
   2   9     f     0.0  -- 

In this case, however, we have two species corresponding to Ca and F, each with their corresponding atomic number.

Next comes the non-equivalent atom list. In this case, the whole crystal is generated by replicating two atoms: one Ca and one F. The positions, multiplicities, and the atomic numbers are indicated:

+ List of non-equivalent atoms in the unit cell (cryst. coords.): 
# nat       x              y              z        spc  name   mult  Z 
   1   0.0000000000   0.0000000000   0.0000000000   1    ca     4  20 
   2   0.2500000000   0.2500000000   0.2500000000   2     f     8   9 

The next table is the complete atom list. Here, critic2 lists all the atoms in the unit cell: four Ca and eight F. The exact same list is repeated in Cartesian coordinates, referred to the internal coordinate system used in critic2. The output also indicates the matrix of lattice vectors in Cartesian coordinates (repeated below).

+ List of atoms in the unit cell (cryst. coords.): 
# at        x              y              z        spc  name    Z 
   1   0.0000000000   0.0000000000   0.0000000000   1    ca    20 
   2   0.0000000000   0.5000000000   0.5000000000   1    ca    20 
   3   0.5000000000   0.0000000000   0.5000000000   1    ca    20 
   4   0.5000000000   0.5000000000   0.0000000000   1    ca    20 
   5   0.2500000000   0.2500000000   0.2500000000   2     f     9 
   6   0.2500000000   0.7500000000   0.7500000000   2     f     9 
   7   0.7500000000   0.2500000000   0.7500000000   2     f     9 
   8   0.7500000000   0.7500000000   0.2500000000   2     f     9 
   9   0.7500000000   0.7500000000   0.7500000000   2     f     9 
  10   0.7500000000   0.2500000000   0.2500000000   2     f     9 
  11   0.2500000000   0.7500000000   0.2500000000   2     f     9 
  12   0.2500000000   0.2500000000   0.7500000000   2     f     9 

+ Lattice vectors (bohr)
    a:   10.3235738640     0.0000000000     0.0000000000 
    b:    0.0000000000    10.3235738640     0.0000000000 
    c:    0.0000000000     0.0000000000    10.3235738640 

+ List of atoms in Cartesian coordinates (bohr): 
# at         x                y                z         spc  name    Z     dnn    
   1     0.0000000000     0.0000000000     0.0000000000   1    ca    20    4.4702  
   2     0.0000000000     5.1617869320     5.1617869320   1    ca    20    4.4702  
   3     5.1617869320     0.0000000000     5.1617869320   1    ca    20    4.4702  
   4     5.1617869320     5.1617869320     0.0000000000   1    ca    20    4.4702  
   5     2.5808934660     2.5808934660     2.5808934660   2     f     9    4.4702  
   6     2.5808934660     7.7426803980     7.7426803980   2     f     9    4.4702  
   7     7.7426803980     2.5808934660     7.7426803980   2     f     9    4.4702  
   8     7.7426803980     7.7426803980     2.5808934660   2     f     9    4.4702  
   9     7.7426803980     7.7426803980     7.7426803980   2     f     9    4.4702  
  10     7.7426803980     2.5808934660     2.5808934660   2     f     9    4.4702  
  11     2.5808934660     7.7426803980     2.5808934660   2     f     9    4.4702  
  12     2.5808934660     2.5808934660     7.7426803980   2     f     9    4.4702  

Following this information comes the cell volume, in atomic units and in angstrom^3:

+ Cell volume (bohr^3): 1100.24704
+ Cell volume (ang^3): 163.03979

And then the list of symmetry operations and the space group and point group information:

+ List of symmetry operations (48):
  Operation 1:
     1.000000  0.000000  0.000000  0.000000
     0.000000  1.000000  0.000000  0.000000
     0.000000  0.000000  1.000000  0.000000
  Operation 2:
     0.000000  0.000000 -1.000000  0.000000
    -1.000000  0.000000  0.000000  0.000000
     0.000000 -1.000000  0.000000  0.000000
[...]
  Operation 48:
     0.000000  1.000000  0.000000  0.000000
     0.000000  0.000000  1.000000  0.000000
    -1.000000  0.000000  0.000000  0.000000

+ List of symmetry operations in crystallographic notation:
   1: x,y,z
   2: -z,-x,-y
   3: -y,x,z
[...]
   47: x,-z,-y
   48: y,z,-x

+ List of centering vectors (4):
  Vector 1: 0.000000  0.000000  0.000000
  Vector 2: 0.000000  0.500000  0.500000
  Vector 3: 0.500000  0.000000  0.500000
  Vector 4: 0.500000  0.500000  0.000000

+ Crystal symmetry information
  Space group (Hermann-Mauguin): Fm-3m (number 225)
  Space group (Hall): -F 4 2 3 (number 523)
  Point group (Hermann-Mauguin): m-3m
  Point group (Schoenflies): Oh
  Holohedry: cubic
  Laue class: m-3m

The Cartesian to crystallographic (“car to crys”) transformation matrices are the transformation operations between the vector basis formed by the cell vectors (crystallographic coordiantes) and the internal Cartesian axes used in critic2 (Cartesian coordinates). The crystallographic to Cartesian matrix (“crys to car”) gives the cell vectors in Cartesian axes. The metric tensor is the transpose of “crys to car” times “crys to car”, and contains the scalar products between lattice vectors.

+ Car/crys coordinate transformation matrices:
  A = car to crys (xcrys = A * xcar, bohr^-1)
       0.0968656798    -0.0000000000    -0.0000000000 
       0.0000000000     0.0968656798    -0.0000000000 
       0.0000000000     0.0000000000     0.0968656798 
  B = crys to car (xcar = B * xcrys, bohr)
      10.3235738640     0.0000000000     0.0000000000 
       0.0000000000    10.3235738640     0.0000000000 
       0.0000000000     0.0000000000    10.3235738640 
  G = metric tensor (B'*B, bohr^2)
     106.5761773245     0.0000000000     0.0000000000 
       0.0000000000   106.5761773245     0.0000000000 
       0.0000000000     0.0000000000   106.5761773245 

The next block in the output gives the calculation of the discrete molecular units in this crystal. By default, critic2 calculates the full atomic connectivity graph in any given input. Based on this graph, critic2 determines whether the crystal is composed of molecules (0D), polymers (1D), slabs (2D) or if it is a three-dimensional periodic structure. In the case of a molecular crystal, critic2 gives the list of all molecules in the unit cell and assigns to them an identifying integer. In this case, the crystal is not molecular:

+ List of fragments in the system (1)
# Id = fragment ID. nat = number of atoms in fragment. C-o-m = center of mass (bohr).
# Discrete = is this fragment finite?
# Id  nat           Center of mass            Discrete  
  1    12     0.871668    0.871668    0.871668   No

+ This is a 3D periodic structure.

In order to perform efficient calculations of distances in the crystal, critic2 sets up an atomic environment, which is the collection of all atoms in a number of unit cells surrounding the cell at the origin. These atoms are placed into bins, which are then used to speed up the calculation of distances and atomic contributions to scalar fields. The information about the atomic environments is given next:

+ Atomic environment
  Number of atoms (reduced cell/environment): 12 / 3056
  Radius of (unit cell/environment) circumscribed sphere (bohr): 8.9405 / 67.0536
  Maximum interaction distance (bohr): 31.4559 
  Covering regions: 
    Total number of regions: 216 (6 6 6)
    Minimum region ID: -3 -3 -3
    Maximum region ID: 2 2 2
    Region side (bohr): 13.3037
    Transformation origin (bohr): 5.1618,5.1618,5.1618
    Search offsets: 2197
    Maximum search offset: 6
    Average number of atoms per region: 14.1481
    Maximum number of atoms in a region: 40

Next the Wigner-Seitz (WS) cell and the reduced Delaunay cell are determined. This information is used in the calculation of shortest distances between lattice translations of two atoms, and for the AUTO and YT tasks, among other things.

+ Vertex of the WS cell in cryst. coords. (8)
# id = vertex ID. xyz = vertex cryst. coords. d = vertex distance to origin (bohr).
   id       x            y            z          d (bohr)   
    1    0.500000     0.500000    -0.500000     8.94047722  
    2    0.500000    -0.500000     0.500000     8.94047722  
    3    0.500000     0.500000     0.500000     8.94047722  
    4   -0.500000     0.500000     0.500000     8.94047722  
    5    0.500000    -0.500000    -0.500000     8.94047722  
    6   -0.500000     0.500000    -0.500000     8.94047722  
    7   -0.500000    -0.500000    -0.500000     8.94047722  
    8   -0.500000    -0.500000     0.500000     8.94047722  

+ Faces of the WS cell (6)
# Face ID: vertexID1 vertexID2 ...
   1: 3  4  8  2 
   2: 3  4  6  1 
   3: 3  1  5  2 
   4: 1  6  7  5 
   5: 2  8  7  5 
   6: 4  8  7  6 

+ Lattice vectors for the Wigner-Seitz neighbors
# FaceID: Voronoi lattice vector (cryst. coords.)
   1:  0  0  1
   2:  0  1  0
   3:  1  0  0
   4:  0  0 -1
   5:  0 -1  0
   6: -1  0  0

+ Lattice vectors for the Delaunay reduced cell (cryst. coords.)
  a:  1  0  0
  b:  0  1  0
  c:  0  0  1
  Delaunay reduced cell lengths: 10.323574 10.323574 10.323574
  Delaunay reduced cell angles: 90.000 90.000 90.000

+ Is the cell orthogonal? T
+ Is the reduced cell orthogonal? T

Critic2 always has a “reference” scalar field defined. The reference field is the primary target for most keywords. For instance, it provides the attraction basins integrated when calculating atomic charges, and it is the field whose critical points are determined by AUTO. In absence of any external field loaded by the user, critic2 defaults to using the promolecular density (the sum of atomic densities) as reference. The promolecular density is made available to the user through the field identifier $0 (also, $rho0).

* List of scalar fields
+ Field number 0
  Name: <promolecular>
  Source: <generated>
  Type: promolecular
  Atoms in the environment: 3056
  Use core densities? F
  Numerical derivatives? F
  Nuclear CP signature: -3
  Number of non-equivalent critical points: 2
  Number of critical points in the unit cell: 12
  Alias for this field (2): $0, $rho0
  This is the REFERENCE field.

A list of the current integrable properties is given next. This is the list of properties that would be integrated in the attraction basins if the user runs INTEGRALS or any of the other basin integration methods. The list of integrable properties can be queried and modified with the INTEGRABLE keyword. Our outupt shows the default integrable properties, which are the atomic volume and the value and Laplacian of the reference field

* List of integrable properties (3)
#  Id  Type  Field  Name
    1   v        0  Volume
    2  fval      0  Pop
    3  lval      0  Lap

Next is the list of additional properties to be calculated at the critical points. These are used at the end of the automatic CP search with AUTO, and can be modified using the POINTPROP keyword. In our example, there are no additional properties.

* List of additional properties at critical points (0)

Each scalar field can be augmented with a core contribution. This can be useful in cases when the source program only provides the valence density, and is activated with the ZPSP keyword. Next in the output is the list of core and pseudopotential charges for all known fields (in this case, the promolecular density, which has neither):

* List of core and pseudopotential charges for each field
# id  type   core?  ZPSP
  0  promol   no  

The execution finishes with a report of the warnings found and the timestamp. It is always a good idea to check for warnings in the output:

CRITIC2 ended succesfully (0 WARNINGS, 0 COMMENTS)

Elapsed wall time: 0s
Elapsed CPU time: 0s
CRITIC2--2019/1/31, 15:45:19.603

Simple Input and Output for a Molecule

Molecular structures are read in critic2 using the MOLECULE keyword. A simple input file for a water molecule is:

MOLECULE
  O 0.000000 0.000000 0.118882
  H 0.000000 0.756653 -0.475529
  H 0.000000 -0.756653 -0.475529
ENDMOLECULE

Unlike in CRYSTAL, the coordinates in the MOLECULE environment are Cartesian coordinates. The default units in and after a MOLECULE keyword are angstrom.

The output starts off with the same header as in CRYSTAL, and then:

%% MOLECULE
%% O 0.000000 0.000000 0.118882
%% H 0.000000 0.756653 -0.475529
%% H 0.000000 -0.756653 -0.475529
%% ENDMOLECULE
* Molecular structure
  From: <input>
  Encompassing cell dimensions (bohr): 37.794523  40.654257  38.917797
  Encompassing cell dimensions (ang): 20.000000  21.513306  20.594411
  Empirical formula: 
    o(1) h(2) 
  Number of atoms: 3
  Number of atomic species: 2
  Number of electrons (with zero atomic charge): 10

The output shows a copy of the input lines (after the “%%” prefix), and some general information about the structure. Critic2 works under periodic boundary conditions, even when dealing with molecular structures. The molecule is placed inside a very large unit cell to mimic gas-phase conditions but critic2 treats the molecule in the same way as a crystal, converting the atomic coordinates to “crystallographic” coordinates inside the supercell. In the output, critic2 shows the dimension of this cell in bohr and angstrom, and the number of atoms and electrons in the molecule. Keywords are available in the MOLECULE keyword and environment for changing the size and shape of the encompassing cell.

After that comes the list of atomic species (same as in a crysatl) and the list of atoms in Cartesian coordinates (angstrom and referred to the same origin as in the input):

+ List of atomic species: 
# spc  Z   name    Q   ZPSP
   1   8     o     0.0  -- 
   2   1     h     0.0  -- 

+ List of atoms in Cartesian coordinates (ang_): 
# at         x                y                z         spc  name    Z     dnn
   1     0.0000000000     0.0000000000     0.1188820000   1     o     8    0.9622
   2     0.0000000000     0.7566530000    -0.4755290000   2     h     1    0.9622
   3     0.0000000000    -0.7566530000    -0.4755290000   2     h     1    0.9622

The list of atoms in crysatllographic coordinates is not given when the structure is a molecule. Likewise, symmetry is not used in a molecular system and hence there is no need for a list of atoms in the asymmetric unit. All atoms in a molecule have multiplicity 1.

The molecule is placed inside a big cell that tries to model the empty space around the molecule. This, however, may lead to some problems with critic2’s methods. For instance, the critical point search will find that at the border of the supercell the density is discontinuous (because critic2 uses periodic boundary conditions) and report spurious CPs. Likewise, the gradient path tracing routines can become trapped at the border of the cell. To prevent this, critic2 defines by default a second cell, slightly smaller than the encompassing cell defined above. This molecular cell represents the valid molecular space for the current structure. Regions outside the molecular cell cannot be traversed by gradient paths and can not hold any critical points. Essentially, the outside border of the encompassing cell becomes a representation of infinity for the molecule under study.

The dimensions of the molecular cell are given next in the output:

+ Limits of the molecular cell (in fractions of the unit cell).
# The part of the unit cell outside the molecular cell represents
# infinity (no CPs or gradient paths in it).
  x-axis: 0.1000 -> 0.9000
  y-axis: 0.0930 -> 0.9070
  z-axis: 0.0971 -> 0.9029

where the limits are given in fractional coordinates of the encompassing cell. That is, the molecular cell goes from 0.1 to 0.9 of the encompassing cell (given above) in the x direction, etc. The remaining 10% of the cell in each direction becomes the forbidden zone for this structure.

After this, the output is very similar to CRYSTAL, except the output related to the crystal symmetry is not present. The atomic environments and list of molecular fragments are shown next:

+ List of fragments in the system (1)
# Id = fragment ID. nat = number of atoms in fragment. C-o-m = center of mass (ang_).
# Discrete = is this fragment finite?
# Id  nat           Center of mass            Discrete
  1    3      0.000000    0.000000    0.052368   Yes

+ Atomic environment
  Number of atoms (reduced cell/environment): 3 / 3
  Radius of (unit cell/environment) circumscribed sphere (ang_): 17.9371 / 0.8129
  Maximum interaction distance (ang_): 11.3820 
  Covering regions: 
    Total number of regions: 4 (1 2 2)
    Minimum region ID: 0 -1 -1
    Maximum region ID: 0 0 0
    Region side (ang_): 2.6400
    Transformation origin (ang_): 10.0000,10.7567,10.2972
    Search offsets: 1331
    Maximum search offset: 5
    Average number of atoms per region: 0.7500
    Maximum number of atoms in a region: 1

As in the case of a crystal, critic2 calculates how many discrete fragments there is in this molecule. In this case, just one. The environment comprises the whole molecule (3 atoms).

The rest of the output is completely equivalent to the crystal case (see the discussion above):

* List of scalar fields
+ Field number 0
  Name: <promolecular>
  Source: <generated>
  Type: promolecular
  Atoms in the environment: 3
  Use core densities? F
  Numerical derivatives? F
  Nuclear CP signature: -3
  Number of non-equivalent critical points: 3
  Number of critical points in the unit cell: 3
  Alias for this field (2): $0, $rho0
  This is the REFERENCE field.

* List of integrable properties (3)
#  Id  Type  Field  Name
    1   v        0  Volume  
    2  fval      0  Pop  
    3  lval      0  Lap  

* List of additional properties at critical points (0)

* List of core and pseudopotential charges for each field
# id  type   core?  ZPSP
  0  promol   no  

CRITIC2 ended succesfully (0 WARNINGS, 0 COMMENTS)

Elapsed wall time: 0s
Elapsed CPU time: 0s
CRITIC2--2019/1/31, 16:10:37.890