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Cost_package/Manuals/dolo_emploi
nadia 45937de5a3 Ajout des manuels
2016-05-03 11:54:25 +02:00

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!
!
! Program dolo
!
!
Files to be read : - molcost files
- an orbital file (RasOrb, ScfOrb...)
output files : - NONORLOC
(Local Orbitals: they are not orthogonal, and are
written in the basis of the OAO (Orthogonalized
Atomic Orbitals))
I.
##############
Preliminairies
##############
design the molecule, with atom names
II.
####
Data
####
1. A DOLOIN file (see "DOLOIN" part)
2. The data to generate local Orbitals (LO) can be given
- interactively
- or can be prepared in the file 'OLD_DATA'
OLD_DATA can be obtained from an interactive run
##############
How it works
##############
---------------------------------------------------
a. Interactive run (program idolo)
---------------------------------------------------
enter:
export CurrDir=...
export WorkDir=...
export Project=...
export PATH=$PATH:...cost/bin
prepare a DOLOIN file
eventually copy an old OLD_DATA_nn file (of a previous run) to OLD_DATA
- enter: idolo
The program starts, and asks for a data to generate one or several LO's
(see below list of commands)
- In the same time, the program generates a new file OLD_DATA_1,
or OLD_DATA_2, or OLD_DATA_n+1, if OLD_DATA_n is the last existing one
In this file, it writes the data you just entered
If the program crashes, or if you stop it, data already entered are
in OLD_DATA_x. Copy OLD_DATA_x to OLD_DATA, verify if everything is OK,
and re-enter "dolo"
----------------------------------------------------
b. background run (program dolo)
----------------------------------------------------
the script looks like:
export CurrDir=...
export WorkDir=...
export Project=...
export PATH=$PATH:...cost/bin
molcost < INPUT
dolo
(proj_scf < INPUT ; cp NONORLOC_scf NONORLOC)
schmudort < INPUT
prepare a DOLOIN file
dolo needs a correct OLD_DATA file
#############
Possible Data
#############
Many possibilities exist to enter a data line which will generate
one or several LO's.
-----------------------------------------
a. Basic generation of one or several LO
-----------------------------------------
The "basic data" correspond to those read by the program
it is easier to use "macro data" (see below)
The program transforms the "macro data" into "basic data"
example:
O_C2H1 C2 1S(2) 2P(1) : H1 1S(1) (1,1)
(not case sensitive)
explanation:
O_C2H1 is the label of the LO('s).
- The first letter (here: O), can be
A: active. C: core. G: frozen. O: other
- _ character number 2: compulsory
- characters 3 to 12. Name of the LO, chosen by the user
C2 1S(2) 2P(1) , H1 1S(1)
atoms and AO's that describe the LO. Here, the LO is described by
atoms C2 and H1. The AO's for C2 are 1S(2) (i.e. the second S in the
ANO basis set, corresponding to the valence shell), and for H1 it is
1S(1)
the atoms are separated by ":"
There is in theory no limitation in the number of atoms/AO.
(1,1): first number: 1 bonding LO
second number: 1 anti-bonding LO
for a double bond, we would have (2,2)
for a core orbital, there would be only one atom, and (1,0)
Warning! For a SINGLE bond, appearing TWICE for symmetry reasons
we would have (2,2)!
-----------------
Macro data
-----------------
The "macro data" are easier to use. In the code, they generate
basic data
There are two main "macro data". Ther names are "bond_" and "deloc_"
Almost everything can be done with these two data
There are other kinds of data (core_, sigma_ etc...)
They may produce errors, if there is symmetry. Be careful, and verify
that you really obtained what you wanted.
-----------------------------------------
b. An macro data: BOND_
-----------------------------------------
a subset of the Lewis structure is given by:
chain='AT1-AT2-AT3...'
where:
ATi are labels of atoms
"-" can be -, =, ~ for single, double and triple bonds
An information may be added to ATi:
ATi(LPn) or ATi(SYn) (lone pairs, bonds invariant under
a symmetry transformation) (see below the examples)
::::::::::::::::::::::::
Give basis set for atoms
::::::::::::::::::::::::
bond_ basref='...'
These is a preliminary data, which defines the default basis set for all
following bond_ data. The default may be changed by another "bas" data.
It can be ignored for a particular bond_ data, by giving "bas=" (as in
many examples below)
example: BOND_ BASREF='O:1S(2) 2P(1),C:1S(2) 2P(1),H:1S(1)'
::::::::::::::::::::::::
Change suffix to ".PI"
::::::::::::::::::::::::
if the suffix of the LO label is ".SG" and it corresponds to a pi LO
it is possible to change the label
Add label='P' to the BOND_ data
bond_ chain='...',label='P'
the name of the generated LO will be:
O_"...".PI
::::::::::::::::::::::::
example 1: (single bond)
::::::::::::::::::::::::
the example of (a) can be written:
bond_ chain='C2-H1',bas='1S(2) 2P(1)','H1 1S(1)'
The label of the LO is chosen by the program (O_C2H1.SG)
n=2: there are 2 atoms (default value: 2)
::::::::::::::::::::::::::::::::::::
example 2: (double and triple bond)
::::::::::::::::::::::::::::::::::::
a) bond_ n=2,chain='C2=C1',bas=2*'1S(2) 2P(1)'
generated labels: O_C2H1.SG O_C2H1.PI
b) bond_ n=2,chain='C2~C1',bas=2*'1S(2) 2P(1)'
generated labels: O_C2H1.SG O_C2H1.P1 O_C2H1.P2
::::::::::::::::::::::::::::::::::
example 3: (bonds and lone pairs)
::::::::::::::::::::::::::::::::::
HO H7
\ _ /
H2-C1 - C3H3 = C4H4 - C5H5 = N - C6H6 = C7
/ \
H1 H8
chain C1-C3=C4-C5=N-C6=C7:
bond_ n=7,chain='C1-C3=C4-C5-N(lp1)=C6-C7',bas=7*'1S(2) 2P(1)',
N(lp1) : atom N has 1 Lone Pair (no limit to n in lpn)
:::::::::::::::::::::::::
example 4: (3 lone pairs)
:::::::::::::::::::::::::
bond_ chain='S1(lp3)-C13',bas=2*'1s(1) 2p(1)'
/
We have: | S1-C13
\
The programm generate the following basic data::
o_s1c13 s1 1s(1) 2p(1) : c13 1s(1) 2p(1) (4 1)
o_s1lp s1 1s(1) 2p(1) (3 0)
The lone pairs were generated twice (once by each basic data).
In o_s1c13, they are "spread" over the 4 occupied
To correct that, the program generates:
subs o_s1c13 o_s1lp
which substracts the lone pairs from the set (LP+sig+sig*). The sigma
appears then to be pure, the LP are unchanged
these generated data appear in OLD_DATA_x
::::::::::::::::::::::::::::::::::::::::
example 5: (bonds invariant by symmetry)
::::::::::::::::::::::::::::::::::::::::
C1
/ \
C2 C3
------ | ---- | ---------------- symmetry plane
C2 C3
\ /
C1
bond_ n=2,chain='C1-C3(sy1)'
sy1 means that There is a C3-C3 bond, invariant by symmetry. The program
will generate the following basic data:
o_C1C3 C1 1s(2) 2p(1) : C3 1s(2) 2p(1) (3 3) (3 occ, 3 anti bonding
corresponding to C1-C3-C3-C1)
O_C3 C3 1s(2) 2p(1) (1 1) (C3-C3 bond)
subs o_C1C3 c_C3 (substract c_C3 from o_C1C3)
After substraction, The orbitals with the label o_C1C3 are really on
the C1-C3 bond, and not on C3-C3
:::::::::::::::::::::
example 6: (pi bonds)
:::::::::::::::::::::
C1 C1
/ /
C2 C3 C2 C3
a) | b) ------ ---- | ---------
C4 C6 C2 C3
\ \
C5 C1
a) bond_ n=2,chain='C1=C2',orth='c1,c2,c3'
b) bond_ n=1,chain='C3(sy2)',orth='c1,c3,c3' (bond invariant by symmetry)
only double bonds are represented (Kékulé).
The 3 centers c1,c2,c3 define a plane.
The pi orbitals are orthogonal to this plane.
(orth='c1,c2,c3' means: no component in plane c1,c2,c3)
:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
example 7: (All p, or d orbitals of an atom. Here: closed shell Fe)
:::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::::
3d of an iron atom:
a) 3 filled LO's
bond_ n=1,chain='fe(lp3)',bas='3d(1)'
b) 2 empty LO's
bond_ n=1,chain='fe',bas='3d(1)',vi=2
:::::::::::::::::::::::::::::::::::::::::::::::::
example 8 (several subgraphs in one "bond_" data)
:::::::::::::::::::::::::::::::::::::::::::::::::
This possibility is sometimes mandatory, if the data (SYn) is used
example of butadiene:
\ /
H1 C2 -
\ //
C1 - C1
// \
- C2 H1
/ \
1. C2-C1-C1-C2 bond: bond_ chain='C1(sy1)=c2'
2. C1-H1 bond: bond_ chain='C1(sy1)-H1'
an atom with (SY.) CANNOT appear in two different bond_ lines
use instead:
bond_ chain='C1(sy1)=c2;C1(sy1)-H1'
NOTE: in general, all bonds can be generated with the BOND_ command
-----------------------------------------
c. An macro data: DELOC_
-----------------------------------------
build a set of orbitals that are deloclized on several atoms
example:
deloc_ n=3,chain='c1-c6-c11',bas=3*'2pz(1)',noc=3,nvirt=3,label='a'
means:
n : number of atoms (can be more by symmetry)
c1-c6-c11 : list of the atoms, separated by "-"
noc, nvirt : number of occupied and anti-bondings (in this example,
we have a 6-atom ring)
label='a' : these orbitals will be active in the MRCI
bas=3*'2pz(1)' : in this example, the Pz pi orbitals were seeked
-----------------------------------------
d. SIGMA_
-----------------------------------------
A set of sigma bonds
sigma_ c* 1S(2) 2P(1) : h* 1S(1) dmax=1.2 ANGSTROM
generates all CH bonds for all (C,H) couples, separated by less
than 1.2 Angstrom.
Note. in C*..., * replaces only NUMBERS, and not letters. So Cu is
not considered as a Carbon atom. Do not call the C atoms Ca, Cb...
NOTE: This data makes sometimes problems if there is symmetry. In this
case, better use BOND_
-----------------------------------------
e. CORE_ , DIFF_
-----------------------------------------
A set of core or diffuse orbitals
CORE_ C* 1S(1) ---> occupation is (1 0)
DIFF_ C* 1S(1) ---> occupation is (0 1)
#############################################
Other macro data (do not une for the moment)
#############################################
-----------------------------------------
f. PI_
-----------------------------------------
similar to SIGMA_, for pi orbitals
example:
PI_ C* 2P(1) : C* 2P(1) DMAX=1.4 ANGSTROM
NOTE: This data makes somtiomes problems if there is symmetry. In this
case, use BOND_c1,c2,c3
-----------------------------------------
g. SUBS
-----------------------------------------
subtraction (or projection) of a set of LO from another set of LO,
as it appears in B. example 4
subs o_s1c13 o_s1lp (the space of o_s1c13 is larger than the space
of o_s1lp)
-----------------------------------------
h. RENAME
-----------------------------------------
If one enters for example
o_s1lp s1 1s(1) 2p(1) (3 0) (basic data)
/
| S1
\
3 lone pairs are generated, with the same name. The names need to
be different in the following of the calculation
a solution is to use BOND_ instead
bond _ n=1,chain='S1(lp3)',bas='1s(2) 2p(1)'
or to rename the bonds
REN o_s1lp o_s1lp1 o_s1lp2 o_s1lp3
(REN common_name individual_names)
-----------------------------------------
i. Multiple data
-----------------------------------------
- using "[", "]"
ex.
BOND_ CHAIN='W1',BAS='3D[0 1+ 2+ 2-](1) 3D[0 1+ 2+ 2-](2)',LP=1,VI=1
generates 4 bond data:
BOND_ CHAIN='W1',BAS='3D0(1) 3D0(2)',LP=1,VI=1
BOND_ CHAIN='W1',BAS='3D1+(1) 3D1+(2)',LP=1,VI=1
...
- using "[["
ex:
BOND_ CHAIN='O[1 2 3 4 5 6 7 11 13 15](LP1)',BAS='2P[[X Y Z]](1) 2P[[X Y Z]](2)'
generates all combinations of the 10 data due to [1 2 3 4 5 6 7 11 13 15]
and the 3 due to [[X Y Z]]
(a total of 30 bond_data)
-----------------------------------------
j. ROT_
-----------------------------------------
- replaces a set of AOs (in general Px,Py,Pz orbitals of an atome) by a
combination of these orbitals
-example
ROT_ ATOM='C1',PARA='0,C1'
for Atom C1, the three AOs Px,Py,Pz are replaced by a combination,
the axis is given by the direction 0 (zero)-C1, where 0 is the Origin.
the AO basis is reduced, to eliminate unwihed LOs
- you can give several ROT_ commands
-example
ROT_ ATOM='C1',PARA='0,C1'
ROT_ ATOM='C2',PARA='0,C2'
ROT_ ATOM='C3',PARA='0,C3'
ROT_ ATOM='C4',PARA='0,C4'
ROT_ ATOM='C5',PARA='0,C5'
DELOC_ CHAIN='C3-C1-C5-C2-C4',BAS=5*'2P(1)',NOC=8,NVIRT=8
ROT_ CLOSE
The DELOC command uses the reduced AOs. The Rot_ commands are valid for all
following commands
ROT_ CLOSE cancels all preceding ROT_ data
####################
Details of Data
####################
--------------
DOLOIN file:
--------------
All data are compulsory
&smufil prefix='Project.' /
&smu
nprint=0,
orb='test.RasOrb' orbital file name, as a result
or a SCF or CASSCF calculation
loc_actives default:T T: localizes active orbitals
F: active orbitals remain unlocal
/
&oao /
Concerns data to build OAO (Orthogonalized Atomic Orbitals)
list of Atomic Orbitals, with priority in the orthogonalization
example:
Fe 1s(1) pr=1
--> first s orbital of atom Fe in the list of AO's
the AO is orthogonalized with highest priority (pr=1)
Fe 2p(1) pr=1
--> idem for all 2px, 2py and 2pz AO's
Fe 3d(1) pr=2
--> idem for the 5 d orbitals. (pr=2: will be orthogonalized, for example,
to the 1s of C which has (pr=1) (projection orthogonalization)
-- etc...
C* 1s(1) pr=2
N* 1s(1) pr=2
H* 1s(1) pr=2
S 1s(1) pr=2
C* 2p(1) pr=2
N* 2p(1) pr=2
H* 2p(1) pr=2
S* 2p(1) pr=2
fin end of AO data
&orb symm='XY' / symm: as given in seward after the line
SYMMetry
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