Recent changes to OrcaExamples

OrcaExamples modified by TimN

TimN — Sun, 13 Jan 2019 12:51:13 -0000

--- v15
+++ v16
@@ -48,6 +48,10 @@

 --------------------------------------------------------

+Note that there was  `-ignorefock` option in JANPA versions prior to 2.02. Using this option was highly recommended for analyzing the orbitals obtained from a correlated wavefunction, since in this case no 'energies' of the orbitals are available. For the same reason the default behaviour has been changed in JANPA v. 2.02, so that the Fock matrix is ignored by default. In case if for some reason the Fock matrix analysis is still needed, the option `-doFock` should be used.
+
+
+
 Hartree-Fock/DFT methods
 ----
 (to be written - but the general idea is still to convert an ORCA's .gbw file
@@ -73,6 +77,8 @@

 --------------------------------------------------------
+
+Note that  no Fock matrix is available for MP2 method.

 General notes for non-variational post-SCF methods (Configuration Interaction, Coupled Cluster)
@@ -99,11 +105,11 @@

 --------------------------------------------------------

-A notes for ORCA post-3.0.0 users
+A notes for ORCA post-3.0.0 (but not v.4.x) users
 ------------

 The following sections require creation of a .47 file with ORCA by using its built-in abilities
-(using *NPA* keyword). However, if the version of ORCA is greater than 3.0.0 this ability will not
+(using *NPA* keyword). However, if the version of ORCA is greater than 3.0.0 this ability will *not*
 work by default due to the fact that ORCA will try to find an executable of an original NBO
 program and will not proceed if this executable is not found. Here is a simple trick to overcome 
 this limitation. 
@@ -180,10 +186,9 @@

 * Run `janpa` to perform analysis

-        java -jar janpa.jar -i bh_oo_oo.PURE -ignorefock > bh_oo_oo.JANPA
-
-Note the `-ignorefock` option, which disables the transformation of the Fock matrix into
-NAO basis. This is necessary since no Fock matrix is available for QCISD method.
+        java -jar janpa.jar -i bh_oo_oo.PURE  > bh_oo_oo.JANPA
+
+Note that no Fock matrix is available for QCISD method.

 You can [Download](http://janpa.sourceforge.net/get.php?file=example_orca3_qcisd.zip) the files of this example.

@@ -234,10 +239,9 @@

 * Run `janpa` to perform analysis

-        java -jar janpa.jar -i HCl.PURE -ignorefock > HCl.JANPA
-
-Note the `-ignorefock` option, which disables the transformation of the Fock matrix into
-NAO basis. This is necessary since no Fock matrix is available for CCSD method.
+        java -jar janpa.jar -i HCl.PURE > HCl.JANPA
+
+Note that  no Fock matrix is available for CCSD method.

 You can [Download](http://janpa.sourceforge.net/get.php?file=example_orca3_ccsd.zip) the files of this example.

OrcaExamples modified by TimN

TimN — Sun, 23 Nov 2014 09:41:53 -0000

--- v14
+++ v15
@@ -1,7 +1,7 @@
 Use of JANPA with ORCA
 =====

-(tested in [Orca](http://cec.mpg.de/forum/) 3.0.0)
+(tested in [Orca](http://cec.mpg.de/forum/) versions 3.0.0 and 3.0.2)

 Some introductory notes
 ----
@@ -50,13 +50,18 @@

 Hartree-Fock/DFT methods
 ----
-(to be written)
+(to be written - but the general idea is still to convert an ORCA's .gbw file
+into a MOLDEN-semi-compatible file using *orca_2mkl* program from the ORCA package,
+and then to use our *molden2molden* program with *-fromorca3bf* and *-orca3signs* options
+to fix MO coefficients and basis function normalization in the obtained MOLDEN-semi-compatible
+file)

 --------------------------------------------------------

 MP2
 ----
-(to be written)
+(to be written - bu the general idea remains the same as for Hartree-Fock/DFT methods with
+the only difference that .mp2nos file created by ORCA should to be used instead of a its .gbw file)

         %mp2 
@@ -107,18 +112,18 @@
 the command line parameters passed to that program. A good candidate for such a program in Linux
 is a standard executable file named *pwd*. Here is an example of a Linux script which does that

-    #!/bin/bash
-    export NBOEXE=pwd
-    export GENEXE=pwd
-    orca file.inp > file.out
+        #!/bin/bash
+        export NBOEXE=pwd
+        export GENEXE=pwd
+        orca file.inp > file.out

 (we assume that *orca* executable can be found in a system's *PATH*). Another variation of the same
 script can be as follows

-    #!/bin/bash
-    export NBOEXE=`which pwd`
-    export GENEXE=`which pwd`
-    orca file.inp > file.out
+        #!/bin/bash
+        export NBOEXE=`which pwd`
+        export GENEXE=`which pwd`
+        orca file.inp > file.out

 so that *NBOEXE* and *GENEXE* environment variables receive a full path to *pwd* program.

OrcaExamples modified by TimN

TimN — Sun, 23 Nov 2014 09:38:15 -0000

--- v13
+++ v14
@@ -94,6 +94,37 @@

 --------------------------------------------------------

+A notes for ORCA post-3.0.0 users
+------------
+
+The following sections require creation of a .47 file with ORCA by using its built-in abilities
+(using *NPA* keyword). However, if the version of ORCA is greater than 3.0.0 this ability will not
+work by default due to the fact that ORCA will try to find an executable of an original NBO
+program and will not proceed if this executable is not found. Here is a simple trick to overcome 
+this limitation. 
+Before running ORCA program simply set *NBOEXE* and *GENEXE* environment variables to *some* program 
+which can be run and which will finish without an error (returning a zero exit code) regardless of
+the command line parameters passed to that program. A good candidate for such a program in Linux
+is a standard executable file named *pwd*. Here is an example of a Linux script which does that
+
+    #!/bin/bash
+    export NBOEXE=pwd
+    export GENEXE=pwd
+    orca file.inp > file.out
+
+(we assume that *orca* executable can be found in a system's *PATH*). Another variation of the same
+script can be as follows
+
+    #!/bin/bash
+    export NBOEXE=`which pwd`
+    export GENEXE=`which pwd`
+    orca file.inp > file.out
+
+so that *NBOEXE* and *GENEXE* environment variables receive a full path to *pwd* program.
+
+
+
+
 QCISD example
 --------

OrcaExamples modified by TimN

TimN — Thu, 07 Aug 2014 13:34:34 -0000

--- v12
+++ v13
@@ -149,7 +149,7 @@
 Note the `-ignorefock` option, which disables the transformation of the Fock matrix into
 NAO basis. This is necessary since no Fock matrix is available for QCISD method.

-You can [Download](http://sourceforge.net/projects/janpa/files/v1.0/example_orca3_qcisd.zip/download) the files of this example.
+You can [Download](http://janpa.sourceforge.net/get.php?file=example_orca3_qcisd.zip) the files of this example.

 --------------------------------------------------------

@@ -203,7 +203,7 @@
 Note the `-ignorefock` option, which disables the transformation of the Fock matrix into
 NAO basis. This is necessary since no Fock matrix is available for CCSD method.

-You can [Download](http://sourceforge.net/projects/janpa/files/v1.0/example_orca3_ccsd.zip/download) the files of this example.
+You can [Download](http://janpa.sourceforge.net/get.php?file=example_orca3_ccsd.zip) the files of this example.

 --------------------------------------------------------

OrcaExamples modified by TimN

TimN — Wed, 11 Jun 2014 20:50:09 -0000

--- v11
+++ v12
@@ -206,3 +206,5 @@
 You can [Download](http://sourceforge.net/projects/janpa/files/v1.0/example_orca3_ccsd.zip/download) the files of this example.

 --------------------------------------------------------
+
+

OrcaExamples modified by TimN

TimN — Wed, 11 Jun 2014 20:29:16 -0000

--- v10
+++ v11
@@ -46,10 +46,13 @@
 it uses only the basis sets defined with 'pure' spherical harmonics while still popular
 Pople's basis sets (6-31G etc) were defined in with 'Cartesian' spherical harmonics.

+--------------------------------------------------------

 Hartree-Fock/DFT methods
 ----
 (to be written)
+
+--------------------------------------------------------

 MP2
 ----
@@ -64,8 +67,10 @@
         end

-
-Non-variational post-SCF methods (Configuration Interaction, Coupled Cluster)
+--------------------------------------------------------
+
+
+General notes for non-variational post-SCF methods (Configuration Interaction, Coupled Cluster)
 ----
 We begin with a quote from ORCA documentation:

@@ -87,6 +92,7 @@

 This will work together with CCSD or QCISD (ORCA's documentation adds that *QCISD and CCSD are identical in the case of OOCCD because of the absence of single excitations*). Note also that an unrelaxed density for CCSD(T) is NOT available in ORCA.

+--------------------------------------------------------

 QCISD example
 --------
@@ -145,6 +151,7 @@

 You can [Download](http://sourceforge.net/projects/janpa/files/v1.0/example_orca3_qcisd.zip/download) the files of this example.

+--------------------------------------------------------

 CCSD example
 ----
@@ -197,3 +204,5 @@
 NAO basis. This is necessary since no Fock matrix is available for CCSD method.

 You can [Download](http://sourceforge.net/projects/janpa/files/v1.0/example_orca3_ccsd.zip/download) the files of this example.
+
+--------------------------------------------------------

OrcaExamples modified by TimN

TimN — Wed, 11 Jun 2014 20:25:20 -0000

--- v9
+++ v10
@@ -1,5 +1,7 @@
 Use of JANPA with ORCA
 =====
+
+(tested in [Orca](http://cec.mpg.de/forum/) 3.0.0)

 Some introductory notes
 ----
@@ -110,7 +112,7 @@
           H   0.56001869207061      0.24271844000000      0.00000000000000 
         * 

-With this input, ORCA will produce `bh_oo_oo.gbw` and `bh_oo_oo.mdcip.47`. Both of them are needed
+With this input, ORCA will produce `bh_oo_oo.gbw` and `bh_oo_oo.mdcip.47` files. Both of them are needed
 for generation of MOLDEN file for JANPA.

 * Use `orca_2mkl` program to prepare MOLDEN-semi-compatible file with SCF molecular orbitals:
@@ -142,3 +144,56 @@
 NAO basis. This is necessary since no Fock matrix is available for QCISD method.

 You can [Download](http://sourceforge.net/projects/janpa/files/v1.0/example_orca3_qcisd.zip/download) the files of this example.
+
+
+CCSD example
+----
+
+A flowchart here is very similar to QCISD example.
+
+Input file (say, `HCl.inp`)
+
+        %MaxCore 2800
+        %pal nprocs 2
+        end
+        
+        
+        %mdci
+         citype CCSD
+         Denmat orbopt
+         density orbopt
+        end
+        
+        ! CCSD cc-pvqz NPA
+        *xyz 0 1 
+            H            0.000000000000     0.000000000000    -1.237032722757
+            CL           0.000000000000     0.000000000000     0.035652086010
+        * 
+
+With this input, ORCA will produce `HCl.gbw` and `HCl.mdcip.47` files. Both of them are needed
+for generation of MOLDEN file for JANPA.
+
+* Use `orca_2mkl` program to prepare MOLDEN-semi-compatible file with SCF molecular orbitals:
+
+        ./orca_2mkl HCl -molden 
+
+here `HCl` is the name of .gbw file (without extension!). This command will produce MOLDEN-semi-
+compatible file `HCl.molden.input` with SCF molecular orbitals from the Hartree-Fock step of 
+CCSD calculation.
+
+* Use `molden2molden` to convert basis set data from `HCl.molden.input` to a conventional
+MOLDEN format and to suppress SCF MO coefficient with CCSD natural orbitals:
+
+        java -jar molden2molden.jar -i HCl.molden.input -o HCl.PURE -fromorca3bf -orca3signs -ds47 HCl.mdcip.47  > M2M.log
+
+This command will create `HCl.PURE ` file which is conventional MOLDEN file and can
+be used for further analysis with Janpa as well as for orbital visualization (in MOLDEN, JMOL etc.).
+
+* Run `janpa` to perform analysis
+
+        java -jar janpa.jar -i HCl.PURE -ignorefock > HCl.JANPA
+
+Note the `-ignorefock` option, which disables the transformation of the Fock matrix into
+NAO basis. This is necessary since no Fock matrix is available for CCSD method.
+
+You can [Download](http://sourceforge.net/projects/janpa/files/v1.0/example_orca3_ccsd.zip/download) the files of this example.

OrcaExamples modified by TimN

TimN — Wed, 11 Jun 2014 20:17:24 -0000

--- v8
+++ v9
@@ -141,4 +141,4 @@
 Note the `-ignorefock` option, which disables the transformation of the Fock matrix into
 NAO basis. This is necessary since no Fock matrix is available for QCISD method.

-You can [Download]() the files of this example.
+You can [Download](http://sourceforge.net/projects/janpa/files/v1.0/example_orca3_qcisd.zip/download) the files of this example.

OrcaExamples modified by TimN

TimN — Wed, 11 Jun 2014 20:15:37 -0000

--- v7
+++ v8
@@ -115,7 +115,30 @@

 * Use `orca_2mkl` program to prepare MOLDEN-semi-compatible file with SCF molecular orbitals:

+        ./orca_2mkl bh_oo_oo -molden 
+
+here `bh_oo_oo` is the name of .gbw file (without extension!). This command will produce MOLDEN-semi-
+compatible file `bh_oo_oo.molden.input` with SCF molecular orbitals from the Hartree-Fock step of 
+QCISD calculation.
+
 * Use `molden2molden` to convert basis set data from `bh_oo_oo.molden.input` to a conventional
 MOLDEN format and to suppress SCF MO coefficient with QCISD natural orbitals:

+        java -jar molden2molden.jar -i bh_oo_oo.molden.input -o bh_oo_oo.PURE -fromorca3bf -orca3signs -ds47 bh_oo_oo.mdcip.47  > M2M.log
+
+where `> M2M.log` is optional, `-fromorca3bf -orca3signs` convert ORCA-style MOLDEN file to a
+conventional MOLDEN file, while `-ds47 bh_oo_oo.mdcip.47` instructs `molden2molden` program
+to suppress molecular orbitals from `bh_oo_oo.molden.input` with those generated from 
+the density matrix from `bh_oo_oo.mdcip.47` by its diagonalization (performed internally
+by `molden2molden`).
+This command will create `bh_oo_oo.PURE` file which is conventional MOLDEN file and can
+be used for further analysis with Janpa as well as for orbital visualization (in MOLDEN, JMOL etc.).
+
 * Run `janpa` to perform analysis
+
+        java -jar janpa.jar -i bh_oo_oo.PURE -ignorefock > bh_oo_oo.JANPA
+
+Note the `-ignorefock` option, which disables the transformation of the Fock matrix into
+NAO basis. This is necessary since no Fock matrix is available for QCISD method.
+
+You can [Download]() the files of this example.

OrcaExamples modified by TimN

TimN — Wed, 11 Jun 2014 19:58:31 -0000

--- v6
+++ v7
@@ -86,3 +86,36 @@
 This will work together with CCSD or QCISD (ORCA's documentation adds that *QCISD and CCSD are identical in the case of OOCCD because of the absence of single excitations*). Note also that an unrelaxed density for CCSD(T) is NOT available in ORCA.

+QCISD example
+--------
+
+Input file (say, `bh_oo_oo.inp`)
+
+        %MaxCore 2800
+        %pal nprocs 2
+        end 
+        
+        
+        %mdci 
+          citype QCISD
+          density orbopt
+          Denmat orbopt
+        end
+        
+        
+        ! QCISD cc-pvtz VeryTightSCF NPA
+        
+        *xyz 0 1
+          B   -0.67451701207061      0.24271844000000      0.00000000000000
+          H   0.56001869207061      0.24271844000000      0.00000000000000 
+        * 
+
+With this input, ORCA will produce `bh_oo_oo.gbw` and `bh_oo_oo.mdcip.47`. Both of them are needed
+for generation of MOLDEN file for JANPA.
+
+* Use `orca_2mkl` program to prepare MOLDEN-semi-compatible file with SCF molecular orbitals:
+
+* Use `molden2molden` to convert basis set data from `bh_oo_oo.molden.input` to a conventional
+MOLDEN format and to suppress SCF MO coefficient with QCISD natural orbitals:
+
+* Run `janpa` to perform analysis