Update

Parallelism.md

@@ -12,7 +12,7 @@ the running program.
 
 The typical scheme is the following:
 
-1. The program (IRPF90) asks `qp_run` to create a new queue for a state of the calculation
+1. The program (Fortran) asks `qp_run` to create a new queue for a state of the calculation
 
 2. The program adds multiple tasks to do to the queue
 
@@ -105,3 +105,9 @@ Now, the main thread can send an `End_job` message to the scheduler to inform
 it that the parallel task is done.
 
 
+MPI layer
+---------
+
+The ZeroMQ slave can be an MPI program. In that case, MPI is used to broadcast large arrays such
+as the wave function, and the input data which are read only by the MPI master. But the communication
+between the ZeroMQ slave and the ZeroMQ master is still done via ZeroMQ.

Requirements.md

@@ -10,4 +10,4 @@
 * EMSL_Basis_Set_Exchange_Local : https://github.com/TApplencourt/EMSL_Basis_Set_Exchange_Local
 * Zlib : http://zlib.net
 * GNU patch : http://savannah.gnu.org/projects/patch
-* ZeroMQ : http://zeromq.org/
+* ZeroMQ : http://zeromq.org/

Tutorial.md

@@ -27,15 +27,31 @@ First, create an `xyz` file containing the coordinates of the molecule. The file
  N    0.0    0.0    -1.156
 ```
 
+Note that you can also input the coordinates using a Z-matrix:
+
+```
+ c
+ n   1 nc2
+ h   1 hc3         2 hcn3
+
+nc2         1.156
+hc3         1.064
+hcn3        180.0
+
+```
+
+
 Now, this `xyz` file is used to generate an `EZFIO` input directory using the ``qp_create_ezfio_from_xyz`` command. The main options of that command are
 
 ```
   -b string      Name of basis set.
+  [-au]          Input geometry is in atomic units.
   [-c int]       Total charge of the molecule. Default is 0.
+  [-cart]        Compute AOs in the Cartesian basis set (6d, 10f, ...)
   [-d float]     Add dummy atoms. x * (covalent radii of the atoms)
   [-m int]       Spin multiplicity (2S+1) of the molecule. Default is 1.
   [-o file]      Name of the created EZFIO file.
-  [-p string]    Using pseudopotentials
+  [-p string]    Name of the pseudopotential
 ```
 
 To generate ``hcn.ezfio`` in the 6-31G basis set, we use::
@@ -43,25 +59,39 @@ To generate ``hcn.ezfio`` in the 6-31G basis set, we use::
 `qp_create_ezfio_from_xyz -b "6-31G" hcn.xyz`
 
 
-You can edit interactively the EZFIO file with all the options available for all the binaries installed using the `qp_edit` command.
+With the `qp_edit` command, you can edit interactively the EZFIO file with all the options available for all the binaries installed.
 
 # Run the SCF and Full-CI calculations
 
 First, create the canonical MOs by running an SCF calculation::
+
 ```
   qp_run SCF hcn.ezfio
 ```
 The expected SCF energy is -92.8278567 au.
 
-Now we want to run the Full-CI calculation. Type
+In the selected FCI calculation, by default the program will stop when the 1.000.000 most important determinants are selected, or when the PT2 correction is below 1.e-4.
+To make a quick test, we want to stop for 10.000 determinants. 
+To change this behavior, edit ``hcn.ezfio`` to modify the options of the selected Full-CI calculation::
+
+```
+  qp_edit hcn.ezfio
+```
+
+This will open a temporary file enabling the modification of the EZFIO directory. Search for the `Determinants` section, and set the ``n_det_max`` option to 10000::
+
+```
+  n_det_max = 10000
+```
+
+Now we can run the Full-CI calculation. Type
 
 ```
   qp_run fci_zmq hcn.ezfio
 ```
 
-By default, this will select the most important 10.000 determinants in the wave-function (this number is set by the `determinants/n_det_max` variable). When this point is reached, the second order perturbative correction is computed (handled by the `do_pt2_end` variable) to generate a really good approximation of the full-ci.
 
-The variational energy should be '-93.043096' and the Full-CI approximation energy should be '-93.051924'.
+The variational energy should be '-93.044945' and the Full-CI approximate energy should be '-93.052019'.
 
 # Freeze core electrons in the CI
 
@@ -74,7 +104,7 @@ Then run the SCF
 ```
   qp_run SCF hcn_large.ezfio
 ```
-The expected SCF energy is -92.8832967.
+The expected SCF energy is -92.8829467.
 
 We want to run the selected Full-CI calculation in the valence only. For this, we will use the ``qp_set_mo_class`` utility. The options are
 ```
@@ -86,15 +116,20 @@ We want to run the selected Full-CI calculation in the valence only. For this, w
 ```
 
 We set 2 first canonical orbitals as `core` and all the remaining MOs are set as active ::
+
 ```
-  qp_set_mo_class hcn_large.ezfio -core "[1,2]" -act "[3-35]"
+  qp_set_mo_class hcn_large.ezfio -core "[1,2]" -act "[3-33]"
 ```
 
 or we can do it automatically:
+
 ```
   qp_set_frozen_core.py hcn_large.ezfio
 ```
 
+The `qp_set_frozen_core.py` script finds the heavy atoms and proposes a set of
+core and active MOs.  For atoms with few electrons in the valence such as Li or
+Na, the script will propose a small core.
 
 Then, edit ``hcn_large.ezfio`` to modify the options of the selected Full-CI calculation::
 ```
@@ -102,26 +137,25 @@ Then, edit ``hcn_large.ezfio`` to modify the options of the selected Full-CI cal
 ```
 
 This will open a temporary file enabling the modification of the EZFIO directory. Search for the `Determinants` section, and set the ``n_det_max`` option to 10000::
+
 ```
   n_det_max = 10000
 ```
-De-activate the calculation of the PT2-energy::
-```
-  do_pt2_end = false
-```
+
 And run the Full-CI calculation::
+
 ```
   qp_run fci_zmq hcn_large.ezfio
 ```
-The expected variational energy is -93.16819314.
+
+The expected variational energy is -93.16482111.
 
 From the current wave function, we can generate the corresponding natural orbitals::
+
 ```
   qp_run save_natorb hcn_large.ezfio
 ```
-Re-activate the calculation of the PT2-energy using qp_edit::
-```
-  do_pt2_end = true
-```
-And run the calculation again. The expected variational energy is -93.176409148 and the energy + the PT2 contribution is -93.194541427.
+
+and run the selected FCI calculation again.
+The expected variational energy is -93.172895441 and the energy + the PT2 contribution is -93.19059084.