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Anthony Scemama 2017-12-18 12:18:08 +01:00
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8
Parallelism.md

@ -12,7 +12,7 @@ the running program.
The typical scheme is the following: 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 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. 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.

68
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 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 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. -b string Name of basis set.
[-au] Input geometry is in atomic units.
[-c int] Total charge of the molecule. Default is 0. [-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) [-d float] Add dummy atoms. x * (covalent radii of the atoms)
[-m int] Spin multiplicity (2S+1) of the molecule. Default is 1. [-m int] Spin multiplicity (2S+1) of the molecule. Default is 1.
[-o file] Name of the created EZFIO file. [-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:: 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` `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 # Run the SCF and Full-CI calculations
First, create the canonical MOs by running an SCF calculation:: First, create the canonical MOs by running an SCF calculation::
``` ```
qp_run SCF hcn.ezfio qp_run SCF hcn.ezfio
``` ```
The expected SCF energy is -92.8278567 au. 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 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 # Freeze core electrons in the CI
@ -74,7 +104,7 @@ Then run the SCF
``` ```
qp_run SCF hcn_large.ezfio 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 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 :: 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: or we can do it automatically:
``` ```
qp_set_frozen_core.py hcn_large.ezfio 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:: 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:: 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 n_det_max = 10000
``` ```
De-activate the calculation of the PT2-energy::
```
do_pt2_end = false
```
And run the Full-CI calculation:: And run the Full-CI calculation::
``` ```
qp_run fci_zmq hcn_large.ezfio 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:: From the current wave function, we can generate the corresponding natural orbitals::
``` ```
qp_run save_natorb hcn_large.ezfio qp_run save_natorb hcn_large.ezfio
``` ```
Re-activate the calculation of the PT2-energy using qp_edit::
``` and run the selected FCI calculation again.
do_pt2_end = true The expected variational energy is -93.172895441 and the energy + the PT2 contribution is -93.19059084.
```
And run the calculation again. The expected variational energy is -93.176409148 and the energy + the PT2 contribution is -93.194541427.