mirror of
https://gitlab.com/scemama/qmcchem.git
synced 2024-10-04 23:35:58 +02:00
Improved README.md
This commit is contained in:
parent
70d2ccdaa9
commit
33637e1ed4
203
README.md
203
README.md
@ -1,2 +1,203 @@
|
|||||||
# qmcchem
|
|
||||||
QMC=Chem : Quantum Monte Carlo for Chemistry
|
QMC=Chem : Quantum Monte Carlo for Chemistry
|
||||||
|
============================================
|
||||||
|
|
||||||
|
|
||||||
|
QMC=Chem is the quantum Monte Carlo program of the
|
||||||
|
[Toulouse group](http://qmcchem.ups-tlse.fr).
|
||||||
|
It is meant to be used in the *post-Full-CI* context : a quasi-Full-CI
|
||||||
|
calculation is done with the
|
||||||
|
[quantum package](https://github.com/LCPQ/quantum_package),
|
||||||
|
and this wave function is used as a trial wave function for the fixed-node
|
||||||
|
diffusion Monte Carlo algorithm.
|
||||||
|
|
||||||
|
|
||||||
|
* Parallel efficiency of 98.3% on 16_000 cores
|
||||||
|
* The load balancing is optimal: the workers always work 100% of the time,
|
||||||
|
independently of their respective CPU speeds
|
||||||
|
* Efficient: 0.96 Pflops/s on 76_800 cores of Curie in 2011
|
||||||
|
* All network communications are non-blocking,
|
||||||
|
with the [ZeroMQ](http://zeromq.org) library
|
||||||
|
* All the implemented algorithms are CPU-bound : the only limit
|
||||||
|
is the available CPU time
|
||||||
|
* The number of simultaneous worker nodes can be variable during a calculation
|
||||||
|
* Fully fault-tolerant (crashing nodes don't stop the running calculation)
|
||||||
|
* QMC=Chem has been used in grid environments (EGI european grid) and
|
||||||
|
in Cloud environments (rance Grilles) coupled to supercomputers
|
||||||
|
|
||||||
|
|
||||||
|
*Warning*: QMC=Chem is under the GPLv2 license. Any modifications to or
|
||||||
|
software including (via compiler) GPL-licensed code must also be made available
|
||||||
|
under the GPL along with build & install instructions.
|
||||||
|
|
||||||
|
Example of a QMC=Chem calculation
|
||||||
|
---------------------------------
|
||||||
|
|
||||||
|
Calculation with the quantum package
|
||||||
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||||
|
|
||||||
|
1) Create the ``xyz`` file containing the nuclear coordinates of the system
|
||||||
|
|
||||||
|
```bash
|
||||||
|
$ cat > h2o.xyz << EOF
|
||||||
|
3
|
||||||
|
Water molecule
|
||||||
|
O 0. 0. 0.
|
||||||
|
H 0.9572 0. 0.
|
||||||
|
H -0.239987 0.926627 0.
|
||||||
|
EOF
|
||||||
|
```
|
||||||
|
|
||||||
|
2) Choose a suitable basis set and create the [EZFIO database](https://github.com/LCPQ/ezfio)
|
||||||
|
|
||||||
|
```bash
|
||||||
|
$ qp_create_ezfio_from_xyz -b cc-pvdz h2o.xyz -o h2o
|
||||||
|
```
|
||||||
|
|
||||||
|
3) Run the SCF calculation
|
||||||
|
|
||||||
|
```bash
|
||||||
|
$ qp_run SCF h2o
|
||||||
|
```
|
||||||
|
4) Run the CIPSI calculation
|
||||||
|
|
||||||
|
```bash
|
||||||
|
$ qp_run full_ci h2o
|
||||||
|
```
|
||||||
|
|
||||||
|
5) Transform the input for use in QMC=Chem
|
||||||
|
|
||||||
|
```bash
|
||||||
|
$ qp_run save_for_qmcchem h2o
|
||||||
|
```
|
||||||
|
|
||||||
|
FN-DMC calculation with QMC=Chem
|
||||||
|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
|
||||||
|
|
||||||
|
Before using QMC=Chem, you need to load the environment variables:
|
||||||
|
|
||||||
|
```bash
|
||||||
|
$ source qmcchem.rc
|
||||||
|
```
|
||||||
|
|
||||||
|
In QMC=Chem, everything goes through the use of the ``qmcchem`` command.
|
||||||
|
When a command is run with no arguments, it prints a help message.
|
||||||
|
This is mainly the manual of QMC=Chem. For example:
|
||||||
|
|
||||||
|
```bash
|
||||||
|
$ qmcchem
|
||||||
|
QMC=Chem command
|
||||||
|
|
||||||
|
qmcchem SUBCOMMAND
|
||||||
|
|
||||||
|
=== subcommands ===
|
||||||
|
|
||||||
|
debug Debug ZeroMQ communications
|
||||||
|
edit Edit input data
|
||||||
|
md5 Manipulate input MD5 keys
|
||||||
|
result Displays the results computed in an EZFIO directory.
|
||||||
|
run Run a calculation
|
||||||
|
stop Stop a running calculation
|
||||||
|
version print version information
|
||||||
|
help explain a given subcommand (perhaps recursively)
|
||||||
|
|
||||||
|
missing subcommand for command qmcchem
|
||||||
|
|
||||||
|
$ qmcchem edit
|
||||||
|
Run a calculation
|
||||||
|
|
||||||
|
qmcchem run EZFIO_FILE
|
||||||
|
|
||||||
|
|
||||||
|
Run QMC=Chem
|
||||||
|
|
||||||
|
|
||||||
|
=== flags ===
|
||||||
|
|
||||||
|
[-a] Add more resources to a running calculation.
|
||||||
|
[-d] Start a dataserver process on the local host.
|
||||||
|
[-q <dataserver_addr>] Start a qmc process on the local host.
|
||||||
|
[-s <host>] Start a qmc process on <host>.
|
||||||
|
[-help] print this help text and exit
|
||||||
|
(alias: -?)
|
||||||
|
|
||||||
|
missing anonymous argument: EZFIO_FILE
|
||||||
|
```
|
||||||
|
|
||||||
|
1) Set the parameters for a VMC calculation to create initial walker positions
|
||||||
|
|
||||||
|
```bash
|
||||||
|
$ qmcchem edit -h
|
||||||
|
Edit input data
|
||||||
|
|
||||||
|
qmcchem edit EZFIO_FILE [INPUT]
|
||||||
|
|
||||||
|
|
||||||
|
Edit input data
|
||||||
|
|
||||||
|
|
||||||
|
=== flags ===
|
||||||
|
|
||||||
|
[-c] Clear blocks
|
||||||
|
[-e energy] Fixed reference energy to normalize DMC weights
|
||||||
|
[-f 0|1] Correct wave function to verify electron-nucleus cusp
|
||||||
|
condition
|
||||||
|
[-j jastrow_type] Type of Jastrow factor [ None | Core | Simple ]
|
||||||
|
[-l seconds] Length (seconds) of a block
|
||||||
|
[-m method] QMC Method : [ VMC | DMC ]
|
||||||
|
[-n norm] Truncation t of the wave function : Remove determinants
|
||||||
|
with a
|
||||||
|
contribution to the norm less than t
|
||||||
|
[-s sampling] Sampling algorithm : [ Langevin | Brownian ]
|
||||||
|
[-t seconds] Requested simulation time (seconds)
|
||||||
|
[-ts time_step] Simulation time step
|
||||||
|
[-w walk_num] Number of walkers per CPU core
|
||||||
|
[-wt walk_num_tot] Total number of stored walkers for restart
|
||||||
|
[-help] print this help text and exit
|
||||||
|
(alias: -?)
|
||||||
|
|
||||||
|
$ qmcchem edit h2o -f 1 -m VMC -n 1.e-5 -s Langevin -t 300 -l 10
|
||||||
|
```
|
||||||
|
|
||||||
|
3) Get info on the wave function
|
||||||
|
|
||||||
|
```bash
|
||||||
|
$ qmcchem info h2o
|
||||||
|
```
|
||||||
|
|
||||||
|
4) Run the VMC calculation
|
||||||
|
|
||||||
|
```bash
|
||||||
|
$ qmcchem run h2o
|
||||||
|
```
|
||||||
|
|
||||||
|
5) Set the correct parameters for FN-DMC
|
||||||
|
|
||||||
|
```bash
|
||||||
|
$ qmcchem edit h2o -e -76.438 -m DMC -s Brownian -ts 3.e-4 -t 3600 -l 30
|
||||||
|
```
|
||||||
|
|
||||||
|
6) Run the FN-DMC calculation
|
||||||
|
|
||||||
|
```bash
|
||||||
|
$ qmcchem run h2o
|
||||||
|
```
|
||||||
|
|
||||||
|
7) Print the result
|
||||||
|
|
||||||
|
```bash
|
||||||
|
$ qmcchem result h2o
|
||||||
|
|
||||||
|
```
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
References
|
||||||
|
----------
|
||||||
|
|
||||||
|
[Quantum Monte Carlo for large chemical systems: Implementing efficient strategies for petascale platforms and beyond](http://dx.doi.org/10.1002/jcc.23216)
|
||||||
|
> Anthony Scemama , Michel Caffarel , Emmanuel Oseret and William Jalby (2013), in: Journal of Computational Chemistry, 34:11(938--951)
|
||||||
|
|
||||||
|
[Quantum Monte Carlo with very large multideterminant wavefunctions](http://arxiv.org/abs/1509.03114)
|
||||||
|
> Anthony Scemama , Thomas Applencourt , Emmanuel Giner and Michel Caffarel (2015), in: ArXiv ePrints:arXiv:1510.00730 [physics.chem-ph]
|
||||||
|
|
||||||
|
Loading…
Reference in New Issue
Block a user