10
1
mirror of https://gitlab.com/scemama/qmcchem.git synced 2024-10-13 03:21:31 +02:00
qmcchem/README.md

259 lines
7.2 KiB
Markdown
Raw Permalink Normal View History

2015-12-18 21:23:12 +01:00
QMC=Chem : Quantum Monte Carlo for Chemistry
2015-12-18 22:12:04 +01:00
============================================
QMC=Chem is the quantum Monte Carlo program of the
2015-12-20 01:43:22 +01:00
[Toulouse (France) group](http://qmcchem.ups-tlse.fr).
2015-12-18 22:12:04 +01:00
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
2015-12-29 01:16:19 +01:00
in Cloud environments (France Grilles) coupled to supercomputers
2015-12-18 22:12:04 +01:00
2015-12-19 03:29:52 +01:00
Warnings:
* 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.
2015-12-18 22:12:04 +01:00
2015-12-18 22:25:32 +01:00
Requirements
------------
2016-01-06 00:50:48 +01:00
* [OCaml compiler with Opam and Core library](http://github.com/ocaml)
2015-12-20 01:09:14 +01:00
* [ZeroMQ high performance communication library](http://www.zeromq.org)
* [F77_ZMQ ZeroMQ Fortran interface](http://github.com/scemama/f77_zmq/)
* [IRPF90 Fortran code generator](http://irpf90.ups-tlse.fr)
* [EZFIO Easy Fortran I/O library generator](http://github.com/scemama/EZFIO)
2019-09-30 20:09:54 +02:00
* GNU C++ Compiler (g++) for ZeroMQ
2015-12-20 01:09:14 +01:00
* Python >= 2.6 for install scripts
2015-12-29 01:16:19 +01:00
* Bash for install scripts
2015-12-20 01:09:14 +01:00
* Fortran compiler, Intel Fortran recommended
* Lapack library, Intel MKL recommended
2020-11-02 18:07:04 +01:00
Most of the dependencies are open-source can be downloaded automatically by
going into the `install` directory and running `make`. It will first download
into the `install/Downloads` directory everything that needs to be installed.
The building of the dependencies takes place in the `install/_build`
2015-12-29 01:16:19 +01:00
directory, and the packages that are being installed can be followed by looking
at the log files in this directory. When a package was successfully installed,
2020-11-02 18:07:04 +01:00
a `*.ok` file is created and the log file is deleted.
2015-12-29 01:16:19 +01:00
If you don't have an internet connection available, you can execute the
downloading step on another computer and transfer all the downloaded files
2020-11-02 18:07:04 +01:00
into the `Downloads` directory.
The Fortran and C++ compilers, Python and Bash interpreters and the Lapack
library need to be installed manually by the user.
Installation
------------
2015-12-29 01:16:19 +01:00
2020-11-02 18:07:04 +01:00
The `make.config` file contains compiler specific parameters. You should change
them to match your hardware. You can copy the `make.config.ifort` or
`make.config.gfortran` as a starting point.
2015-12-20 01:09:14 +01:00
Before using or compiling QMC=Chem, environment variables need to be loaded. The
2020-11-02 18:07:04 +01:00
environment variables are located in the `qmcchemrc` file:
2015-12-20 01:09:14 +01:00
```bash
$ source qmcchemrc
```
2020-11-02 18:07:04 +01:00
The `QMCCHEM_NIC` environment variable should be set to the proper network interface,
usually `ib0` on HPC machines.
2019-09-30 20:09:54 +02:00
2015-12-20 01:09:14 +01:00
To compile the program, run
```bash
2019-09-30 20:09:54 +02:00
$ make
2015-12-20 01:09:14 +01:00
```
2015-12-18 22:25:32 +01:00
2015-12-18 22:12:04 +01:00
Example of a QMC=Chem calculation
---------------------------------
2019-09-30 20:09:54 +02:00
1.Calculation with the [quantum package](http://github.com/QuantumPackage/qp2)
2015-12-18 22:12:04 +01:00
Create the `xyz` file containing the nuclear coordinates of the system
```bash
2015-12-18 22:12:04 +01:00
$ cat > h2o.xyz << EOF
3
Water molecule
O 0. 0. 0.
H 0.9572 0. 0.
H -0.239987 0.926627 0.
EOF
```
Choose a suitable basis set and create the [EZFIO database](https://github.com/LCPQ/ezfio)
2015-12-18 22:12:04 +01:00
```bash
2019-09-30 20:09:54 +02:00
$ qp_create_ezfio -b cc-pvdz h2o.xyz -o h2o
2015-12-18 22:12:04 +01:00
```
Run the SCF calculation
2015-12-18 22:12:04 +01:00
```bash
2019-09-30 20:09:54 +02:00
$ qp_run scf h2o
2015-12-18 22:12:04 +01:00
```
Run the CIPSI calculation
2015-12-18 22:12:04 +01:00
```bash
2019-09-30 20:09:54 +02:00
$ qp_run fci h2o
2015-12-18 22:12:04 +01:00
```
Transform the input for use in QMC=Chem
2015-12-18 22:12:04 +01:00
```bash
$ qp_run save_for_qmcchem h2o
```
2.FN-DMC calculation with QMC=Chem
2015-12-18 22:12:04 +01:00
Before using QMC=Chem, you need to load the environment variables:
```bash
2019-09-30 20:09:54 +02:00
$ source qmcchemrc
2015-12-18 22:12:04 +01:00
```
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:
2015-12-29 01:16:19 +01:00
```
2015-12-18 22:12:04 +01:00
$ 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
2015-12-29 01:16:19 +01:00
```
2015-12-18 22:12:04 +01:00
$ 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)
2015-12-29 02:19:08 +01:00
[Quantum Monte Carlo with very large multideterminant wavefunctions](http://arxiv.org/abs/1510.00730)
2015-12-29 01:16:19 +01:00
> Anthony Scemama , Thomas Applencourt , Emmanuel Giner and Michel Caffarel (2015), in: ArXiv ePrints:arXiv:1510.00730v2 [physics.chem-ph]
2015-12-18 22:12:04 +01:00