mirror of https://gitlab.com/scemama/qmcchem.git
259 lines
7.2 KiB
Markdown
259 lines
7.2 KiB
Markdown
QMC=Chem : Quantum Monte Carlo for Chemistry
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============================================
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QMC=Chem is the quantum Monte Carlo program of the
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[Toulouse (France) group](http://qmcchem.ups-tlse.fr).
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It is meant to be used in the *post-Full-CI* context : a quasi-Full-CI
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calculation is done with the
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[quantum package](https://github.com/LCPQ/quantum_package),
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and this wave function is used as a trial wave function for the fixed-node
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diffusion Monte Carlo algorithm.
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* Parallel efficiency of 98.3% on 16_000 cores
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* The load balancing is optimal: the workers always work 100% of the time,
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independently of their respective CPU speeds
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* Efficient: 0.96 Pflops/s on 76_800 cores of Curie in 2011
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* All network communications are non-blocking,
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with the [ZeroMQ](http://zeromq.org) library
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* All the implemented algorithms are CPU-bound : the only limit
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is the available CPU time
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* The number of simultaneous worker nodes can be variable during a calculation
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* Fully fault-tolerant (crashing nodes don't stop the running calculation)
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* QMC=Chem has been used in grid environments (EGI european grid) and
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in Cloud environments (France Grilles) coupled to supercomputers
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Warnings:
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* QMC=Chem is under the GPLv2 license. Any modifications to or
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software including (via compiler) GPL-licensed code must also be made available
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under the GPL along with build & install instructions.
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Requirements
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------------
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* [OCaml compiler with Opam and Core library](http://github.com/ocaml)
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* [ZeroMQ high performance communication library](http://www.zeromq.org)
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* [F77_ZMQ ZeroMQ Fortran interface](http://github.com/scemama/f77_zmq/)
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* [IRPF90 Fortran code generator](http://irpf90.ups-tlse.fr)
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* [EZFIO Easy Fortran I/O library generator](http://github.com/scemama/EZFIO)
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* GNU C++ Compiler (g++) for ZeroMQ
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* Python >= 2.6 for install scripts
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* Bash for install scripts
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* Fortran compiler, Intel Fortran recommended
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* Lapack library, Intel MKL recommended
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Most of the dependencies are open-source can be downloaded automatically by
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going into the `install` directory and running `make`. It will first download
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into the `install/Downloads` directory everything that needs to be installed.
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The building of the dependencies takes place in the `install/_build`
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directory, and the packages that are being installed can be followed by looking
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at the log files in this directory. When a package was successfully installed,
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a `*.ok` file is created and the log file is deleted.
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If you don't have an internet connection available, you can execute the
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downloading step on another computer and transfer all the downloaded files
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into the `Downloads` directory.
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The Fortran and C++ compilers, Python and Bash interpreters and the Lapack
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library need to be installed manually by the user.
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Installation
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------------
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The `make.config` file contains compiler specific parameters. You should change
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them to match your hardware. You can copy the `make.config.ifort` or
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`make.config.gfortran` as a starting point.
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Before using or compiling QMC=Chem, environment variables need to be loaded. The
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environment variables are located in the `qmcchemrc` file:
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```bash
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$ source qmcchemrc
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```
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The `QMCCHEM_NIC` environment variable should be set to the proper network interface,
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usually `ib0` on HPC machines.
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To compile the program, run
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```bash
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$ make
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```
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Example of a QMC=Chem calculation
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---------------------------------
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1.Calculation with the [quantum package](http://github.com/QuantumPackage/qp2)
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Create the `xyz` file containing the nuclear coordinates of the system
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```bash
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$ cat > h2o.xyz << EOF
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3
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Water molecule
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O 0. 0. 0.
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H 0.9572 0. 0.
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H -0.239987 0.926627 0.
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EOF
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```
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Choose a suitable basis set and create the [EZFIO database](https://github.com/LCPQ/ezfio)
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```bash
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$ qp_create_ezfio -b cc-pvdz h2o.xyz -o h2o
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```
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Run the SCF calculation
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```bash
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$ qp_run scf h2o
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```
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Run the CIPSI calculation
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```bash
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$ qp_run fci h2o
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```
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Transform the input for use in QMC=Chem
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```bash
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$ qp_run save_for_qmcchem h2o
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```
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2.FN-DMC calculation with QMC=Chem
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Before using QMC=Chem, you need to load the environment variables:
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```bash
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$ source qmcchemrc
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```
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In QMC=Chem, everything goes through the use of the ``qmcchem`` command.
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When a command is run with no arguments, it prints a help message.
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This is mainly the manual of QMC=Chem. For example:
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```
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$ qmcchem
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QMC=Chem command
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qmcchem SUBCOMMAND
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=== subcommands ===
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debug Debug ZeroMQ communications
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edit Edit input data
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md5 Manipulate input MD5 keys
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result Displays the results computed in an EZFIO directory.
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run Run a calculation
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stop Stop a running calculation
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version print version information
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help explain a given subcommand (perhaps recursively)
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missing subcommand for command qmcchem
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$ qmcchem edit
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Run a calculation
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qmcchem run EZFIO_FILE
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Run QMC=Chem
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=== flags ===
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[-a] Add more resources to a running calculation.
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[-d] Start a dataserver process on the local host.
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[-q <dataserver_addr>] Start a qmc process on the local host.
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[-s <host>] Start a qmc process on <host>.
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[-help] print this help text and exit
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(alias: -?)
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missing anonymous argument: EZFIO_FILE
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```
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1) Set the parameters for a VMC calculation to create initial walker positions
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```
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$ qmcchem edit -h
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Edit input data
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qmcchem edit EZFIO_FILE [INPUT]
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Edit input data
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=== flags ===
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[-c] Clear blocks
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[-e energy] Fixed reference energy to normalize DMC weights
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[-f 0|1] Correct wave function to verify electron-nucleus cusp
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condition
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[-j jastrow_type] Type of Jastrow factor [ None | Core | Simple ]
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[-l seconds] Length (seconds) of a block
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[-m method] QMC Method : [ VMC | DMC ]
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[-n norm] Truncation t of the wave function : Remove determinants
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with a
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contribution to the norm less than t
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[-s sampling] Sampling algorithm : [ Langevin | Brownian ]
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[-t seconds] Requested simulation time (seconds)
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[-ts time_step] Simulation time step
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[-w walk_num] Number of walkers per CPU core
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[-wt walk_num_tot] Total number of stored walkers for restart
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[-help] print this help text and exit
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(alias: -?)
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$ qmcchem edit h2o -f 1 -m VMC -n 1.e-5 -s Langevin -t 300 -l 10
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```
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3) Get info on the wave function
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```bash
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$ qmcchem info h2o
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```
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4) Run the VMC calculation
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```bash
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$ qmcchem run h2o
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```
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5) Set the correct parameters for FN-DMC
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```bash
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$ qmcchem edit h2o -e -76.438 -m DMC -s Brownian -ts 3.e-4 -t 3600 -l 30
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```
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6) Run the FN-DMC calculation
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```bash
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$ qmcchem run h2o
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```
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7) Print the result
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```bash
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$ qmcchem result h2o
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```
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References
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----------
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[Quantum Monte Carlo for large chemical systems: Implementing efficient strategies for petascale platforms and beyond](http://dx.doi.org/10.1002/jcc.23216)
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> Anthony Scemama , Michel Caffarel , Emmanuel Oseret and William Jalby (2013), in: Journal of Computational Chemistry, 34:11(938--951)
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[Quantum Monte Carlo with very large multideterminant wavefunctions](http://arxiv.org/abs/1510.00730)
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> Anthony Scemama , Thomas Applencourt , Emmanuel Giner and Michel Caffarel (2015), in: ArXiv ePrints:arXiv:1510.00730v2 [physics.chem-ph]
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