# Release66:Gaussian Basis AIMD

### From NWChem

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- | Overview | + | ==Overview== |

- | + | ||

This module performs adiabatic ab initio molecular dynamics on finite systems. The nuclei are integrated using the velocity-Verlet algorithm, and the electronic potential can be provided by any of the Gaussian basis set based methods in NWChem, e.g. DFT, TDDFT, TCE, MP2, SCF, MCSCF, etc. If analytic gradients are not available for the selected level of theory, numerical gradients will automatically be used. Initial velocities are randomly selected from the Maxwell-Boltzmann distribution at the specified temperature, unless a restart file (.qmdrst) is present. If a restart file is present, the trajectory information will be read from that file and the trajectory will resume from that point. | This module performs adiabatic ab initio molecular dynamics on finite systems. The nuclei are integrated using the velocity-Verlet algorithm, and the electronic potential can be provided by any of the Gaussian basis set based methods in NWChem, e.g. DFT, TDDFT, TCE, MP2, SCF, MCSCF, etc. If analytic gradients are not available for the selected level of theory, numerical gradients will automatically be used. Initial velocities are randomly selected from the Maxwell-Boltzmann distribution at the specified temperature, unless a restart file (.qmdrst) is present. If a restart file is present, the trajectory information will be read from that file and the trajectory will resume from that point. | ||

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S. A. Fischer, T. W. Ueltschi, P. Z. El-Khoury, A. L. Mifflin, W. P. Hess, H.F. Wang, C. J. Cramer, N. Govind | S. A. Fischer, T. W. Ueltschi, P. Z. El-Khoury, A. L. Mifflin, W. P. Hess, H.F. Wang, C. J. Cramer, N. Govind | ||

"Infrared and Raman Spectroscopy from Ab Initio Molecular Dynamics and Static Normal Mode Analysis: The CH Region of DMSO as a | "Infrared and Raman Spectroscopy from Ab Initio Molecular Dynamics and Static Normal Mode Analysis: The CH Region of DMSO as a | ||

- | Case Study" J. Phys. Chem. B, DOI: 10.1021/acs.jpcb.5b03323 (2015) | + | Case Study" J. Phys. Chem. B, 120 (8), pp 1429–1436 (2016), DOI: 10.1021/acs.jpcb.5b03323 (2015) |

Publication Date (Web): July 29, 2015 | Publication Date (Web): July 29, 2015 | ||

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[com_step <integer default 100>] | [com_step <integer default 100>] | ||

[print_xyz <integer default 1>] | [print_xyz <integer default 1>] | ||

- | [linear] | + | [linear] |

END | END | ||

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where <level of theory> is any Gaussian basis set method in NWChem | where <level of theory> is any Gaussian basis set method in NWChem | ||

- | QMD Keywords | + | ==QMD Keywords== |

- | + | ||

- | + | ||

- | + | ||

- | + | ===dt_nucl -- Nuclear time step=== | |

- | + | ||

- | + | This specifies the nuclear time step in atomic units (1 a.u. = 0.02419 fs). Default 10.0 a.u. | |

- | + | ||

- | thermostat -- Thermostat for controling temperature of the simulation | + | ===nsteps_nucl -- Simulation steps=== |

- | + | ||

- | + | This specifies the number of steps to take in the nuclear dynamics. Default 1000 | |

+ | |||

+ | ===targ_temp -- Temperature of the system=== | ||

+ | |||

+ | This specifies the temperature to use with the thermostat. Also it is used in generating initial velocities from the Maxwell-Boltzmann distribution. Default 298.15 K | ||

+ | |||

+ | ===thermostat -- Thermostat for controling temperature of the simulation=== | ||

+ | |||

+ | This specifies the thermostat to use for regulating the temperature of the nuclei. Possible options are: | ||

+ | *none | ||

No thermostat is used, i.e. an NVE ensemble is simulated. Default | No thermostat is used, i.e. an NVE ensemble is simulated. Default | ||

- | + | *svr <double default 1000.0> | |

Stochastic velocity rescaling thermostat of Bussi, Donadio, and Parrinello J. Chem. Phys. 126, 014101 (2007) | Stochastic velocity rescaling thermostat of Bussi, Donadio, and Parrinello J. Chem. Phys. 126, 014101 (2007) | ||

Number sets the relaxation parameter of the thermostat | Number sets the relaxation parameter of the thermostat | ||

- | + | *langevin <double default 0.1> | |

Langevin dynamics, implementation according to Bussi and Parrinello Phys. Rev. E 75, 056707 (2007) | Langevin dynamics, implementation according to Bussi and Parrinello Phys. Rev. E 75, 056707 (2007) | ||

Number sets the value of the friction | Number sets the value of the friction | ||

- | + | *berendsen <double default 1000.0> | |

Berendsen thermostat, number sets the relaxation parameter of the thermostat | Berendsen thermostat, number sets the relaxation parameter of the thermostat | ||

- | + | *rescale | |

Velocity rescaling, i.e. isokinetic ensemble | Velocity rescaling, i.e. isokinetic ensemble | ||

- | rand_seed -- Seed for the random number generator | + | ===rand_seed -- Seed for the random number generator=== |

- | + | ||

+ | This specifies the seed for initializing the random number generator. If not given, a unique random seed will be generated. Even without a thermostat, this will influence the initial velocities. | ||

+ | |||

+ | ===com_step -- How often center-of-mass translations and rotations are removed=== | ||

+ | |||

+ | This specifies that center-of-mass translations and rotations will be removed every com_step steps. Default 10 | ||

+ | COM translations and rotations are removed on startup (either randomized initial velocities or those read from the restart file). | ||

+ | |||

+ | ===print_xyz -- How often to print trajectory information to xyz file=== | ||

+ | |||

+ | This specifies that the trajectory information (coordinates, velocities, total energy, step number, dipole (if available)) to the xyz file. The units for the coordinates and velocities in the xyz file are Angstrom and Angstrom/fs, respectively. | ||

+ | |||

+ | ===linear -- Flag for linear molecules=== | ||

+ | |||

+ | If present, the code assumes the molecule is linear. | ||

+ | |||

+ | |||

+ | ==Sample input== | ||

+ | |||

+ | The following is a sample input for a ground state MD simulation. The simulation is 200 steps long with a 10 a.u. time step, using the stochastic velocity rescaling thermostat with a relaxation parameter of 100 a.u. and a target temperature of 200 K. Center-of-mass rotations and translations will be removed every 10 steps and trajectory information will be output to the xyz file every 5 steps. | ||

+ | |||

+ | start qmd_dft_h2o_svr | ||

+ | echo | ||

+ | print low | ||

+ | geometry noautosym noautoz | ||

+ | O 0.00000000 -0.01681748 0.11334792 | ||

+ | H 0.00000000 0.81325914 -0.34310308 | ||

+ | H 0.00000000 -0.67863597 -0.56441201 | ||

+ | end | ||

+ | basis | ||

+ | * library 6-31G* | ||

+ | end | ||

+ | dft | ||

+ | xc pbe0 | ||

+ | end | ||

+ | qmd | ||

+ | nstep_nucl 200 | ||

+ | dt_nucl 10.0 | ||

+ | targ_temp 200.0 | ||

+ | com_step 10 | ||

+ | thermostat svr 100.0 | ||

+ | print_xyz 5 | ||

+ | end | ||

+ | task dft qmd | ||

+ | |||

+ | The following is a sample input for an excited state MD simulation on the first excited state. The simulation is 200 steps long with a 10 a.u. time step, run in the microcanonical ensemble. Center-of-mass rotations and translations will be removed every 10 steps and trajectory information will be output to the xyz file every 5 steps. | ||

+ | |||

+ | start qmd_tddft_h2o_svr | ||

+ | echo | ||

+ | print low | ||

+ | geometry noautosym noautoz | ||

+ | O 0.00000000 -0.01681748 0.11334792 | ||

+ | H 0.00000000 0.81325914 -0.34310308 | ||

+ | H 0.00000000 -0.67863597 -0.56441201 | ||

+ | end | ||

+ | basis | ||

+ | * library 6-31G* | ||

+ | end | ||

+ | dft | ||

+ | xc pbe0 | ||

+ | end | ||

+ | tddft | ||

+ | nroots 5 | ||

+ | notriplet | ||

+ | target 1 | ||

+ | civecs | ||

+ | grad | ||

+ | root 1 | ||

+ | end | ||

+ | end | ||

+ | qmd | ||

+ | nstep_nucl 200 | ||

+ | dt_nucl 10.0 | ||

+ | com_step 10 | ||

+ | thermostat none | ||

+ | print_xyz 5 | ||

+ | end | ||

+ | task tddft qmd | ||

+ | |||

+ | Additional sample inputs can be found in $NWCHEM_TOP/QA/tests/qmd_* | ||

+ | |||

+ | ==Processing the output of a QMD run== | ||

+ | |||

+ | The xyz file produced by the QMD module contains the velocities (given in Angstrom/fs), in addition to the coordinates (given in Angstrom). The comment lines also contain the time step, total energy (atomic units), and dipole moment (atomic units). In $NWCHEM_TOP/contrib/qmd_tools is a code that will take the xyz trajectory and calculate the IR spectrum and vibrational density of states from Fourier transforms of the dipole and atomic momenta autocorrelation functions, respectively. The code needs to be linked to a LAPACK library when compiled; the Makefile in the directory will compile the code with the LAPACK routines included with the NWChem source. | ||

+ | |||

+ | Here we compute the IR spectrum and the element-wise breakdown of the vibrational density of states for silicon tetrachloride (SiCl4). The following input file was used. | ||

+ | |||

+ | start SiCl4 | ||

+ | echo | ||

+ | print low | ||

+ | geometry noautosym noautoz | ||

+ | Si -0.00007905 0.00044148 0.00000001 | ||

+ | Cl 0.71289590 1.00767685 1.74385011 | ||

+ | Cl -2.13658008 -0.00149375 -0.00000001 | ||

+ | Cl 0.71086735 -2.01430142 -0.00000001 | ||

+ | Cl 0.71289588 1.00767684 -1.74385011 | ||

+ | end | ||

+ | basis | ||

+ | * library 6-31G | ||

+ | end | ||

+ | dft | ||

+ | xc hfexch 1.0 | ||

+ | end | ||

+ | qmd | ||

+ | nstep_nucl 20000 | ||

+ | dt_nucl 10.0 | ||

+ | targ_temp 20.0 | ||

+ | com_step 10 | ||

+ | rand_seed 12345 | ||

+ | thermostat none | ||

+ | end | ||

+ | task dft qmd | ||

+ | |||

+ | |||

- | + | The IR spectrum and vibrational density of states were generated from the [[Media:qmd_tools.tar.gz|qmd_analysis code]] with the following command. | |

- | + | ||

- | + | ||

- | + | ./qmd_analysis -xyz SiCl4.xyz -steps 15000 -skip 5000 -ts 10.0 -temp 20.0 -smax 800 -width 10.0 | |

- | + | ||

- | + | where we have skipped the first 5000 steps from the simulation and only used the data from the last 15000 steps to compute the spectra. The time step is given as 10 a.u. since that was the time step in the simulation and we output the trajectory information every step. The temperature was set to 20 K (for analysis, this is only used in the calculation of the quantum correction factor for the autocorrelation function of the dipole moment). The option smax sets the maximum of the spectral window that is output to 800 wave numbers. The width option sets the full-width at half-maximum of the peaks in the resulting spectra. | |

- | + | ||

+ | The computed IR spectrum and vibrational density of states are shown here. | ||

- | + | [[File:SiCl4IR.png|400px|]],[[File:SiCl4VDOS.png|400px|]] | |

- | + |

## Latest revision as of 10:09, 11 December 2016

## Overview

This module performs adiabatic ab initio molecular dynamics on finite systems. The nuclei are integrated using the velocity-Verlet algorithm, and the electronic potential can be provided by any of the Gaussian basis set based methods in NWChem, e.g. DFT, TDDFT, TCE, MP2, SCF, MCSCF, etc. If analytic gradients are not available for the selected level of theory, numerical gradients will automatically be used. Initial velocities are randomly selected from the Maxwell-Boltzmann distribution at the specified temperature, unless a restart file (.qmdrst) is present. If a restart file is present, the trajectory information will be read from that file and the trajectory will resume from that point.

For computational details and a case study using the module, please refer to the following paper: S. A. Fischer, T. W. Ueltschi, P. Z. El-Khoury, A. L. Mifflin, W. P. Hess, H.F. Wang, C. J. Cramer, N. Govind "Infrared and Raman Spectroscopy from Ab Initio Molecular Dynamics and Static Normal Mode Analysis: The CH Region of DMSO as a Case Study" J. Phys. Chem. B, 120 (8), pp 1429–1436 (2016), DOI: 10.1021/acs.jpcb.5b03323 (2015) Publication Date (Web): July 29, 2015

QMD [dt_nucl <double default 10.0>] [nstep_nucl <integer default 1000>] [targ_temp <double default 298.15>] [thermostat <string default none> <thermostat parameters>] [rand_seed <integer default new one generated for each run>] [com_step <integer default 100>] [print_xyz <integer default 1>] [linear] END

The module is called as:

task <level of theory> qmd

where <level of theory> is any Gaussian basis set method in NWChem

## QMD Keywords

### dt_nucl -- Nuclear time step

This specifies the nuclear time step in atomic units (1 a.u. = 0.02419 fs). Default 10.0 a.u.

### nsteps_nucl -- Simulation steps

This specifies the number of steps to take in the nuclear dynamics. Default 1000

### targ_temp -- Temperature of the system

This specifies the temperature to use with the thermostat. Also it is used in generating initial velocities from the Maxwell-Boltzmann distribution. Default 298.15 K

### thermostat -- Thermostat for controling temperature of the simulation

This specifies the thermostat to use for regulating the temperature of the nuclei. Possible options are:

- none

No thermostat is used, i.e. an NVE ensemble is simulated. Default

- svr <double default 1000.0>

Stochastic velocity rescaling thermostat of Bussi, Donadio, and Parrinello J. Chem. Phys. 126, 014101 (2007) Number sets the relaxation parameter of the thermostat

- langevin <double default 0.1>

Langevin dynamics, implementation according to Bussi and Parrinello Phys. Rev. E 75, 056707 (2007) Number sets the value of the friction

- berendsen <double default 1000.0>

Berendsen thermostat, number sets the relaxation parameter of the thermostat

- rescale

Velocity rescaling, i.e. isokinetic ensemble

### rand_seed -- Seed for the random number generator

This specifies the seed for initializing the random number generator. If not given, a unique random seed will be generated. Even without a thermostat, this will influence the initial velocities.

### com_step -- How often center-of-mass translations and rotations are removed

This specifies that center-of-mass translations and rotations will be removed every com_step steps. Default 10 COM translations and rotations are removed on startup (either randomized initial velocities or those read from the restart file).

### print_xyz -- How often to print trajectory information to xyz file

This specifies that the trajectory information (coordinates, velocities, total energy, step number, dipole (if available)) to the xyz file. The units for the coordinates and velocities in the xyz file are Angstrom and Angstrom/fs, respectively.

### linear -- Flag for linear molecules

If present, the code assumes the molecule is linear.

## Sample input

The following is a sample input for a ground state MD simulation. The simulation is 200 steps long with a 10 a.u. time step, using the stochastic velocity rescaling thermostat with a relaxation parameter of 100 a.u. and a target temperature of 200 K. Center-of-mass rotations and translations will be removed every 10 steps and trajectory information will be output to the xyz file every 5 steps.

start qmd_dft_h2o_svr echo print low geometry noautosym noautoz O 0.00000000 -0.01681748 0.11334792 H 0.00000000 0.81325914 -0.34310308 H 0.00000000 -0.67863597 -0.56441201 end basis * library 6-31G* end dft xc pbe0 end qmd nstep_nucl 200 dt_nucl 10.0 targ_temp 200.0 com_step 10 thermostat svr 100.0 print_xyz 5 end task dft qmd

The following is a sample input for an excited state MD simulation on the first excited state. The simulation is 200 steps long with a 10 a.u. time step, run in the microcanonical ensemble. Center-of-mass rotations and translations will be removed every 10 steps and trajectory information will be output to the xyz file every 5 steps.

start qmd_tddft_h2o_svr echo print low geometry noautosym noautoz O 0.00000000 -0.01681748 0.11334792 H 0.00000000 0.81325914 -0.34310308 H 0.00000000 -0.67863597 -0.56441201 end basis * library 6-31G* end dft xc pbe0 end tddft nroots 5 notriplet target 1 civecs grad root 1 end end qmd nstep_nucl 200 dt_nucl 10.0 com_step 10 thermostat none print_xyz 5 end task tddft qmd

Additional sample inputs can be found in $NWCHEM_TOP/QA/tests/qmd_*

## Processing the output of a QMD run

The xyz file produced by the QMD module contains the velocities (given in Angstrom/fs), in addition to the coordinates (given in Angstrom). The comment lines also contain the time step, total energy (atomic units), and dipole moment (atomic units). In $NWCHEM_TOP/contrib/qmd_tools is a code that will take the xyz trajectory and calculate the IR spectrum and vibrational density of states from Fourier transforms of the dipole and atomic momenta autocorrelation functions, respectively. The code needs to be linked to a LAPACK library when compiled; the Makefile in the directory will compile the code with the LAPACK routines included with the NWChem source.

Here we compute the IR spectrum and the element-wise breakdown of the vibrational density of states for silicon tetrachloride (SiCl4). The following input file was used.

start SiCl4 echo print low geometry noautosym noautoz Si -0.00007905 0.00044148 0.00000001 Cl 0.71289590 1.00767685 1.74385011 Cl -2.13658008 -0.00149375 -0.00000001 Cl 0.71086735 -2.01430142 -0.00000001 Cl 0.71289588 1.00767684 -1.74385011 end basis * library 6-31G end dft xc hfexch 1.0 end qmd nstep_nucl 20000 dt_nucl 10.0 targ_temp 20.0 com_step 10 rand_seed 12345 thermostat none end task dft qmd

The IR spectrum and vibrational density of states were generated from the qmd_analysis code with the following command.

./qmd_analysis -xyz SiCl4.xyz -steps 15000 -skip 5000 -ts 10.0 -temp 20.0 -smax 800 -width 10.0

where we have skipped the first 5000 steps from the simulation and only used the data from the last 15000 steps to compute the spectra. The time step is given as 10 a.u. since that was the time step in the simulation and we output the trajectory information every step. The temperature was set to 20 K (for analysis, this is only used in the calculation of the quantum correction factor for the autocorrelation function of the dipole moment). The option smax sets the maximum of the spectral window that is output to 800 wave numbers. The width option sets the full-width at half-maximum of the peaks in the resulting spectra.

The computed IR spectrum and vibrational density of states are shown here.