Release66:Hessians & Vibrational Frequencies
From NWChem
(→Controlling the Step Size of the Finite difference Hessian) 
(→Controlling the Step Size of the Finite difference Hessian) 

(6 intermediate revisions not shown)  
Line 87:  Line 87:  
<real temperature1 temperature2 ...>]  <real temperature1 temperature2 ...>]  
[animate [<real step_size_for_animation>]]  [animate [<real step_size_for_animation>]]  
  [fd_delta [<real  +  [fd_delta [<real step_size_for_fd_hessian>]] 
[filename <string file_set_name> [overwrite]]  [filename <string file_set_name> [overwrite]]  
end  end  
Line 179:  Line 179:  
====Controlling the Step Size Along the Mode Vector====  ====Controlling the Step Size Along the Mode Vector====  
  By default, the step size used is 0.15 a.u. which will give reliable animations for most systems. This can be changed via the input directive  +  By default, the step size used is 0.15 a.u. which will give reliable animations for most systems. This can be changed via the animate input directive, e.g. 
  +  vib  
+  animate 0.20  
+  end  
where <step_size> is the real number that is the magnitude of each step along the eigenvector of each nuclear hessian mode in atomic units.  where <step_size> is the real number that is the magnitude of each step along the eigenvector of each nuclear hessian mode in atomic units.  
Line 197:  Line 199:  
===Controlling the Step Size of the Finite difference Hessian===  ===Controlling the Step Size of the Finite difference Hessian===  
  By default, the step size used for calculating the finite difference Hessian is 0.010 a.u. for DFT and NWPW modules, and 0.001 a.u. otherwise This can be changed via the input directive  +  By default, the step size used for calculating the finite difference Hessian is 0.010 a.u. for DFT and NWPW modules, and 0.001 a.u. otherwise This can be changed via the fd_delta input directive, e.g. 
  +  vib  
  +  fd_delta 0.005  
  where <fd_hessian_step_size> is the real number that is the magnitude of each displacement in atomic units for the calculation of the finite difference Hessian.  +  end 
+  where <fd_hessian_step_size> is the real number that is the magnitude of each displacement in atomic units for the calculation of the finite difference Hessian. For older versions of NWChem without the fd_delta option just set the "stpr_gen:delta" value on the runtime database, e.g.  
+  set stpr_gen:delta 0.005  
===An Example Input Deck===  ===An Example Input Deck=== 
Latest revision as of 12:54, 7 February 2017
Contents

Hessians
This section relates to the computation of analytic hessians which are available for open and closed shell SCF, except ROHF and for closed shell and unrestricted open shell DFT ^{[1]}. Analytic hessians are not currently available for SCF or DFT calculations relativistic allelectron methodologies or for charge fitting with DFT. The current algorithm is fully incore and does not use symmetry.
There is no required input for the Hessian module. This module only impacts the hessian calculation. For options for calculating the frequencies, please see the Vibrational module.
Hessian Module Input
All input for the Hessian Module is optional since the default definitions are usually correct for most purposes. The generic module input begins with hessian and has the form:
hessian thresh <real tol default 1d6> print ... profile end
Defining the wavefunction threshold
You may modify the default threshold for the wavefunction. This keyword is identical to THRESH in the SCF, and the CONVERGENCE gradient in the DFT. The usual defaults for the convergence of the wavefunction for single point and gradient calculations is generally not tight enough for analytic hessians. Therefore, the hessian, by default, tightens these up to 1d6 and runs an additional energy point if needed. If, during an analytic hessian calculation, you encounter an error:
cphf_solve:the available MOs do not satisfy the SCF equations
the convergence criteria of the wavefunction generally needs to be tightened.
Profile
The PROFILE keyword provides additional information concerning the computation times of different sections of the hessian code. Summary information is given about the maximum, minimum and average times that a particular section of the code took to complete. This is normally only useful for developers.
Print Control
Known controllable print options are shown in the table below:
Name  Print Level  Description 
"hess_follow"  high  more information about where the calculation is 
"cphf_cont"  debug  detailed CPHF information 
"nucdd_cont"  debug  detailed nuclear contribution information 
"onedd_cont"  debug  detailed one electron contribution information 
"twodd_cont"  debug  detailed two electron contribution information 
"fock_xc"  debug  detailed XC information during the fock builds 
Vibrational frequencies
The nuclear hessian which is used to compute the vibrational frequencies can be computed by finite difference for any ab initio wavefunction that has analytic gradients or by analytic methods for SCF and DFT (see Hessians for details). The appropriate nuclear hessian generation algorithm is chosen based on the user input when TASK <theory> frequencies is the task directive.
The vibrational package was integrated from the Utah Messkit and can use any nuclear hessian generated from the driver routines, finite difference routines or any analytic hessian modules. There is no required input for the "VIB" package. VIB computes the Infra Red frequencies and intensities for the computed nuclear hessian and the "projected" nuclear hessian. The VIB module projects out the translations and rotations of the nuclear hessian using the standard Eckart projection algorithm. It also computes the zero point energy for the molecular system based on the frequencies obtained from the projected hessian.
The default mass of each atom is used unless an alternative mass is provided via the geometry input or redefined using the vibrational module input. The default mass is the mass of the most abundant isotope of each element. If the abundance was roughly equal, the mass of the isotope with the longest half life was used.
In addition, the vibrational analysis is given at the default standard temperature of 298.15 degrees.
Vibrational Module Input
All input for the Vibrational Module is optional since the default definitions will compute the frequencies and IR intensities. The generic module input can begin with vib, freq, frequency and has the form:
{freq  vib  frequency} [reuse [<string hessian_filename>]] [mass <integer lexical_index> <real new_mass>] [mass <string tag_identifier> <real new_mass>] [{temp  temperature} <integer number_of_temperatures> \ <real temperature1 temperature2 ...>] [animate [<real step_size_for_animation>]] [fd_delta [<real step_size_for_fd_hessian>]] [filename <string file_set_name> [overwrite]] end
Hessian File Reuse
By default the task <theory> frequencies directive will recompute the hessian. To reuse the previously computed hessian you need only specify reuse in the module input block. If you have stored the hessian in an alternate place you may redirect the reuse directive to that file by specifying the path to that file.
reuse /path_to_hessian_file
This will reuse your saved Hessian data but one caveat is that the geometry specification at the point where the hessian is computed must be the default "geometry" on the current runtimedatabase for the projection to work properly.
Redefining Masses of Elements
You may also modify the mass of a specific center or a group of centers via the input.
To modify the mass of a specific center you can simply use:
mass 3 4.00260324
which will set the mass of center 3 to 4.00260324 AMUs. The lexical index of centers is determined by the geometry object.
To modify all Hydrogen atoms in a molecule you may use the tag based mechanism:
mass hydrogen 2.014101779
The mass redefinitions always start with the default masses and change the masses in the order given in the input. Care must be taken to change the masses properly. For example, if you want all hydrogens to have the mass of Deuterium and the third hydrogen (which is the 6th atomic center) to have the mass of Tritium you must set the Deuterium masses first with the tag based mechanism and then set the 6th center's mass to that of Tritium using the lexical center index mechanism.
The mass redefinitions are not fully persistent on the runtimedatabase. Each input block that redefines masses will invalidate the mass definitions of the previous input block. For example,
freq reuse mass hydrogen 2.014101779 end task scf frequencies freq reuse mass oxygen 17.9991603 end task scf frequencies
will use the new mass for all hydrogens in the first frequency analysis. The mass of the oxygen atoms will be redefined in the second frequency analysis but the hydrogen atoms will use the default mass. To get a modified oxygen and hydrogen analysis you would have to use:
freq reuse mass hydrogen 2.014101779 end task scf frequencies freq reuse mass hydrogen 2.014101779 mass oxygen 17.9991603 end task scf frequencies
Temp or Temperature
The "VIB" module can generate the vibrational analysis at various temperatures other than at standard room temperature. Either temp or temperature can be used to initiate this command.
To modify the temperature of the computation you can simply use:
temp 4 298.15 300.0 350.0 400.0
At this point, the temperatures are persistant and so the user must "reset" the temperature if the standard behavior is required after setting the temperatures in a previous "VIB" command, i.e.
temp 1 298.15
Animation
The "VIB" module also can generate mode animation input files in the standard xyz file format for graphics packages like RasMol or XMol There are scripts to automate this for RasMol in $NWCHEM_TOP/contrib/rasmolmovie. Each mode will have 20 xyz files generated that cycle from the equilibrium geometry to 5 steps in the positive direction of the mode vector, back to 5 steps in the negative direction of the mode vector, and finally back to the equilibrium geometry. By default these files are not generated. To activate this mechanism simply use the following input directive
animate
anywhere in the frequency/vib input block.
Given an ordered list of files containing molecular coordinates in XYZ format, the rasmolmovie shell script generates an animated gif for each of the six possible views down a Cartesian axis.
It uses the free utilities
 rasmol (http://www.umass.edu/microbio/rasmol) to manipulate the molecule and generate the individual frames  convert from ImageMagick (http://www.imagemagick.org/) to combine the frames into an animated gif
It should be easy to modify the script to other file formats or animation tools.
Controlling the Step Size Along the Mode Vector
By default, the step size used is 0.15 a.u. which will give reliable animations for most systems. This can be changed via the animate input directive, e.g.
vib animate 0.20 end
where <step_size> is the real number that is the magnitude of each step along the eigenvector of each nuclear hessian mode in atomic units.
Specifying filenames for animated normal modes
By default, normal modes will be stored in files that start with "freq.m<mode number>". This is inconvenient if more than vibrational analysis is run in a single input file. To specify different filename for a particular vibrational analysis use the directive
filename <file_set_name> [overwrite]
where <file_set_name> is the name that will be prepended to the usual filenames. In addition the code by default requires all files to be new files. When the option "overwrite" is provided any preexisting files will simply be overwritten.
Controlling the Step Size of the Finite difference Hessian
By default, the step size used for calculating the finite difference Hessian is 0.010 a.u. for DFT and NWPW modules, and 0.001 a.u. otherwise This can be changed via the fd_delta input directive, e.g.
vib fd_delta 0.005 end
where <fd_hessian_step_size> is the real number that is the magnitude of each displacement in atomic units for the calculation of the finite difference Hessian. For older versions of NWChem without the fd_delta option just set the "stpr_gen:delta" value on the runtime database, e.g.
set stpr_gen:delta 0.005
An Example Input Deck
This example input deck will optimize the geometry for the given basis set, compute the frequencies for H_{2}O, H_{2}O at different temperatures, D_{2}O, HDO, and TDO.
start h2o title Water geometry units au autosym O 0.00000000 0.00000000 0.00000000 H 0.00000000 1.93042809 1.10715266 H 0.00000000 1.93042809 1.10715266 end basis noprint H library sto3g O library sto3g end scf; thresh 1e6; end driver; tight; end task scf optimize scf; thresh 1e8; print none; end task scf freq freq reuse; temp 4 298.15 300.0 350.0 400.0 end task scf freq freq reuse; mass H 2.014101779 temp 1 298.15 end task scf freq freq reuse; mass 2 2.014101779 end task scf freq freq reuse; mass 2 2.014101779 ; mass 3 3.01604927 end task scf freq
References
 ↑ Johnson, B.G. and Frisch, M.J. (1994) "An implementation of analytic second derivatives of the gradientcorrected density functional energy", Journal of Chemical Physics 100 74297442, doi:10.1063/1.466887