Input description

Input description#

There are two major types of input that are allowed in the input file.

Keyword input
Section input

Besides the input file that can be edited by the users, URVA needs input data files which record necessary information along the IRC path.

Input Browsing Data Files#

The browsing files are in a compact form generated from any quantum chemistry package, e.g. Gaussian, that can do a reaction path calculation (i.e. IRC).

There are currently two types or versions of browsing file. The first one can be generated with Gaussian.

In Gaussian package, the functionality to generate the first version of browsing files has been implemented in 09. D and later versions, where we can specify IOp(1/45D=1000000) to ask the program to dump the URVA input file.

For the other version, which is a newer version of browsing file, only COLOGNE program (modified Gaussian links) could generate it by specifying IOp(1/169=1). [Please confirm with Niraj Verma for the latest implementation.]

An old version of browsing file IRC.forward looks like this:

BEGIN  -3.4799                                                                  
IAnZ,IZ1,IZ2,IZ3,IZ4,LBl,LAlpha,LBeta                                           
   6   0   0   0   0   1   2   3                                                
   1   0   0   0   0   4   5   6                                                
   1   0   0   0   0   7   8   9                                                
   1   0   0   0   0  10  11  12                                                
   1   0   0   0   0  13  14  15                                                
   1   0   0   0   0  16  17  18                                                                                                                                               
NAtom,NAt3,NAt3TT                                                               
   6  18 171                                                                    
CC                                                                              
-0.941587149013747D-07 0.887602257564275D+00 0.387104565790869D-11              
 0.475914479534898D-06-0.448641107198881D+01-0.308906876973208D-10              
 0.203051702502061D+01 0.914272813247156D+00 0.967689526182865D-07              
-0.101525874179257D+01 0.914272490133307D+00 0.175847936210061D+01              
-0.101525857419142D+01 0.914272490191794D+00-0.175847945885654D+01              
 0.623157481730462D-06-0.587443354575896D+01-0.284199869112849D-10              
FX_ZMat_Orientation                                                             
 0.469464169647529D-10-0.442597030751934D-03-0.846736108686104D-14              
-0.296968235944851D-10 0.279948023513574D-03-0.261963070566768D-14              
 0.571395806000380D-07-0.390328441440883D-04 0.466646816576250D-14              
-0.285635804236559D-07-0.390328441499423D-04 0.494807437002864D-07              
-0.285635750963201D-07-0.390328441522112D-04-0.494807411380999D-07              
-0.296748342948419D-10 0.279747539684463D-03 0.301039777958092D-14              
FFX_ZMat_Orientation                                                            
 0.673727728741553D+00 0.692347311037514D-07 0.170456711270361D-01              
-0.142202709459861D-09-0.177377578309433D-10 0.673727726266388D+00              
-0.191679729818407D-03-0.479224072006179D-10 0.378322845985903D-12              
 0.147755444717779D-02-0.138211260433442D-09 0.960597359254672D-04              
-0.287797932559476D-12-0.425785997622094D-07 0.402775274510450D+00              
-0.430506740849085D-13-0.523665237476869D-13-0.191679765460043D-03              
 0.352355949134907D-12-0.540346943834321D-12 0.147755444745623D-02              
-0.387536631729866D+00-0.414026953359867D-02-0.154234759429327D-07              
-0.117425946477113D-03-0.112436935526389D-03-0.444090507638634D-11              
 0.401322170387265D+00-0.588193654684310D-02-0.520381152108751D-02              
-0.281010181951143D-09-0.206369601668985D-03-0.233149951634369D-03              
-0.205318044421773D-10 0.479441566840071D-02 0.195486092279551D-02              
-0.155301628991545D-07-0.195194077923833D-09-0.616272603921819D-01              
-0.762240847096698D-11-0.435605540864809D-11 0.907481129750354D-05              
 0.167052222382542D-07 0.186312095497300D-09 0.507182683619605D-01              
-0.143104617223255D+00 0.207010024264664D-02 0.141122905348142D+00              
-0.225504606243053D-04 0.562185534893163D-04 0.547764897356356D-04              
-0.688249763679878D-02 0.595533403248963D-03 0.261284817447027D-01              
 0.138369258716501D+00 0.294093384568847D-02-0.520381045134077D-02              
-0.509385437008933D-02 0.103184838389051D-03-0.233149475303471D-03              
-0.178721319565060D-03-0.303476604562444D-03 0.167239471788411D-02              
 0.512454696643599D-03-0.239717207421547D-02 0.195485918582516D-02              
 0.141122906666171D+00-0.358552887255165D-02-0.306059274737216D+00              
 0.547765519077780D-04-0.973732685280769D-04-0.858008128951657D-04              
-0.474652854896711D-02-0.659176682864509D-05 0.546238156311338D-02              
-0.151815952001706D+00 0.415203202968296D-02 0.313671180937373D+00              
-0.143104590471927D+00 0.207009989554119D-02-0.141122889785943D+00              
-0.225504756746668D-04 0.562185494452985D-04-0.547764851787939D-04              
-0.688249550574728D-02 0.595533229841313D-03-0.261284829183172D-01              
 0.116348193463472D-01-0.292058056346915D-03 0.154375056093259D-01              
 0.138369229837513D+00 0.294093344368605D-02-0.520381046055451D-02              
 0.509385466904043D-02 0.103184845022906D-03-0.233149477699420D-03              
 0.178721339964697D-03-0.303476649403728D-03 0.167239499530266D-02              
-0.512454686050758D-03-0.292058091903389D-03 0.167239550140436D-02              
-0.519041077056318D-03-0.239717158599157D-02 0.195485891935188D-02              
-0.141122890997321D+00 0.358552908535406D-02-0.306059301869659D+00              
-0.547765445277776D-04 0.973732731880967D-04-0.858008458520807D-04              
 0.474652726888300D-02 0.659186837107873D-05 0.546237954400947D-02              
-0.154375033814465D-01 0.519040923681797D-03-0.130549363172571D-01              
 0.151815935387051D+00-0.415203219254843D-02 0.313671210091786D+00              
 0.209790412629678D-03 0.208601959286366D-09 0.310537117161714D-11              
-0.112334783458490D-02 0.425494030467413D-07-0.425207326856537D-12              
 0.968804316269098D-04 0.102823847021022D-03 0.617615472492293D-11              
 0.558725783258865D-05-0.514119489526909D-04-0.527082767312573D-04              
 0.558726948715399D-05-0.514119614100895D-04 0.527082673563188D-04              
 0.805502463008145D-03 0.160948311638988D-09-0.153029843061379D-02              
 0.846911585308464D-13 0.425447797184725D-07-0.402171885341740D+00              
 0.724646901596527D-12 0.652440546906607D-04 0.137310836744148D-03              
 0.264515359911154D-11-0.326220332661966D-04 0.137310521530052D-03              
 0.565029552816523D-04-0.326220324891689D-04 0.137310522194380D-03              
-0.565029580463852D-04-0.426946633198162D-07 0.403290251891884D+00              
 0.356454359158440D-11 0.181879037025892D-12 0.209790496952807D-03              
-0.488244236063045D-12 0.523246865345788D-12-0.112334783454515D-02              
 0.277851875936917D-11 0.136875162335107D-10-0.248438882056150D-04              
-0.527081994294628D-04 0.890480396461679D-04 0.664493668847341D-04              
 0.527081930560261D-04-0.890480533496732D-04 0.664493969755311D-04              
 0.518629751010695D-12-0.689114415888392D-12 0.805502461937890D-03              
IPoCou,Energy,XXIRC                                                             
                  -174  -40.8508514503203       -3.47985399601697               
END   

This is all browsing information for one point along the reaction path, a complete browsing file contains many points.

The line starting with BEGIN is the starting line for this point. Followed by a negative floating number which is the reaction coordinate(parameter) for the current point.

The first column of numbers in IAnZ section is the atomic number for each atoms.

The first number in NAtom section is the number of atoms.

The CC section is the cartesian coordinates, the unit here is Bohr instead of Angstrom. It takes the dimension of 3*NAtom.

The FX_ZMat_Orientation section is the Gradient information. It takes the dimension of 3*NAtom.

The FFX_ZMat_Orientation section is the Hessian(Force constant) information. It takes the dimension of 3*NAtom*(3*NAtom-1)/2+3*NAtom in a lower-triangular form.

The IPoCou, Energy, XXIRC section gives the label of points along the reaction path, electronic structure energy in Hartree and reaction coordinate(parameter).

A new version of browsing file for.urv looks like this:

BEGIN (no Hessian)
Natoms,NatomQ
9   3
Atomic masses needed for the decomposition
 0.120000000000000E+02 0.100782503700000E+01 0.100782503700000E+01
 0.100782503700000E+01 0.140030740080000E+02 0.120000000000000E+02
 0.100782503700000E+01 0.100782503700000E+01 0.100782503700000E+01
CC
 0.169697225005739E+02-0.811648210965859E+01 0.879761988944722E+00
 0.159209800896797E+02-0.838486471114676E+01-0.864827429826200E+00
 0.171599259287420E+02-0.608371464802783E+01 0.124374604451643E+01
 0.188600877428366E+02-0.893158523127136E+01 0.686890601243498E+00
 0.156179697313045E+02-0.936119388026272E+01 0.292541201747129E+01
 0.168297577763089E+02-0.926062502202836E+01 0.542514992931659E+01
 0.186745689197338E+02-0.836556547206232E+01 0.521353822888859E+01
 0.157188537240959E+02-0.813405460399106E+01 0.675235970615032E+01
 0.171250765149637E+02-0.111468436635420E+02 0.622006357374161E+01
Tangent vector eta (mass-weighted)
 0.174213796695604E-01-0.144341082676468E-01-0.144712984770885E-01
 0.106559266035991E+00-0.525263178710592E-01-0.779829795435399E-01
 0.428422033827948E-01-0.410026270711606E-01-0.461627751504783E-01
 0.628457355549446E-01-0.535353718231013E-01 0.884511052422221E-02
-0.131423149702742E-01-0.178021411679630E-01-0.843875746820369E-02
-0.250804846404081E-01-0.116384505518228E-01-0.200777100845307E-01
-0.497329644893999E-01-0.385596025012369E-01 0.265160704500627E-02
-0.102357371260773E+00-0.407454382444974E-01-0.885924194092035E-01
-0.374311612282349E-01-0.669037059819530E-02-0.168663007762965E-01
Curvature vector kappa (mass-weighted)
 0.337785215308511E+02-0.372550029743592E+02-0.193722187694327E+02
 0.446689084318519E+02-0.181668802761675E+02-0.519031862427770E+01
 0.163559643890897E+02 0.279570494078686E+02-0.955109485969388E+01
-0.491951230454485E+02 0.128446274928335E+02 0.202643132986328E+02
-0.601368290001503E+01-0.724854755773568E+01-0.148369225090863E+02
-0.332619489451996E+02-0.187272016313164E+02-0.142066560380431E+02
 0.360153147718756E+02 0.197721658603493E+02 0.155718008332464E+01
-0.414157897737381E+02 0.872858252777357E+00-0.763890527166036E+01
-0.139871605949416E+02-0.940435296948506E+01-0.112954431794456E+01
IPoCou,Energy,XXIRC
   0 -0.119999056211247E+04  0.000000000000000E+00
END

To distinguish from old browsing file, the first line is BEGIN (no Hessian), indicating that this browsing file does not contains Hessian information and is a new browsing file.

The second section of Natoms,NatomQ gives the total number of atoms in the system and number of atoms in the QM part. If the latter is smaller than the previous, it means this is an QMMM calculation. (in gaussian, it is an ONIOM calculation.)

The Atomic mass section gives all atomic masses for atoms in the system.

The CC section gives the cartesian coordinates information, the unit here is Bohr instead of Angstrom. It takes the dimension of 3*NAtom.

The Tangent section gives the mass-weighted path direction vector which has been mass-weighted. It takes the dimension of 3*NAtom.

The Curvature section gives the mass-weighted curvature vector which has been mass-weighted. It takes the dimension of 3*NAtom.

The IPoCou, Energy, XXIRC section firstly gives the point label along the reaction path, which can range from a very negative integer to a very positive integer. The second number is the electronic structure energy in Hartree. The last number is the reaction coordinate(parameter) which can range from a very negative floating number to a very positive floating number.

Keyword input#

Just for convenience, keyword input is often written before section input. The format of keyword input line is:

@keyword_name = [keyword_value]

The @ symbol should be in the first column. No space is allowed after it. On both sides of = sign, it should be space. There might be several optional keyword values available, however, only one option is accepted.

`@DATAFILETYPE` keyword#

This keywords specifies the format of input data source file for URVA analysis.

@DATAFILETYPE = old/new/xyz

old: The input data source file is generated by Gaussian package by setting corresponding IOp(1/45). This type of data contains most complete information.

Note

If the data file is generated by Gaussian with version number lower than 16.A, all floating numbers should be converted from “D” into “E” format.

new: The input data source file is generated by a modified version of Gaussian package. This type of data has no Hessian and gradient stored.

xyz: XYZ file containing the Cartesian coordinates of multiple snapshots.

`@DATAFILEPATH` keyword#

This keyword specifies the path of the input data file.

@DATAFILEPATH = "../path/to/data/file"

The quotation marks should be included.

`@ENERGY` keyword#

This keyword specifies whether SCF energy and its first and second derivatives will be calculated.

@ENERGY = on/off

`@PARM` keyword#

This keyword specifies the way to deal with internal coordinates parameters provided by user.

@PARM = No/GeomOnly/All

No: Do nothing with regard to these internal coordinates specifications.

GeomOnly: Only calculate the value of these internal coordinates.

All: Besides the value of internal coordinates, other properties related to these internal coordinates will be calculated.

`@VIBRATION` keyword#

This keyword specifies whether or not to do normal mode analysis.

@VIBRATION = on/off

If the keyword value is set to on, the @DATAFILETYPE must be set to old.

`@DIRCURV` keyword#

This keyword decides whether or not to calculate reaction path direction \(\boldsymbol {\eta(s)}\) and curvature \(\boldsymbol {\kappa(s)}\).

@DIRCURV = on/off

If the keyword value is set to on, the @DATAFILETYPE must be set to old or new.

`@AVAM` keyword#

This keyword specifies whether or not to calculate the adiabatic mode coupling coefficient \(\boldsymbol{ A_{n,s}(s)}\).

@AVAM = on/off

If the keyword value is set to on, the @DATAFILETYPE must be set to old, the @PARM must be set to All, the @VIBRATION must be set to on and the @DIRCURV must be set to on

`@CURVCPL` keyword#

This keyword specifies whether or not to calculate the curvature coupling coefficient \(\boldsymbol{B_{\mu,s}(s)}\).

@CURVCPL = on/off

If the keyword value is set to on, the @DATAFILETYPE must be set to old, the @VIBRATION must be set to on, and the @DIRCURV must be set to on.

`@CORIOLIS` keyword#

This keyword specifies whether or not to calculate the Coriolis mode-mode coupling coefficient \(\boldsymbol{B_{\mu,\nu}(s)}\).

@CORIOLIS = on/off

If the keyword value is set to on, the @DATAFILETYPE must be set to old and the @VIBRATION must be set to on.

`@ADIABFC` keyword#

This keyword specifies whether or not to calculate adiabatic force constant \(\mathbf{k^a}\).

@ADIABFC = on/off

If the keyword value is set to on, the @DATAFILETYPE must be set to old and the @PARM must be set to All.

Section input#

Section input is used when multiple parameters need to be read in, the format of the section input is:

SECTION_NAME
parameter line_1
parameter line_2
...
END SECTION_NAME

`TITLE` section#

This section accepts remarks provided by user. The content will be displayed in standard output.

TITLE
Please put remarks here.
Multiple lines are accepted.
END TITLE

This section is quite useful to take note of the parameters we use for URVA calculations.

`PARAMETER` section#

This section contains the internal coordinates specifications provided by the user. Different types of internal coordinates including ring coordinates are acceptable.

Bond length, bond angle, dihedral angle, out-of-plane angle, pyramidalization angle, ring puckering amplitude, ring puckering phase angle, ring deformation amplitude and ring deformation phase angle are supported.

PARAMETER
Internal coordinate specification
END PARAMETER

Bond length:

`std N_1 N_2 : “bond_name”

Bond angle:

std N_1 N_2 N_3: "angle_name"

Dihedral angle:

std N_1 N_2 N_3 N_4 : "dihedral_name"

Out of plane angle(the angle between the bond length \(N_1\)-\(N_2\) and the plane \(N_2\)-\(N_3\)-\(N_4\)):

oop N_1 N_2 N_3 N_4 : "out_of_plane_name"

Pyramidalization angle(the angle \(\theta_P\) is related to the three bond angles \(N_2\)-\(N_1\)-\(N_3\), \(N_3\)-\(N_1\)-\(N_4\), \(N_4\)-\(N_1\)-\(N_2\)):

pyr N_1 N_2 N_3 N_4 : "pyramidalization_angle_name"

Radius of planar reference ring(\(R\))(\(N_{ring}\): number of ring atoms):

ring N_{ring}- (N_1 N_2 ... N_{atoms}) -[0 0]: "ring_breathing_name"

Planar deformation amplitude(\(t_n\))(n=1\(\sim\)\(N_{ring}-2\)):

ring N_{ring}- (N_1 N_2 ... N_{atoms}) -[1 n]: "deformation_amplitude_name"

Planar deformation phase angle(\(\tau_n\))(n=1\(\sim\)\(N_{ring}-2\)):

ring N_{ring}- (N_1 N_2 ... N_{atoms}) -[2 n]: "deformation_phase_angle_name"

Puckering amplitude(\(q_n\))(n=2\(\sim\)(\(N_{ring}-1\))/2 for odd \(N_{ring}\) or 2\(\sim\)\(N_{ring}\)/2 for even \(N_{ring}\)):

ring N_{ring}- (N_1 N_2 ... N_{atoms}) -[3 n]: "puckering_amplitude_name"

Puckering phase angle(\(\phi_n\))(n=2\(\sim\)(\(N_{ring}-1\))/2 for odd \(N_{ring}\) or 2\(\sim\)\(N_{ring}\)/2-1 for even \(N_{ring}\)):

ring N_{ring}- (N_1 N_2 ... N_{atoms}) -[4 n]: "puckering_phase_angle_name"

`CURVCOR` section#

The CURVCOR interface will be activated if this section is found.

For most situations, it is usually enough for \(N_l\) and \(N_r\) to take the value of 25.

CURVCOR
Ln = $N_l$
Rn = $N_r$
END CURVCOR

`AUTOSMTH` section#

The AUTOSMTH interface will be activated if this section is found.

AUTOSMTH interface requires the activation of CURVCOR interface.

\(\delta s\) is the stepsize of mass-weighted IRC with the unit of amu\(^{1/2}\)-Bohr.

Using the value of 3 is usually enough for \(N_l\) and \(N_r\).

\(t\) is a cut-off for second derivative of smoothened curve. Increase it when necessary. Recommended value: 2.5.

AUTOSMTH
StepSize = $\delta s$
Ln = $N_l$
Rn = $N_r$
d2ythresh = $t$
END AUTOSMTH

`RMSPK` section#

The RMSPK interface will be activated if this section is found.

RMSPK interface requires the activation of AUTOSMTH.

Any points in the curvature plot having the value larger than \(k\) will be left out as spike.

The value of \(p\) ranges from 0.5 to 1.0 as a percentage number. Any points leading to consecutive difference larger than the percentile of \(p\) will be labeled as spike condidates. Recommened value: 0.85.

Gradient check threshold \(g\) is used to filter out normal points from spike candidates. Recommended value: 1.2.

RMSPK
CutHigh = $k$
Percentage = $p$
GradRatio = $g$
END RMSPK

`DMO` section#

If this section input is not found, default parameter values will be used.

\(s_{max}\) is an overlap threshold after each mode reordering step. If the overlap criteria of \(s_{max}\) could not be reached, the criteria will be reduced to \(s_{min}\) gradually. Recommend values for \(s_{max}\) and \(s_{min}\): 0.990 and 0.890.

If local difficulty is encountered, linear interpolation will be adopted, space between two consecutive points will be divided into \(N_{min}\) pieces. If the difficulty is still not solved, \(N_{min}\) will be increased up to \(N_{max}\). Recommended values for \(N_{min}\) and \(N_{max}\): 30 and 200.

If the DMO could not get through for a specific point due to the following reasons:

Change of symmetry of reaction complex, e.g. linear \(\rightarrow\) non-linear
Discontinuity of reaction path
Failure of reaction path following close to local minimum region

one solution to circumvent this problem is to calculate and re-order the vibrational frequencies for a specific region of reaction path. This function could be activated by setting \(IO_{cut}\) to 1. In this way, the reaction path with its \(\mathbf{s}\) value ranging from \(s_{start}\) to \(s_{end}\) will have vibrational frequencies calculated.

In some situations, due to the innate difficulty of path following algorithm, the DMO might fail at the transition state(TS) point. And also the first point off TS point in either forward or reverse direction might also lead to problems. In order to remediate this problem, we can skip a few points in that region by setting \(IO_{skip}\) to 1. If one point off the TS point in reverse(or forward) direction also needs to be skipped, \(N_{left}\)( or \(N_{right}\)) should be set to 1.

DMO 
Sthresh = $s_{max}$
Slowest = $s_{min}$
Np = $N_{min}$
NMax = $N_{max}$
Cut = $IO_{cut}$
CutA = $s_{start}$
CutB = $s_{end}$
Skip = $IO_{skip}$
SkipA = $N_{left}$
SkipB = $N_{right}$
END DMO

Input description

Contents

Input description#

Input Browsing Data Files#

Keyword input#

@DATAFILETYPE keyword#

@DATAFILEPATH keyword#

@ENERGY keyword#

@PARM keyword#

@VIBRATION keyword#

@DIRCURV keyword#

@AVAM keyword#

@CURVCPL keyword#

@CORIOLIS keyword#

@ADIABFC keyword#