The IRC method

.coveragerc

@@ -19,6 +19,7 @@ exclude_lines =
     raise NEBChainRespaceError
     raise NEBStructureError
     raise NEBBandGradientError
+    raise IRCError
     def visualize
     verbose:
     if verbose >=

README.md

@@ -16,7 +16,7 @@ Documentation is hosted at https://geometric.readthedocs.io/ .
 
 Authors: Lee-Ping Wang, Chenchen Song
 
-Contributors: Heejune Park (Nudged elastic band); Yudong Qiu (Psi4 engine, error handling); Daniel G. A. Smith (Testing framework, QCEngine JSON API);
+Contributors: Heejune Park (Nudged elastic band, Intrinsic reaction coordinate); Yudong Qiu (Psi4 engine, error handling); Daniel G. A. Smith (Testing framework, QCEngine JSON API);
 Tamas K. Stenczel (GitHub Actions, ASE engine); Sebastian Lee (Molpro engine); Chaya Stern (Travis, Conda); Qiming Sun (Custom engine); 
 Alberto Gobbi (Batch energy/gradient, logging); Josh Horton (Convergence criteria, Gaussian engine); Akhil Shajan (QUICK engine)
 

docs/source/citation.rst

@@ -17,7 +17,7 @@ Credits
 
 Authors: Lee-Ping Wang, Chenchen Song
 
-Contributors: Heejune Park (Nudged elastic band); Yudong Qiu (Psi4 engine, error handling); Daniel G. A. Smith (Testing framework, QCEngine JSON API);
+Contributors: Heejune Park (Nudged elastic band, Intrinsic reaction coordinate); Yudong Qiu (Psi4 engine, error handling); Daniel G. A. Smith (Testing framework, QCEngine JSON API);
 Tamas K. Stenczel (GitHub Actions, ASE engine); Sebastian Lee (Molpro engine); Chaya Stern (Travis, Conda); Qiming Sun (Custom engine); 
 Alberto Gobbi (Batch energy/gradient, logging); Josh Horton (Convergence criteria, Gaussian engine); Akhil Shajan (QUICK engine)
 
@@ -40,7 +40,7 @@ License
 
     Authors: Lee-Ping Wang, Chenchen Song
 
-    Contributors: Yudong Qiu, Daniel G. A. Smith, Sebastian Lee, Chaya Stern, Qiming Sun,
+    Contributors: Heejune Park, Yudong Qiu, Daniel G. A. Smith, Sebastian Lee, Chaya Stern, Qiming Sun,
     Alberto Gobbi, Josh Horton, Tamas K. Stenczel, Akhil Shajan
 
     Redistribution and use in source and binary forms, with or without modification,

examples/1-simple-examples/hcn_hnc_irc/gaussian/command.sh

@@ -0,0 +1,2 @@
+geometric-optimize start.gjf --irc yes --nt 6 --trust 0.05 --engine gaussian --converge set GAU_LOOSE
+

examples/1-simple-examples/hcn_hnc_irc/gaussian/start.gjf

@@ -0,0 +1,10 @@
+%Mem=4GB
+# hf/3-21g Force=NoStep SCF=(XQC, VeryTightLinEq)
+
+Downloaded from PubChem
+
+0 1
+C       -0.1088783634   -0.6365101639    0.0043221742
+N       -0.6393457902    0.4205365638    0.0052498438
+H        0.7532976101    0.2173493463   -0.0090384631
+

examples/1-simple-examples/hcn_hnc_irc/gaussian/start_irc.vdata_first

@@ -0,0 +1,69 @@
+    #==========================================#
+    #|   File containing vibrational modes    |#
+    #|      generated by geomeTRIC and        |#
+    #|       readable by ForceBalance         |# 
+    #|                                        |#
+    #| Octothorpes are comments               |#
+    #| This file should be formatted like so: |#
+    #| (Full XYZ file for the molecule)       |#
+    #| Number of atoms                        |#
+    #| Comment line                           |#
+    #| a1 x1 y1 z1 (xyz for atom 1)           |#
+    #| a2 x2 y2 z2 (xyz for atom 2)           |#
+    #|                                        |#
+    #| These coords will be actually used     |#
+    #|                                        |#
+    #| (Followed by vibrational modes)        |#
+    #| Do not use mass-weighted coordinates   |#
+    #| ...                                    |#
+    #| v (Eigenvalue in wavenumbers)          |#
+    #| dx1 dy1 dz1 (Eigenvector for atom 1)   |#
+    #| dx2 dy2 dz2 (Eigenvector for atom 2)   |#
+    #| ...                                    |#
+    #| (Empty line is optional)               |#
+    #| v (Eigenvalue)                         |#
+    #| dx1 dy1 dz1 (Eigenvector for atom 1)   |#
+    #| dx2 dy2 dz2 (Eigenvector for atom 2)   |#
+    #| ...                                    |#
+    #| and so on                              |#
+    #|                                        |#
+    #| Please list freqs in increasing order  |#
+    #==========================================#
+
+# 
+# == Summary of harmonic free energy analysis ==
+# Note: Rotational symmetry is set to 1 regardless of true symmetry
+# 1 Imaginary Frequencies (cm^-1): 1215.859i
+# Note: Free energy does not include contribution from imaginary mode(s)
+# 
+# Free energy contributions calculated at @ 300.00 K:
+# Zero-point vibrational energy:                                    6.5453 kcal/mol 
+# H   (Trans + Rot + Vib = Tot):   1.4904 +   0.8942 +   0.0003 =   2.3849 kcal/mol 
+# S   (Trans + Rot + Vib = Tot):  35.8748 +  16.3847 +   0.0010 =  52.2605 cal/mol/K
+# TS  (Trans + Rot + Vib = Tot):  10.7624 +   4.9154 +   0.0003 =  15.6782 kcal/mol 
+# 
+# Ground State Electronic Energy    : E0                        =   -92.24604266 au (    -57885.2657 kcal/mol)
+# Free Energy Correction (Harmonic) : ZPVE + [H-TS]_T,R,V       =    -0.01075349 au (        -6.7479 kcal/mol)
+# Gibbs Free Energy (Harmonic)      : E0 + ZPVE + [H-TS]_T,R,V  =   -92.25679615 au (    -57892.0136 kcal/mol)
+# 
+
+3
+Iteration 0 Energy -92.24604266
+ C   -0.1088783634   -0.6365101639    0.0043221742
+ N   -0.6393457902    0.4205365638    0.0052498438
+ H    0.7532976101    0.2173493463   -0.0090384631
+
+-1215.858933
+-0.043293 -0.081607  0.000849
+ 0.075287  0.009576 -0.000867
+-0.530324  0.839319  0.001930
+
+ 2126.655388
+-0.335109  0.647241  0.000681
+ 0.302446 -0.563902 -0.000708
+-0.209774  0.123745  0.001723
+
+ 2451.859833
+-0.057515 -0.023525  0.000737
+-0.012776 -0.015886  0.000213
+ 0.862859  0.501058 -0.011742