ONIOM (#763)

* small changes to .gitignore Signed-off-by: Abylay „Albert“ Katbashev <[email protected]> * Allocation of solvation Signed-off-by: Abylay „Albert“ Katbashev <[email protected]> * Default methods (gfn2:gfnff) for the ONIOM calculation Signed-off-by: Abylay „Albert“ Katbashev <[email protected]> * .gitignore Signed-off-by: Abylay „Albert“ Katbashev <[email protected]> * license update for man/xtb.1.adoc Signed-off-by: Abylay „Albert“ Katbashev <[email protected]> * ONIOM Jacobian matrix Signed-off-by: Abylay „Albert“ Katbashev <[email protected]> * Changes related to the ONIOM Signed-off-by: Abylay „Albert“ Katbashev <[email protected]> * Turbomole settings for ONIOM Signed-off-by: Abylay „Albert“ Katbashev <[email protected]> * general changes Signed-off-by: Abylay „Albert“ Katbashev <[email protected]> * Comments Signed-off-by: Abylay „Albert“ Katbashev <[email protected]> * inner:outer charges Signed-off-by: Abylay „Albert“ Katbashev <[email protected]> * To change setparam for ONIOM Signed-off-by: Abylay „Albert“ Katbashev <[email protected]> * allocate wfn for oniom in main Signed-off-by: Abylay „Albert“ Katbashev <[email protected]> * oniom_settings data type to control ONIOM Signed-off-by: Abylay „Albert“ Katbashev <[email protected]> * ONIOM: option to print inner region logs Signed-off-by: Abylay „Albert“ Katbashev <[email protected]> * ONIOM: to change k factor from fixed to derive Signed-off-by: Abylay „Albert“ Katbashev <[email protected]> * add ONIOM specs in man Signed-off-by: Abylay „Albert“ Katbashev <[email protected]> * Add --ceasfiles to delete all external files Signed-off-by: Abylay „Albert“ Katbashev <[email protected]> * add 'mute' to redirect ORCA and TURBOMOLE output Signed-off-by: Abylay „Albert“ Katbashev <[email protected]> * add protectCoord subroutine: 1) To copy coord file if it exists to protect it from the rewrite Signed-off-by: Abylay „Albert“ Katbashev <[email protected]> * add silent into xcontrol Signed-off-by: Abylay „Albert“ Katbashev <[email protected]> * Pretty headers Signed-off-by: Abylay „Albert“ Katbashev <[email protected]> * fixed rdrm reference Signed-off-by: Abylay „Albert“ Katbashev <[email protected]> * Cleaning the source Signed-off-by: Abylay „Albert“ Katbashev <[email protected]> * fixed class default statement Signed-off-by: Abylay „Albert“ Katbashev <[email protected]> * Update bias_path.f90 * Update optimizer.f90 * Update scf_module.F90 * Update anc.f90 removing double damping * Update main.F90 remove unrelated comments * tests added Signed-off-by: Abylay „Albert“ Katbashev <[email protected]> * new test for iniom Signed-off-by: Abylay „Albert“ Katbashev <[email protected]> * Update xtb.1.adoc * Update orca.f90 --------- Signed-off-by: Abylay „Albert“ Katbashev <[email protected]> Signed-off-by: Abylay „Albert“ Katbashev <[email protected]> Co-authored-by: Abylay „Albert“ Katbashev <[email protected]> Co-authored-by: Abylay „Albert“ Katbashev <[email protected]> Co-authored-by: Christoph Plett <[email protected]>
grimme-lab · Feb 1, 2023 · 9f0c28c · 9f0c28c
1 parent c6e56db
commit 9f0c28c
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diff --git a/man/xcontrol.7.adoc b/man/xcontrol.7.adoc
@@ -326,6 +326,19 @@ $modef
 *mode*='int'::
     can set by --modef via cmdline
 
+$oniom
+~~~~~~
+*inner logs*='bool'::
+   to print optimization log files for model region geometry (`high.inner_region.log` and `low.inner_region.log`)
+
+*derived k*='bool'::
+   to calculate prefactor *k* and create jacobian dynamically (see more )
+
+*silent*='bool'::
+   to hide the execution runs of external software 
+
+
+
 $opt
 ~~~~
 *engine*='method'::

diff --git a/man/xtb.1.adoc b/man/xtb.1.adoc
@@ -24,8 +24,8 @@ geometries, frequencies and non-covalent interactions (GFN)
 as well as with the ionisation potential and
 electron affinity (IPEA) parametrisation of the GFN1 Hamiltonian.
 The generalized born (GB) model with solvent accessable surface area (SASA)
-is also available available in this version.
-Ground state calculations for the simplified Tamm-Danceoff approximation (sTDA)
+is also available in this version.
+Ground state calculations for the simplified Tamm-Dancoff approximation (sTDA)
 with the vTB model are currently not implemented.
 
 GEOMETRY INPUT
@@ -66,6 +66,9 @@ OPTIONS
 *-c, --chrg* 'INT':: 
     specify molecular charge as 'INT', overrides `.CHRG` file and `xcontrol` option
 
+*-c, --chrg* 'INT:INT':: 
+    specify charges for 'inner region:outer region' for `oniom` calculation, overrides `.CHRG` file and `xcontrol` option
+
 *-u, --uhf* 'INT'::
     specify number of unpaired electrons as 'INT', overrides `.UHF` file and `xcontrol` option
 
@@ -79,10 +82,10 @@ OPTIONS
     use tblite library as implementation of for xTB
 
 *--oniom* 'METHOD' 'LIST'::
-    use subtractive embedding via ONIOM method. 'METHOD' is given as `inner:outer`
-    where `inner` can be 'orca', 'turbomole', 'gfn2', 'gfn1', or 'gfnff' and
-    `outer` can be 'gfn2', 'gfn1', or 'gfnff'.
-    The inner region is given as a comma separated indices directly in the commandline
+    use subtractive embedding via ONIOM method. 'METHOD' is given as `high:low`
+    where `high` can be 'orca', 'turbomole', 'gfn2', 'gfn1', or 'gfnff' and
+    `low` can be 'gfn2', 'gfn1', or 'gfnff'.
+    The inner region is given as comma-separated indices directly in the commandline
     or in a file with each index on a separate line.
 
 *--etemp* 'REAL'::
@@ -263,6 +266,9 @@ GENERAL
 *-h, --help*::
      show help page
 
+*--cut*::
+      create inner region for `oniom` calculation without performing any calcultion
+
 ENVIRONMENT VARIABLES
 ---------------------
 `xtb(1)` accesses a path-like variable to determine the location of its
@@ -421,7 +427,7 @@ After `xtb(1)` has evaluated the all input sources it immediately enters
 the production mode. Severe errors will lead to an abnormal termination
 which is signalled by the printout to STDERR and a non-zero return value
 (usually 128). All non-fatal errors are summerized in the end of the calculation
-in one block, right bevor the timing analysis.
+in one block, right before the timing analysis.
 
 To aid the user to fix the problems generating these warnings a brief
 summary of each warning with its respective string representation in the

diff --git a/src/bias_path.f90 b/src/bias_path.f90
@@ -282,7 +282,7 @@ subroutine bias_path(env, mol, chk, calc, egap, et, maxiter, epot, grd, sigma)
       enddo
       factor2= factor2 + alp_change
    enddo bias_loop
-
+   
    !! ------------------------------------------------------------------------
    ! output and find path yielding product
    !! ------------------------------------------------------------------------

diff --git a/src/extern/driver.f90 b/src/extern/driver.f90
@@ -117,7 +117,7 @@ subroutine singlepoint(self, env, mol, chk, printlevel, restart, &
     !$omp critical (turbo_lock)
     inquire (file='gradient', exist=exist)
     if (exist) then
-      call rdtm(mol%n, .true., energy, gradient, xyz_cached)
+      call rdtm(env,mol%n, .true., energy, gradient, xyz_cached)
       cache = all(abs(xyz_cached - mol%xyz) < 1.e-10_wp)
     end if
     if (.not. cache) then
@@ -135,7 +135,7 @@ subroutine singlepoint(self, env, mol, chk, printlevel, restart, &
       end if
       write (env%unit, '(72("="))')
 
-      call rdtm(mol%n, .true., energy, gradient, xyz_cached)
+      call rdtm(env,mol%n, .true., energy, gradient, xyz_cached)
     end if
     !$omp end critical (turbo_lock)