Version 5.2.0 update (#55)

* visual/output fixes * initialize mult. and neg. charges * fixed neg. charge population distr. * rebuild -> charge determines runtype * updated fractional charges for single charges * negative charges and bugfix for fractional charges * fractional mult. chrgs.; neg. EAs * version number and output update * added eTemp manipulation; corrected 3d-metals w. mult. chrgs * modified No_eTemp * NoeTemp update; version * re-introduced random seed manipulation * added write-out if ESI frags. but no ESI run * remove ORCA.INPUT files for next CID run * added charge info at end * added time restrictions to MFP-MD * temprun fix * switched off no_eTemp for MDs, but remains for IP-ORCA * add pbeh-3c to turbomole input * visual/output fixes * initialize mult. and neg. charges * fixed neg. charge population distr. * rebuild -> charge determines runtype * updated fractional charges for single charges * negative charges and bugfix for fractional charges * fractional mult. chrgs.; neg. EAs * version number and output update * added eTemp manipulation; corrected 3d-metals w. mult. chrgs * modified No_eTemp * NoeTemp update; version * re-introduced random seed manipulation * remove ORCA.INPUT files for next CID run * added charge info at end * temprun fix * switched off no_eTemp for MDs, but remains for IP-ORCA * gcc bug fix * changed eimpw use * init ReBuild * re-structured wr/rdstart (working) * changed eimpw use * init ReBuild * re-structured wr/rdstart (working) * add error stop input.f90 for GCC * error output for commandline fail * updated version * init rmsd; update avg write-out * add rmsd subroutine; check 50 frag steps * added 50 steps to CID * write out nxyz fragment structures * rmsd completely implemented; errors with changing frag size * write out structures with RMSD > 1AA * bugfix modules * init rmsd; update avg write-out * added 50 steps to CID * write out nxyz fragment structures * rmsd completely implemented; errors with changing frag size * write out structures with RMSD > 1AA * reduce steps after collision * delete egrad to iniqm * init nuc dependend esi scaling * moved dist from iee to main * reversed scaling; used impactscale for CID * reworked ESI scaling * reworked ESI scaling; now in step2 * fixed noESI bug * version and orca setting * increased MD for larger strucs * tmax for CID; reworked t-scaling routine in MD * added long after-fragmentation MD for chrg > 1 * working version 5.2.0 * cid update for avg strucs * tblite reset * latest subprojects version updates * updated README infos * v520 steps working, all rebased on main * reduced MFP steps by nuc * 100; reduced lchamb default to 0.2m; calculate Mol. radius with c-o-geometry; moved com and cog to utility * timings fix; accuracy * deleted read_coordinates; deleted comments
qcxms · Jul 25, 2022 · 6d88c06 · 6d88c06
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diff --git a/README.md b/README.md
@@ -21,8 +21,28 @@ The following files are being extracted: `qcxms` `pqcxms` `q-batch` `getres` `.X
 
 Place the executables into your ``$HOME/bin/`` directory or path. Place the `.XTBPARAM` folder and `.mass_raw.arg` file into your `$HOME` directory (these files can appear to be hidden). 
 
-### Spectra Plotting
-To evaluate the results and create a spectrum, download and use the [PlotMS](https://github.com/qcxms/PlotMS) program. For visualization of the calculated spectra, we recommend the usage of the **xmgrace** program. Furthermore, *JCAMP-DX* and *.csv* are plotted. Versions PlotMS v.6.0 and higher now provide **exact masses**. The `.mass_raw.agr` file was moved to the [PlotMS](https://github.com/qcxms/PlotMS) repository. 
+### Conda
+
+[![Conda Version](https://img.shields.io/conda/vn/conda-forge/qcxms.svg)](https://anaconda.org/conda-forge/qcxms)
+
+Installing `qcxms` from the `conda-forge` channel can be achieved by adding `conda-forge` to your channels with:
+
+```
+conda config --add channels conda-forge
+```
+
+Once the `conda-forge` channel has been enabled, `qcxms` can be installed with:
+
+```
+conda install qcxms
+```
+
+It is possible to list all of the versions of `qcxms` available on your platform with:
+
+```
+conda search qcxms --channel conda-forge
+```
+
 
 ### Meson
 
@@ -34,18 +54,37 @@ export FC=ifort CC=icc
 meson setup build -Dfortran_link_args=-static
 ninja -C build 
 ```
-Copy the binary from the `build/qcxms` file into a directory in your path, e.g. `~/bin/`.
 
-**Documentation**
+This will build a static linked binary in the ``build`` folder. Copy the binary from ``build/qcxms`` file into a directory in your path, e.g. ``~/bin/``.
 
-A more detailed documentation on topics like installation and input settings can be fond at [read-the-docs](https://xtb-docs.readthedocs.io/en/latest/qcxms_doc/qcxms.html). Examples to test QCxMS can be found in the `EXAMPLES` folder. Here, input and coordinate files are provided for either EI or CID run modes. 
 
+**Documentation**
+
+A more detailed documentation on topics like input settings can be fond at [read-the-docs](https://xtb-docs.readthedocs.io/en/latest/qcxms_doc/qcxms.html). 
+Examples to test QCxMS can be found in the `EXAMPLES` folder. Here, input and coordinate files are provided for either EI or CID run modes. 
 
 
 **From QCEIMS to QCxMS:**
 - All names have been changed from `qceims.xxx` to `qcxms.xxx`.
 - The `q-batch`, `pqcxms` and `plotms` script have been updated.
-- Collision induced dissociation (CID) calculations are now available. Set *cid* in the `qcxms.in` file. 
+- Collision induced dissociation (CID) calculations are now available. Set *cid* in the `qcxms.in` file (see
+  documentation) 
 
 **The tblite library for xTB calculations**
 - The [tblite](https://github.com/awvwgk/tblite) library has been included into the program code. This keeps xtb up-to-date and decreases the computational time for calculations done with GFN1- and GFN2-xTB when compared to earlier versions. 
+
+
+**Plotting Spectra**
+
+To evaluate the results and create a spectrum, download and use the [PlotMS](https://github.com/qcxms/PlotMS) program. 
+The [documentation](https://xtb-docs.readthedocs.io/en/latest/qcxms_doc/qcxms_plot.html) explains the basic
+functionalities of the program. 
+
+The program provides *mass.agr*, *JCAMP-DX* and *.csv* are files that can be analyzed. 
+For visualization of the calculated spectra, we recommend the usage of the **xmgrace** program. 
+
+### Updates
+
+Versions PlotMS v.6.0 and higher now provide **exact masses**.
+Experimental files in `.csv` format can now be read and plotted against the computed spectra.
+The `.mass_raw.agr` file was moved to the [PlotMS](https://github.com/qcxms/PlotMS) repository. 
diff --git a/config/meson.build b/config/meson.build
@@ -124,3 +124,12 @@ exe_deps += tblite_dep
 if tblite_dep.version().version_compare('>=0.3')
   error('tblite version 0.3 or higher is not supported yet.')
 endif
+
+# Create the rmsd tool as subproject
+rmsd_dep = dependency(
+  'rmsd-tool',
+  version: '>=0.1',
+  fallback: ['rmsd-tool', 'rmsd_dep'],
+  default_options: ['default_library=static'],
+)
+exe_deps += rmsd_dep
diff --git a/meson.build b/meson.build
@@ -3,7 +3,7 @@
 project(
   'qcxms',
   'fortran',
-  version: '5.1.3',
+  version: '5.2.0',
   license: 'LGPL-3.0-or-later',
   meson_version: '>=0.55',
   default_options: [

diff --git a/src/.gitignore b/src/.gitignore
@@ -0,0 +1 @@
+*.swp
diff --git a/src/Makefile b/src/Makefile