Remove binaries.

fix typo in file extension

.forgeignore

@@ -0,0 +1,6 @@
+*~
+TrimSPweb.js
+TrimSP.cfg
+ToDo.txt
+#*
+Readme.md

.gitignore

@@ -0,0 +1,122 @@
+# Logs
+logs
+*.log
+npm-debug.log*
+yarn-debug.log*
+yarn-error.log*
+lerna-debug.log*
+.pnpm-debug.log*
+
+# Diagnostic reports (https://nodejs.org/api/report.html)
+report.[0-9]*.[0-9]*.[0-9]*.[0-9]*.json
+
+# Runtime data
+pids
+*.pid
+*.seed
+*.pid.lock
+
+# Directory for instrumented libs generated by jscoverage/JSCover
+lib-cov
+
+# Coverage directory used by tools like istanbul
+coverage
+*.lcov
+
+# nyc test coverage
+.nyc_output
+
+# Grunt intermediate storage (https://gruntjs.com/creating-plugins#storing-task-files)
+.grunt
+
+# Bower dependency directory (https://bower.io/)
+bower_components
+
+# node-waf configuration
+.lock-wscript
+
+# Compiled binary addons (https://nodejs.org/api/addons.html)
+build/Release
+
+# Dependency directories
+node_modules/
+jspm_packages/
+
+# Snowpack dependency directory (https://snowpack.dev/)
+web_modules/
+
+# TypeScript cache
+*.tsbuildinfo
+
+# Optional npm cache directory
+.npm
+
+# Optional eslint cache
+.eslintcache
+
+# Microbundle cache
+.rpt2_cache/
+.rts2_cache_cjs/
+.rts2_cache_es/
+.rts2_cache_umd/
+
+# Optional REPL history
+.node_repl_history
+
+# Output of 'npm pack'
+*.tgz
+
+# Yarn Integrity file
+.yarn-integrity
+
+# dotenv environment variables file
+.env
+.env.test
+.env.production
+
+# parcel-bundler cache (https://parceljs.org/)
+.cache
+.parcel-cache
+
+# Next.js build output
+.next
+out
+
+# Nuxt.js build / generate output
+.nuxt
+dist
+
+# Gatsby files
+.cache/
+# Comment in the public line in if your project uses Gatsby and not Next.js
+# https://nextjs.org/blog/next-9-1#public-directory-support
+# public
+
+# vuepress build output
+.vuepress/dist
+
+# Serverless directories
+.serverless/
+
+# FuseBox cache
+.fusebox/
+
+# DynamoDB Local files
+.dynamodb/
+
+# TernJS port file
+.tern-port
+
+# Stores VSCode versions used for testing VSCode extensions
+.vscode-test
+
+# yarn v2
+.yarn/cache
+.yarn/unplugged
+.yarn/build-state.yml
+.yarn/install-state.gz
+.pnp.*
+
+# my additions
+package-lock.json
+*~

LICENSE

@@ -0,0 +1,674 @@
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+                            Preamble
+
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+software and other kinds of works.
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+  The licenses for most software and other practical works are designed
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+for and in connection with specific products or compilations that
+contain the covered work, unless you entered into that arrangement,
+or that patent license was granted, prior to 28 March 2007.
+
+  Nothing in this License shall be construed as excluding or limiting
+any implied license or other defenses to infringement that may
+otherwise be available to you under applicable patent law.
+
+  12. No Surrender of Others' Freedom.
+
+  If conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License.  If you cannot convey a
+covered work so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you may
+not convey it at all.  For example, if you agree to terms that obligate you
+to collect a royalty for further conveying from those to whom you convey
+the Program, the only way you could satisfy both those terms and this
+License would be to refrain entirely from conveying the Program.
+
+  13. Use with the GNU Affero General Public License.
+
+  Notwithstanding any other provision of this License, you have
+permission to link or combine any covered work with a work licensed
+under version 3 of the GNU Affero General Public License into a single
+combined work, and to convey the resulting work.  The terms of this
+License will continue to apply to the part which is the covered work,
+but the special requirements of the GNU Affero General Public License,
+section 13, concerning interaction through a network will apply to the
+combination as such.
+
+  14. Revised Versions of this License.
+
+  The Free Software Foundation may publish revised and/or new versions of
+the GNU General Public License from time to time.  Such new versions will
+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+  Each version is given a distinguishing version number.  If the
+Program specifies that a certain numbered version of the GNU General
+Public License "or any later version" applies to it, you have the
+option of following the terms and conditions either of that numbered
+version or of any later version published by the Free Software
+Foundation.  If the Program does not specify a version number of the
+GNU General Public License, you may choose any version ever published
+by the Free Software Foundation.
+
+  If the Program specifies that a proxy can decide which future
+versions of the GNU General Public License can be used, that proxy's
+public statement of acceptance of a version permanently authorizes you
+to choose that version for the Program.
+
+  Later license versions may give you additional or different
+permissions.  However, no additional obligations are imposed on any
+author or copyright holder as a result of your choosing to follow a
+later version.
+
+  15. Disclaimer of Warranty.
+
+  THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW.  EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE.  THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+  16. Limitation of Liability.
+
+  IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+  17. Interpretation of Sections 15 and 16.
+
+  If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    TrimSP
+    Copyright (C) 2023  salman
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+  If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+    <program>  Copyright (C) 2023  salman
+    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+  You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<https://www.gnu.org/licenses/>.
+
+  The GNU General Public License does not permit incorporating your program
+into proprietary programs.  If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.  But first, please read
+<https://www.gnu.org/licenses/why-not-lgpl.html>.

Readme.md

@@ -0,0 +1,86 @@
+# Trim.SP - TRIM simulation #
+
+### Contents ###
+
+This repository contains the [Fortran] source code and an accompanying
+graphical user interface ([GUI]) for TrimSP -
+an application for performing [Monte Carlo] simulations of ion implantation. 
+
+* This code is specifically tuned to simulate implantation of low-energy projectiles in materials.
+* The code is maintained by the Low Energy Muons ([LEM]) group at the Paul Scherrer Institute ([PSI]). 
+* The [GUI] is written in [Node.js], [JavaScript] and [Electron]. 
+* The binary (statically linked) from the [Fortran] code is also included.
+* [RPM] and [DEB] packages are also included.
+
+Further information can be found in the following publications:
+
+- J. P. Biersack and W. Eckstein,
+  <i>Sputtering studies with the Monte Carlo program TRIM.SP</i>,
+  Appl. Phys. A <b>34</b> (2), 73-94 (1984).
+  <https://doi.org/10.1007/BF00614759>
+- W. Eckstein,
+  <i>Computer Simulation of Ion-Solid Interactions</i>,
+  Springer Series in Materials Science Vol. 10
+  (Springer-Verlag, Berlin, Heidelberg, 1991).
+  <https://doi.org/10.1007/978-3-642-73513-4>
+- W. Eckstein,
+  <i>Backscattering and sputtering with the Monte-Carlo program TRIM.SP</i>,
+  Radiat. Eff. Defects Solids <b>130-131</b> (1), 239-250 (1994).
+  <https://doi.org/10.1080/10420159408219787>
+- E. Morenzoni et al.,
+  <i>Implantation studies of keV positive muons in thin metallic layers</i>,
+  Nucl. Instrum. Methods Phys. Res., Sect. B <b>192</b> (3), 245-266 (2002).
+  <https://doi.org/10.1016/S0168-583X(01)01166-1>
+
+### Supported platforms ###
+
+* [Linux]
+* Online at: http://musruser.psi.ch/TrimSP/
+
+### Installation ###
+
+For a simple installation you may use the included RPM or Debian packages which come with statically linked binaries. See instructions below if you prefer a manual installation. 
+
+###### Fortran code compilation ######
+
+Install the `gfortran` compiler, then:
+
+```bash
+cd trimsp/fortran
+make
+make install
+```
+    
+This will install the `trimspNL` binary in `/usr/local/bin`,
+but it can be moved to any other directory in your `PATH`.
+
+###### Running the GUI ######
+
+Install [Node.js] (`nodejs`, `nodejs-libs` and `npm`),
+then run:
+
+```bash
+cd trimsp
+npm install
+npm start
+```
+
+Note: you do not need to run `npm install` every time.
+Next time you can simply run `npm start` only. 
+
+### Contact ###
+
+Zaher Salman <zaher.salman@psi.ch>
+
+
+[Fortran]: https://fortran-lang.org/
+[Node.js]: https://nodejs.org/en/
+[JavaScript]: https://www.javascript.com/
+[Electron]: https://www.electronjs.org/
+[PSI]: https://www.psi.ch/en
+[LEM]: https://www.psi.ch/en/low-energy-muons
+[RPM]: https://rpm.org/
+[DEB]: https://en.wikipedia.org/wiki/Deb_(file_format)
+[Linux]: https://en.wikipedia.org/wiki/Linux
+[Monte Carlo]: https://en.wikipedia.org/wiki/Monte_Carlo_method
+[GUI]: https://en.wikipedia.org/wiki/Graphical_user_interface

ToDo.txt

@@ -0,0 +1,2 @@
+- Increase the number of elements acceptable for each layer, currently up to 5
+- Stop using the tandard filenames eingabe/ausgabe etc. Take input filename as an argument and produce output files with the same name.

TrimSP.html

@@ -1,18 +1,14 @@
 <!DOCTYPE html>
-<html class="mcss">
+<html>
 <head>
   <meta http-equiv="Content-type" content="text/html;charset=UTF-8">
   <link rel="stylesheet" href="ZGUI.css">
   <link rel="stylesheet" href="https://www.w3schools.com/w3css/4/w3.css">
-  <script src="TrimSPlib.js"></script>
   <script src="TrimSPelec.js"></script>
+  <!script src="TrimSPWeb.js"></script>
+  <script src="TrimSPlib.js"></script>
   <script src="myplots.js"></script>
-  <script type="text/javascript">
-    const ipcRenderer = require('electron').ipcRenderer;
-    const fs = require('fs');
-    const exec = require('child_process').execSync;
-  </script>
-
+  <!script src="https://cdn.plot.ly/plotly-latest.min.js"></script>
   <title>Trim.SP</title>
 </head>
 <body onresize="resizePl()" onload="adjust_table();adjust_scans();">
@@ -23,27 +19,35 @@
 	  <button class="tablinks" onclick="openTab(event,'Layers')" id="btnLayers">Layers</button>
 	  <button class="tablinks" onclick="openTab(event,'Scans')" id="btnScans">Scans</button>
 	  <button class="tablinks" onclick="openTab(event,'Plots')" id="btnPlots">Plots</button>
-	  <button class="tablinks" onclick="openTab(event,'Other')" id="btnOther">Other Params</button>
+	  <button class="tablinks" onclick="openTab(event,'Other')" id="btnOther">Other Parameters</button>
 	</div>
 	<div id="Layers" class="tabcontent">
 	  <table style="width: 100%;">
 	    <tr>
 	      <td style="vertical-align: top;">
 		<table cellpadding="5">
-		  <tr>
-		    <td><label>File name prefix:</label><input name="fileNamePrefix" id="fileNamePrefix" type="text" size="7" value="SrTiO3"/>
-		      <label>saved in:</label><input type="text" id="workPath" name="workPath" value="/tmp/test" onchange="console.log(this.value);"/>
+		  <tr id="FileRow">
+		    <td><label>File name prefix:</label></td>
+		    <td>
+		      <input name="fileNamePrefix" id="fileNamePrefix" type="text" style="width:70%" value="SrTiO3"/>
+		      <input name="trimPath" id="trimPath" type="text" style="width:70%;visibility:hidden;"/>
+		    </td>
 		  </tr>
-		  <tr><td>
-		      <b>Layers</b>
-		  </td></tr>
-		  <tr><td>
-		      <label>Number of
-		      Layers: </label><input name="numLayer" id="numLayer" type="number" size="3" step="1" min="1" max="100" value="1" onchange="adjust_table()">
-		  </td></tr>
-		  <tr><td>
+		  <tr id="FolderRow">
+		    <td><label>Save folder:</label></td>
+		    <td>
+		      <input type="text" style="width:70%" id="workPath" name="workPath" readonly/>
+		      <input type="button" value="Browse"
+			     id="browseFolde" onclick="ipcRenderer.send('browseFolder');">
+		    </td>
+		  </tr>
+		  <tr>
+		    <td><label>Number of Layers:</label></td>
+		    <td><input name="numLayer" id="numLayer" type="number" size="3" step="1" min="1" max="100" value="1" onchange="adjust_table()"></td>
+		  </tr>
+		  <tr><td colspan="2">
 		      <table id="LTable" border="2" cellpadding="10">
-			<tr><td><b>Layer #</b></td><td><b>Composition</b></td><td><b>Density [g/cm<sup>3</sup>]</b></td><td><b>Thickness [A]</b></td></tr>
+			<tr><td><b>Layer #</b></td><td><b>Composition</b></td><td><b>Density [g/cm<sup>3</sup>]</b></td><td><b>Thickness [Å]</b></td></tr>
 		      </table>
 		  </td></tr>
 		</table>
@@ -53,24 +57,27 @@
 		  <tr><td collspan="2"><b>Projectile parameters</b></td></tr>
 		  <tr><td>Projectile</td>
 		    <td><select name="ProjType" id="ProjType" onchange="ProjSmartDefaults()" onload="ProjSmartDefaults()">
-			<option selected="selected" value="Muon">Muon</option>
-			<option  value="Li8">Li8</option>
-			<option  value="B12">B12</option>
-			<option  value="H">H</option>
+			<option selected="selected" value="muon">muon</option>
+			<option value="Li-8">Li-8</option>
+			<option value="B-12">B-12</option>
+			<option value="Mg-31">Mg-31</option>
+			<option value="H">H</option>
+			<option value="He">He</option>
+			<option value="Ar">Ar</option>
 		      </select>
 		    </td>
 		  </tr>
 		  <tr><td>Number of projectiles</td>
 		    <td><input name="numberProj" id="numberProj" type="text" size="7" value="1000" onchange="//ProjNumberLimit()"></td>
 		  </tr>
-		  <tr><td>Starting depth [A]</td><td><input name="z0" id="z0" type="text" size="7" value="0"></td></tr>
-		  <tr><td>Depth increment [A]</td><td><input name="dz" id="dz" type="text" size="7" value="20"></td></tr>
+		  <tr><td>Starting depth [Å]</td><td><input name="z0" id="z0" type="text" size="7" value="0"></td></tr>
+		  <tr><td>Depth increment [Å]</td><td><input name="dz" id="dz" type="text" size="7" value="20"></td></tr>
 		  <tr><td>Energy [eV]</td><td><input name="valEnergy" id="valEnergy" type="text" size="7" value="2000"></td></tr>
 		  <tr><td>Energy sigma [eV]</td><td><input name="sigEnergy" id="sigEnergy" type="text" size="7" value="450"></td></tr>
-		  <tr><td>Angel [deg]</td><td><input name="valAngle" id="valAngle" type="text" size="7" value="0"></td></tr>
+		  <tr><td>Angle [deg]</td><td><input name="valAngle" id="valAngle" type="text" size="7" value="0"></td></tr>
 		  <tr><td>Angle sigma [deg]</td><td><input name="sigAngle" id="sigAngle" type="text" size="7" value="15"></td></tr>
 		  <tr><td>Random seed</td><td><input name="ranSeed" id="ranSeed" type="text" size="7" value="78741"></td></tr>
-		  <tr><td><button onclick="document.getElementById('btnPlots').click();tester();">Start</button></td><td></td></tr> 
+		  <tr><td><button onclick="startSim();">Start</button></td><td></td></tr> 
 		</table>
 	      </td>
 	    </tr>
@@ -80,22 +87,22 @@
 	  <input type="checkbox" name="scanSeq" id="scanSeq" onChange="adjust_scans();">   Enable scan on
 	  <select name="scanType" id="scanType" onchange="adjust_scans();">
 	    <option value="scanLoop">Loop</option>
-	    <option value="scanVals">Set of Values</option>		  
+	    <option value="scanVals">Set of values</option>
 	  </select>
 	  <div id="ScansLine" style="visibility: hidden;">
-	    <br>Set of Values: <input name="scanList" id="scanList" type="text" value="1000">
-	    corresponding depth increment <input name="scanListdz" id="scanListdz" type="text" value="">
+	    <br>Set of values: <input name="scanList" id="scanList" type="text" value="1000">
+	    Corresponding depth increment: <input name="scanListdz" id="scanListdz" type="text" value="">
 	  </div>
 	  <table id="ScansTable" style="width: 100%;visibility: hidden;">
 	    <tr>
 	      <td colspan="3">Scan parameter
 		<select name="comboScan" id="comboScan" onchange="">
-		  <option value="EScan">Energy</option>
-		  <option value="SigEScan">Energy Sigma</option>
-		  <option value="AngleScan">Angle</option>
-		  <option value="SigAngleScan">Angle Sigma</option>
-		  <option value="NProjScan">Number of Projectiles</option>
-		  <option value="dScan">Thickness of layer1</option>
+		  <option value="EScan">Energy [eV]</option>
+		  <option value="SigEScan">Energy sigma [eV]</option>
+		  <option value="AngleScan">Angle [deg]</option>
+		  <option value="SigAngleScan">Angle sigma [deg]</option>
+		  <option value="NProjScan">Number of projectiles</option>
+		  <option value="dScan">Thickness of layer # 1</option>
 		</select>
 	      </td>
 	    </tr>
@@ -125,129 +132,261 @@
 	<div id="Other" class="tabcontent">
 	  <table cellpadding="5">
 	    <tr>
-	      <td>EF</td>
+	      <td class="tooltip">
+		EF
+		<span class="tooltiptext">
+		  Cutoff energy of projectiles (in eV); must be
+		  greater than zero. Used for low projectile energies
+		  (< 1000 eV) and ESB = 0. EF should be of the order
+		  of ~0.2 eV, but not above SBE (for sputtering
+		  data). With increasing projectile energy, EF can be
+		  increased to save computing time.
+		</span>
+	      </td>
 	      <td>
 		<input name="parEF" id="parEF" type="number" size="7" step="0.1" value="0.5">
 	      </td>
-	      <td>KK0</td>
+	      <td class="tooltip">
+	        KK0
+		<span class="tooltiptext">
+	          Maximum order of weak (simultaneous) collisions between projectile and target atoms:
+	          <ol>
+	            <li value="0">No weak collisions included.</li>
+	            <li value="1">???</li>
+	            <li value="2">Sufficient for most calculations.</li>
+	            <li value="3">Only useful for very heavy particles; increases computing time.</li>
+	            <li value="4">Only useful for very heavy particles; increases computing time.</li>
+	          </ol>
+	        </span>
+	      </td>
 	      <td>
 		<input name="parKK0" id="parKK0" type="number" step="1" min="0" max="4" value="2">
 	      </td>
 	    </tr>
 	    <tr>
-	      <td>ESB</td>
+	      <td class="tooltip">
+	   	ESB
+		<span class="tooltiptext">
+	          Surface binding energy for projectiles (in eV).
+	          This value is zero for the noble gases,
+	          but ESB should be larger than zero if the projectile is an active
+	          chemically species.
+	          ESB = SBE for self-sputtering calculations.
+	        </span>
+	      </td>
 	      <td>
 		<input name="parESB" id="parESB" type="number" size="7" step="0.1" value="0.0">
 	      </td>
-	      <td>KK0R</td>
+	      <td class="tooltip">
+	        KK0R
+		<span class="tooltiptext">
+	          Maximum order of weak (simultaneous) collisions between target atoms:
+	          <ol>
+	            <li value="0">No weak collisions included.</li>
+	            <li value="1">???</li>
+	            <li value="2">Sufficient for most calculations.</li>
+	            <li value="3">Only useful for very heavy particles; increases computing time.</li>
+	            <li value="4">Only useful for very heavy particles; increases computing time.</li>
+	          </ol>
+	        </span>
+	      </td>
 	      <td>
 		<input name="parKK0R" id="parKK0R" type="number" step="1" min="0" max="4" value="2">
 	      </td>
 	    </tr>
 	    <tr>
-	      <td>SHEATH</td>
+	      <td class="tooltip">
+	        SHEATH
+		<span class="tooltiptext">
+	          Sheath potential (in eV);
+	          typically 3 * kT (i.e.,  3 * |projectile energy|).
+	        </span>
+	      </td>
 	      <td>
 		<input name="parSHEATH" id="parSHEATH" type="number" size="7" step="0.1" value="0.0">
 	      </td>
-	      <td>KDEE1</td>
+	      <td class="tooltip">
+	        KDEE1
+		<span class="tooltiptext">
+	          Inelastic energy loss model for projectiles:
+	          <ol>
+	            <li value="1">Nonlocal (Lindhard-Scharff).</li>
+	            <li value="2">Local (Oen-Robinson).</li>
+	            <li value="3">Equipartition of local and nonlocal models (i.e., options 1 & 2).</li>
+	            <li value="4">Nonlocal (Anderson-Ziegler tables for hydrogen); must be used for hydrogen-like projectile with energies > 10 keV.</li>
+	            <li value="5">Nonlocal (Ziegler tables for helium); must be used for helium-like projectiles with energies > 50 keV.</li>
+	          </ol>
+	          Note: options 1, 2, and 3 can only be used at energies below the stopping power maximum.
+	        </span>
+	      </td>
 	      <td>
 		<input name="parKDEE1" id="parKDEE1" type="number" step="1" min="1" max="5" value="4">
 	      </td>
 	    </tr>
 	    <tr>
-	      <td>ERC</td>
+	      <td class="tooltip">
+	        ERC
+		<span class="tooltiptext">
+	          Recoil cutoff energy (in eV);
+	          usually equal to the surface binding energy.
+	        </span>
+	      </td>
 	      <td>
 		<input name="parERC" id="parERC" type="number" size="7" step="0.1" value="0.0">
 	      </td>
-	      <td>KDEE2</td>
+	      <td class="tooltip">
+	        KDEE2
+		<span class="tooltiptext">
+	          Inelastic energy loss for target atoms:
+	          <ol>
+	            <li value="1">Nonlocal (Lindhard-Scharff).</li>
+	            <li value="2">Local (Oen-Robinson).</li>
+	            <li value="3">Equipartition of local and nonlocal models (i.e., options 1 & 2).
+	            </li>
+	          </ol>
+	          Note: options 1, 2, and 3 can only be used at energies below the stopping power maximum.
+	        </span>
+	      </td>
 	      <td>
 		<input name="parKDEE2" id="parKDEE2" type="number" step="1" min="1" max="3" value="3">
 	      </td>
 	    </tr>
 	    <tr>
-	      <td>RD</td>
+	      <td class="tooltip">
+	      	RD
+		<span class="tooltiptext">
+	          Depth (in Å) to which recoils are followed.
+	          RD = 50 is usually sufficient for sputtering
+	          (if the projectile energy is not too high).
+	          Use RD = 100 * CW (i.e., the depth increment)
+	          for following the full collision cascade.
+	        </span>
+	      </td>
 	      <td>
 		<input name="parRD" id="parRD" type="number" size="7" step="0.1" value="50.0">
 	      </td>
-	      <td>IPOT</td>
+	      <td class="tooltip">
+	      	IPOT
+		<span class="tooltiptext">
+	          Interaction potential between projectile and target atoms:
+	          <ol>
+	            <li value="1">Krypton-Carbon (Kr-C) potential.</li>
+	            <li value="2">Molière potential.</li>
+	            <li value="3">Ziegler-Biersack-Littmark (ZBL) potential.</li>
+	          </ol>
+	        </span>
+	      </td>
 	      <td>
 		<input name="parIPOT" id="parIPOT" type="number" step="1" min="1" max="3" value="2">
 	      </td>
 	    </tr>
 	    <tr>
-	      <td>CA</td>
+	      <td class="tooltip">
+	        CA
+		<span class="tooltiptext">
+	          Correction factor to the Firsov screening length for
+	          collisions between projectile and target atoms
+	          (only used in the application of the Molière potential);
+	          usually on the order of ~1.0.
+	        </span>
+	      </td>
 	      <td>
 		<input name="parCA" id="parCA" type="number" size="7" step="0.1" value="1.0">
 	      </td>
-	      <td>IPOTR</td>
+	      <td class="tooltip">
+	        IPOTR
+		<span class="tooltiptext">
+	          Interaction potential between target atoms:
+	          <ol>
+	            <li value="1">Krypton-Carbon (Kr-C) potential.</li>
+	            <li value="2">Molière potential.</li>
+	            <li value="3">Ziegler-Biersack-Littmark (ZBL) potential.</li>
+	          </ol>
+	        </span>
+	      </td>
 	      <td>
 		<input name="parIPOTR" id="parIPOTR" type="number" step="1" min="0" max="3" value="1">
 	      </td>
 	    </tr>
 	    <tr>
-	      <td></td>
-	      <td></td>
-	      <td>IRL</td>
+	      <td class="tooltip">
+		<input type="checkbox" id="flagICRU" checked>
+		<span class="tooltiptext">
+		  Force the TRIM.SP code to use stopping power
+		  parameters from the old ICRU tables. 
+		</span>
+	      </td>
 	      <td>
-		<input name="parIRL" id="parIRL" type="number" step="1" min="0" max="2" value="0">
+		Use ICRU parameters
+	      </td>
+	      <td class="tooltip">
+	        IRL
+		<span class="tooltiptext">
+	          Collision recoils:
+	          <ol>
+	            <li value="0">
+	              No recoils are generated (i.e., no sputtering effects);
+	              used to speed up the calculation if only projectile ranges are of interest.
+	            </li>
+	            <li value="1">Calculate collision recoils.</li>
+	          </ol>
+	        </span>
+	      </td>
+	      <td>
+		<input name="parIRL" id="parIRL" type="number" step="1" min="0" max="1" value="0">
 	      </td>
 	    </tr>
-	  </table>
+          </table>
+	  <p>
+	    For further details see:
+	  </p>
+	  <p>
+	    W. Eckstein, <i>Computer Simulation of Ion-Solid Interactions</i>,<br>
+	    Springer Series in Materials Science, Vol. 10 (Springer-Verlag, Berlin, 1991).<br>
+	    <a href="https://doi.org/10.1007/978-3-642-73513-4">
+	      https://doi.org/10.1007/978-3-642-73513-4
+	    </a>
+	  </p>
 	</div>
       </div>
   </td></tr>
-  <!tr>
-    <!td>
-      <!progress id="myBar" max=100 min=0><!/progress>
-    <!/td>
-  <!/tr>
+  <tr style="width: 100%;//visibility: hidden;">
+    <td>
+      <div class="w3-light-grey">
+	<div id="pBar" class="w3-container w3-green w3-center" style="width:0%">0%</div>
+      </div> 
+    </td>
+  </tr>
 </table>
 </body>
 <script>
-  // Catch calls for open file
-  ipcRenderer.on('openFile', function(event, filename) {
-      console.log('Open file '+filename);
-      fs.readFile(filename.toString(), function read(err, data) {
-	  if (err) {
-	      throw err;
-	  }
-	  setValues(data);
-      });
-  });
-  // Catch calls for selectfolder
-  ipcRenderer.on('selectFolder', function(event, foldername) {
-      // If foldername is empty use default value
-      if (foldername == '') {foldername ="/tmp/test";}
-      document.getElementById("workPath").value = foldername;
-      console.log("folder="+foldername);
-  });
-  // Catch calls for save as
-  ipcRenderer.on('saveFile', function(event, filename) {
-      // If filename is empty use default value
-      if (filename == '') {filename='TrimSP.cfg';}
-      // Get values from all fields and prepare config file
-      let trimSPcfg=prep_cfg(0);
-      // Save file to filename
-      console.log('Save file to '+filename);
-      try { fs.writeFileSync(filename, trimSPcfg, 'utf-8'); }
-      catch(e) { alert('Failed to save the file !'); }
-  });
-  // Catch calls for plotProf
-  ipcRenderer.on('plotProf', function(event, filename) {
-      console.log("filename="+filename);
-      plotProfiles(filename);
-  });
-  // Catch calls for plotFrac
-  ipcRenderer.on('plotFrac', function(event, filename) {
-      console.log("filename="+filename);
-      plotFractions(filename);
-  });
-  // Catch calls for plotMean
-  ipcRenderer.on('plotMean', function(event, filename) {
-      console.log("filename="+filename);
-      plotMean(filename);
-  });
-  // Get the element with id="defaultOpen" and click on it
+
+  let workPath = document.getElementById("workPath");
+  // If empty or undefined use local folder as default
+  if (workPath.value == '' || workPath.value == undefined ) {
+       //     workPath.value = process.cwd();
+            workPath.value = '/tmp';
+      //app.setPath('temp',process.cwd());
+  }
+  // Open the default Layers tab
   document.getElementById("btnLayers").click();
+
+  let webOrApp = amIWeb();
+  
+  if (webOrApp) {
+      console.log('this script is not running in Node.js');
+      // Run as a web app
+      //let row = document.getElementById("FileRow");
+      //row.parentNode.removeChild(row);
+      //row = document.getElementById("FolderRow");
+      //row.parentNode.removeChild(row);
+      document.getElementById("FileRow").style.visibility = "hidden";;
+      document.getElementById("FolderRow").style.visibility = "hidden";;
+  } else {
+      console.log('this script is running in Node.js');
+      // Run as standalone app
+      // Set up after first load (electron specific menu calls)
+      firstLoad();
+  }
 </script>
 </html>

TrimSPelec.js

@@ -1,4 +1,12 @@
-// This file contains function that are Electron/Node specific
+// This file contains function that are Electron/Node.JS specific
+
+// Load required packages
+const Plotly = require('plotly.js-dist');
+const ipcRenderer = require('electron').ipcRenderer;
+const fs = require('fs');
+const exec = require('child_process').execSync;
+const remote = require('electron').remote;
+
 function getFiles(dir, filelist){
     fileList = [];
     var files = fs.readdirSync(dir);
@@ -17,7 +25,7 @@ function execute(command) {
 }
 
 function checkDir(directory) {
-    // Check whether director exists, if not create it
+    // Check whether directory exists, if not create it
     if (!fs.existsSync(directory)) {
 	// Folder does not exist try to create it
 	fs.mkdir(directory,{recursive: true}, (err) => {
@@ -54,10 +62,72 @@ function readAsciiFile(filename) {
     return(content);
 }
 	       
-function appPath() {
-    // return the path where the app resides
-//    let path = require('app').getAppPath();
-    //    console.log(path);
-    let path = "./";
-    return path;
+function fileExists(filename) {
+    try {
+	if (fs.existsSync(filename)) {
+	    return 1;
+	}
+    }catch(err) {
+	console.log(err);
+    }
+    return 0;
+}
+
+function firstLoad() {
+    document.getElementById("trimPath").value = remote.getGlobal('path');
+    
+    // Catch calls for open file
+    ipcRenderer.on('openFile', function(event, filename) {
+	console.log('Open file '+filename);
+	fs.readFile(filename.toString(), function read(err, data) {
+	    if (err) {
+		throw err;
+	    }
+	    setValues(data);
+	});
+    });
+    
+    // Catch calls for selectfolder
+    ipcRenderer.on('selectFolder', function(event, foldername) {
+	if (foldername.length != 0) {
+	    document.getElementById("workPath").value = foldername[0];
+	    // Change process directory
+	    process.chdir(foldername[0]);
+	}
+	console.log("currentdir",process.cwd());
+    });
+    // Catch calls for save as
+    ipcRenderer.on('saveFile', function(event, filename) {
+	// If filename is empty use default value
+	if (filename == '') {filename='TrimSP.cfg';}
+	// Get values from all fields and prepare config file
+	let trimSPcfg=prep_cfg(0);
+	// Save file to filename
+	console.log('Save file to '+filename);
+	try { fs.writeFileSync(filename, trimSPcfg, 'utf-8'); }
+	catch(e) { alert('Failed to save the file !'); }
+    });
+    // Catch calls for plotProf
+    ipcRenderer.on('plotProf', function(event, filename) {
+	console.log("filename="+filename);
+	plotProfiles(filename);
+    });
+    // Catch calls for plotFrac
+    ipcRenderer.on('plotFrac', function(event, filename) {
+	console.log("filename="+filename);
+	plotFractions(filename);
+    });
+    // Catch calls for plotMean
+    ipcRenderer.on('plotMean', function(event, filename) {
+	console.log("filename="+filename);
+	plotMean(filename);
+    });
+    // Catch clicks for Browse button
+    ipcRenderer.on('browseFolder', function(event, foldername) {
+	if (foldername.length != 0) {
+	    document.getElementById("workPath").value = foldername[0];
+	    // Change process directory
+	    process.chdir(foldername[0]);
+	}
+    });
 }

TrimSPweb.js

@@ -0,0 +1,124 @@
+// This file contains function that are web app specific
+
+function writeAsciiFile(filename,content) {
+    // Write string content into ascii file filename
+    // Go via CGI script
+    //console.log(filename, content);
+    // Prepare CGI args use POST for long files
+    let cgiargs = "fn="+filename; // POST
+    let lines = content.split(/\n/);
+    let prefix = filename.split(/\//);
+    for (let i=0; i<lines.length; i++) {
+	cgiargs += "&line" + i + "=" + lines[i].replace(/\s\s+/g, ' ');
+    }
+
+    var xhttp;
+    xhttp = new XMLHttpRequest();
+    xhttp.onreadystatechange = function() {
+        if (this.readyState == 4 && this.status == 200) {
+	    console.log("response=",xhttp.responseText);
+	} else if (this.readyState == 4) {
+	    console.log(xhttp.status, xhttp.statusText);
+	}
+    }
+    let request = "/cgi-bin/singleTrimSP.cgi"; //POST
+    xhttp.open("POST", request, false);   //POST
+
+    //Send the proper header information along with the request
+    xhttp.setRequestHeader('Content-type', 'application/x-www-form-urlencoded'); //POST
+    xhttp.send(cgiargs); //POST
+    // Now you can add a link to the files
+    let d = document.getElementById("linkDiv");
+    if (!d) {
+	d = document.createElement("div");
+	d.id = "linkDiv";
+	document.body.appendChild(d);
+    }
+    let htmlLink = "Download files: <a href='";
+    htmlLink += "/tmp/" + prefix[2] + ".tgz'>";
+    htmlLink += prefix[2] + ".tgz</a>";
+    d.innerHTML = htmlLink;
+	
+    return(1);
+}
+
+function writeAsciiFile2(filename,content) {
+    // Write string content into ascii file filename
+    // Go via CGI script
+    //console.log(filename, content);
+    // Prepare CGI args use GET for short files
+    let cgiargs = "?fn="+filename; // GET
+    let lines = content.split(/\n/);
+    let prefix = filename.split(/\//);
+    for (let i=0; i<lines.length; i++) {
+	cgiargs += "&line" + i + "=" + lines[i].replace(/\s\s+/g, ' ');
+    }
+
+    var xhttp;
+    xhttp = new XMLHttpRequest();
+    xhttp.onreadystatechange = function() {
+        if (this.readyState == 4 && this.status == 200) {
+	    console.log("response=",xhttp.responseText);
+	} else if (this.readyState == 4) {
+	    console.log(xhttp.status, xhttp.statusText);
+	}
+    }
+    let request = "/cgi-bin/singleTrimSP.cgi"+cgiargs; // GET
+    xhttp.open("GET", request, false);   //GET
+
+    //Send the proper header information along with the request
+    xhttp.send(); // GET
+    // Now you can add a link to the files
+    let d = document.getElementById("linkDiv");
+    if (!d) {
+	d = document.createElement("div");
+	d.id = "linkDiv";
+	document.body.appendChild(d);
+    }
+    let htmlLink = "Download files: <a href='";
+    htmlLink += "/tmp/" + prefix[2] + ".tgz'>";
+    htmlLink += prefix[2] + ".tgz</a>";
+    d.innerHTML = htmlLink;
+	
+    return(1);
+}
+
+function readAsciiFile(filename) {
+    // Read ascii file filename and return content in a string
+    var xhttp;
+    let file = filename;
+    if (filename == "" || filename == undefined || filename == null) {
+        return 0;
+    } else {
+        // Make an HTTP request
+        xhttp = new XMLHttpRequest();
+        xhttp.onreadystatechange = function() {
+            if (this.readyState == 4) {
+		if (this.status == 404) {
+                    console.log("File "+file+" not found.");
+		    return(0);
+                }
+	    }
+	}
+	// Force refresh, do not use cache
+	filename += "?" + Date();
+	//filename = "http://musruser.psi.ch" + filename;
+        xhttp.open("GET", filename, false);
+	xhttp.overrideMimeType("text/plain");
+        xhttp.send();
+	return(xhttp.responseText);
+    }
+}
+	       
+function fileExists(filename) {
+    var xhr = new XMLHttpRequest();
+    xhr.open('HEAD', filename, false);
+    xhr.send();
+     
+    if (xhr.status == "404") {
+        return 0;
+    } else {
+        return 1;
+    }
+}
+

ZGUI.css

@@ -3,7 +3,7 @@
 }
 
 td {
-    white-space: nowrap;
+    white-space: wrap;
 }
 
 .guitable {
@@ -140,7 +140,7 @@ td {
 }
     
 .tabcontent {
-    animation: fadeEffect 1s; /* Fading effect takes 1 second */
+/*    animation: fadeEffect 1s; /* Fading effect takes 1 second */
 }
     
 /* Go from zero to full opacity */
@@ -175,3 +175,30 @@ td {
     line-height: 30px; /* To center it vertically */
     color: white;
 }
+
+/* Tooltip container */
+.tooltip {
+  position: relative;
+  display: inline-block;
+  /* border-bottom: 1px dotted black; /* If you want dots under the hoverable text */
+}
+
+/* Tooltip text */
+.tooltip .tooltiptext {
+  visibility: hidden;
+  width: 320px;
+  background-color: black;
+  color: #fff;
+  text-align: left;
+  padding: 5px;
+  border-radius: 6px;
+ 
+  /* Position the tooltip text - see examples below! */
+  position: absolute;
+  z-index: 1;
+}
+
+/* Show the tooltip text when you mouse over the tooltip container */
+.tooltip:hover .tooltiptext {
+  visibility: visible;
+}

fortran/Makefile

@@ -0,0 +1,33 @@
+# Makefile MAKEFILE_unix_trimsp.
+#
+# 17-Jun-2002 TP, use standard f77 code; use
+#             ranlux random number generator of the CERN mathlib
+#
+# 4-Feb-2013 ZS, clean up makefile and include random number
+#            generator in the code. Use gfortran which is now
+#            a standard part of gcc in moder systems.
+#
+
+FC = gfortran
+DEBUG = # -g -O -fbacktrace -ffpe-trap='underflow'
+WARN = # -Wall -Wextra
+DIALECT = -std=gnu
+prefix = /usr/local
+# OPS = -c $(DIALECT) $(WARN) $(DEBUG)
+#FCFLAGS = $(DIALECT) $(WARN) $(DEBUG) -O3 -mcmodel=large
+FCFLAGS = $(DIALECT) $(WARN) $(DEBUG) -O3 -mcmodel=medium
+
+all : trimspNL
+
+trimspNL : trimspNL.F
+	$(FC) $(FCFLAGS) -o $@ $<
+
+clean:
+	rm -f *.o *~ \#* .#* trimspNL
+
+install:
+	mv trimspNL $(prefix)/bin/.
+
+trimspNL-static : trimspNL.F
+	$(FC) $(FCFLAGS) -static -o $@ $<
+

main.js

@@ -1,27 +1,30 @@
 const { app, BrowserWindow, Menu, dialog, ipcMain, fs } = require('electron');
-
 function createWindow () {
     const win = new BrowserWindow({
 	width: 950,
 	height: 580,
+	icon: "/usr/lib/TrimSP/resources/app/icon.png",
 	webPreferences: {
+	    contextIsolation: false,
 	    nodeIntegration: true,
-	    nativeWindowOpen: true
+	    nativeWindowOpen: true,
+	    enableRemoteModule: true,
 	}
     })
 
     
-    const template = [
+    let template = [
 	{
 	    label: 'File',
 	    submenu: [
 		{
 		    label: 'Open',
+		    id : 'openItem',
 		    accelerator: 'CmdOrCtrl+O',
 		    click () {
 			dialog.showOpenDialog(win,
 					      { title : "Load configuration file", 
-						defaultPath : "./",
+						defaultPath : app.getPath('temp'),
 						//buttonLabel : "Custom button",
 						filters :[
 						    {name: 'Config file type', extensions: ['cfg']},
@@ -31,8 +34,10 @@ function createWindow () {
 						 console.log(result.canceled);
 						 console.log(result.filePaths);
 						 if (!result.canceled) {
-						     var focusedWindow = BrowserWindow.getFocusedWindow();
-						     focusedWindow.webContents.send('openFile',result.filePaths);
+						     setImmediate(function() {
+							 var focusedWindow = BrowserWindow.getFocusedWindow();
+							 focusedWindow.webContents.send('openFile',result.filePaths);
+						     });
 						 }
 					     }).catch(err => {
 						 console.log(err);
@@ -45,12 +50,14 @@ function createWindow () {
 		    click () {
 			dialog.showOpenDialog(win,
 					      { title: "Select folder",
-						defaultPath : "./",
+						defaultPath :  app.getPath('temp'),
 						properties:["openDirectory"]}
 					     ).then(result => {
-						 console.log(result.filePaths)
-						 var focusedWindow = BrowserWindow.getFocusedWindow();
-						 focusedWindow.webContents.send('selectFolder',result.filePaths);
+						 setImmediate(function() {
+						     console.log(result.filePaths)
+						     var focusedWindow = BrowserWindow.getFocusedWindow();
+						     focusedWindow.webContents.send('selectFolder',result.filePaths);
+						 });
 					     }).catch(err => {
 						 console.log(err);
 					     })
@@ -60,8 +67,10 @@ function createWindow () {
 		    label: 'Save',
 		    accelerator: 'CmdOrCtrl+S',
 		    click () {
-			var focusedWindow = BrowserWindow.getFocusedWindow();
-			focusedWindow.webContents.send('saveFile','');
+			setImmediate(function() {
+			    var focusedWindow = BrowserWindow.getFocusedWindow();
+			    focusedWindow.webContents.send('saveFile','');
+			});
 		    }
 		},
 		{
@@ -70,15 +79,17 @@ function createWindow () {
 		    click () {
 			dialog.showSaveDialog(win,
 					      { title : "Save configuration file", 
-						defaultPath : "./",
+						defaultPath : app.getPath('temp'),
 						filters :[
 						    {name: 'Config file type', extensions: ['cfg']},
 						    {name: 'All Files', extensions: ['*']}
 						],
 						properties: ['showOverwriteConfirmation']}
 					     ).then(result => {
-						 var focusedWindow = BrowserWindow.getFocusedWindow();
-						 focusedWindow.webContents.send('saveFile',result.filePath);
+						 setImmediate(function() {
+						     var focusedWindow = BrowserWindow.getFocusedWindow();
+						     focusedWindow.webContents.send('saveFile',result.filePath);
+						 });
 					     }).catch(err => {
 						 console.log(err);
 					     })
@@ -88,11 +99,13 @@ function createWindow () {
 		    label: 'Print',
 		    accelerator: 'CmdOrCtrl+P',
 		    click () {
-			var focusedWindow = BrowserWindow.getFocusedWindow();
-			const options = {};
-			focusedWindow.webContents.print(options, (success, errorType) => {
-			    if (!success) console.log(errorType)
-			})
+			setImmediate(function() {
+			    var focusedWindow = BrowserWindow.getFocusedWindow();
+			    const options = {};
+			    focusedWindow.webContents.print(options, (success, errorType) => {
+				if (!success) console.log(errorType)
+			    });
+			});
 		    }
 		},
 		{
@@ -121,8 +134,10 @@ function createWindow () {
 						 console.log(result.canceled);
 						 console.log(result.filePaths);
 						 if (!result.canceled) {
-						     var focusedWindow = BrowserWindow.getFocusedWindow();
-						     focusedWindow.webContents.send('plotProf',result.filePaths);
+						     setImmediate(function() {
+							 var focusedWindow = BrowserWindow.getFocusedWindow();
+							 focusedWindow.webContents.send('plotProf',result.filePaths);
+						     });
 						 }
 					     }).catch(err => {
 						 console.log(err);
@@ -144,8 +159,10 @@ function createWindow () {
 						 console.log(result.canceled);
 						 console.log(result.filePaths);
 						 if (!result.canceled) {
-						     var focusedWindow = BrowserWindow.getFocusedWindow();
-						     focusedWindow.webContents.send('plotFrac',result.filePaths);
+						     setImmediate(function() {
+							 var focusedWindow = BrowserWindow.getFocusedWindow();
+							 focusedWindow.webContents.send('plotFrac',result.filePaths);
+						     });
 						 }
 					     }).catch(err => {
 						 console.log(err);
@@ -167,8 +184,10 @@ function createWindow () {
 						 console.log(result.canceled);
 						 console.log(result.filePaths);
 						 if (!result.canceled) {
-						     var focusedWindow = BrowserWindow.getFocusedWindow();
-						     focusedWindow.webContents.send('plotMean',result.filePaths);
+						     setImmediate(function() {
+							 var focusedWindow = BrowserWindow.getFocusedWindow();
+							 focusedWindow.webContents.send('plotMean',result.filePaths);
+						     });
 						 }
 					     }).catch(err => {
 						 console.log(err);
@@ -196,7 +215,7 @@ function createWindow () {
 	    ]
 	}
     ]
-    const menu = Menu.buildFromTemplate(template)
+    let menu = Menu.buildFromTemplate(template)
     Menu.setApplicationMenu(menu)
     
     win.loadFile('TrimSP.html');
@@ -205,7 +224,8 @@ function createWindow () {
 }
 
 app.whenReady().then(createWindow)
-console.log(app.getAppPath());
+global.path = app.getAppPath();
+//console.log("From main: ",global.path);
 
 app.on('window-all-closed', () => {
   if (process.platform !== 'darwin') {
@@ -219,15 +239,32 @@ app.on('activate', () => {
   }
 })
 
-ipcMain.on('folderSelect', (event) => {
+// Reply to calls from browser button
+ipcMain.on('browseFolder', (event, args) => {
+    console.log('received a message: '+args);
     dialog.showOpenDialog({ title: "Select folder",
-			    defaultPath : "./",
+			    defaultPath : app.getPath('temp'),
 			    properties:["openDirectory"]}
 			 ).then(result => {
-			     console.log(result.filePaths)
-			     var focusedWindow = BrowserWindow.getFocusedWindow();
-			     focusedWindow.webContents.send('selectFolder',result.filePaths);
+			     console.log(result)
+			     setImmediate(function() {
+				 var focusedWindow = BrowserWindow.getFocusedWindow();
+				 focusedWindow.webContents.send('browseFolder',result.filePaths);
+				 app.setPath('temp',result.filePaths[0]);
+			     });
 			 }).catch(err => {
 			     console.log(err);
 			 })
 });
+
+//ipcMain.on('browseFolder-send', (event, args) => {
+//    dialog.showOpenDialog(null, args).then(filePaths => {
+//	event.sender.dend('browseFolder', filePaths);
+//    }).catch(err => {
+//	console.log(err);
+//    })
+//});
+
+
+//menuItem = menu.getMenuItemById('openItem');
+//console.log(menuItem);

myplots.js

@@ -1,5 +1,3 @@
-const Plotly = require('plotly.js-dist');
-
 function Plot_xy(plotdiv,x,y,labels){
     // Plot (x,y) scatter with x/ylabels
     // place generated plot in div named plotdiv
@@ -97,7 +95,7 @@ function sizePlot(){
 
 function resizePl(flag){
     let newx=this.innerWidth/2-50;
-    let newy=this.innerHeight-85;
+    let newy=this.innerHeight-185;
     var plotDiv1=this.document.getElementById("plotRge");
     var plotDiv2=this.document.getElementById("plotFrac");
     var update ={

package.json

@@ -1,6 +1,6 @@
 {
   "name": "TrimSP",
-  "version": "1.0.0",
+  "version": "1.0.2",
   "description": "Trim.SP simulation to calculate stopping profile of implanted probes.",
   "main": "main.js",
   "scripts": {
@@ -8,7 +8,10 @@
     "package": "electron-forge package",
     "make": "electron-forge make"
   },
-  "keywords": [],
+  "keywords": [
+    "TRIM",
+    "SRIM"
+  ],
   "author": "Zaher Salman",
   "license": "GPL2",
   "devDependencies": {
@@ -20,12 +23,19 @@
     "electron": "^11.2.1"
   },
   "dependencies": {
-    "electron-squirrel-startup": "^1.0.0",
     "plotly.js-dist": "^1.58.4"
   },
   "config": {
     "forge": {
-      "packagerConfig": {},
+      "packagerConfig": {
+        "icon": "appicons/icons/png/1024x1024.png",
+        "ignore": [
+          "Readme.md",
+          "ToDo.txt",
+          "TrimSP.cfg",
+          "fortran/*"
+        ]
+      },
       "makers": [
         {
           "name": "@electron-forge/maker-squirrel",