more fixes for lab3

git-svn-id: https://subversion.assembla.com/svn/qmcdev/trunk@6971 e5b18d87-469d-4833-9cc0-8cdfa06e9491

labs/lab3_advanced_molecules/exercises/ex1_first-run-hartree-fock/convert/h2o.hf.out

@@ -1 +0,0 @@
-../gms/h2o.hf.out

labs/lab3_advanced_molecules/exercises/ex1_first-run-hartree-fock/convert/h2o.ptcl.xml

@@ -1,43 +0,0 @@
-<?xml version="1.0"?>
-<qmcsystem>
-  <particleset name="e">
-    <group name="u" size="4">
-      <parameter name="charge">-1</parameter>
-      <attrib name="position" datatype="posArray">
- -6.6027728640e-01  2.5780019676e-01 -1.4667985018e-01
-  2.2161708024e-02  6.4959700188e-02 -7.2057692919e-01
- -1.7154101002e-02  3.2910251634e-01 -6.4446821907e-01
-  6.8623254359e-01 -1.5032219953e+00  1.3264698787e+00
-</attrib>
-    </group>
-    <group name="d" size="4">
-      <parameter name="charge">-1</parameter>
-      <attrib name="position" datatype="posArray">
- -2.3973462188e-01  6.8167605170e-01  4.2273945152e-02
- -2.1914254639e-01  6.8676896037e-01  6.5321927941e-02
-  1.3382082573e-01 -1.3409754056e-01  6.9860707916e-01
-  4.6552136660e-01  8.7657082698e-01  1.1137241817e+00
-</attrib>
-    </group>
-  </particleset>
-  <particleset name="ion0" size="3">
-    <group name="O">
-      <parameter name="charge">6</parameter>
-      <parameter name="valence">4</parameter>
-      <parameter name="atomicnumber">8</parameter>
-    </group>
-    <group name="H">
-      <parameter name="charge">1</parameter>
-      <parameter name="valence">1</parameter>
-      <parameter name="atomicnumber">1</parameter>
-    </group>
-    <attrib name="position" datatype="posArray">
-  0.0000000000e+00  0.0000000000e+00  0.0000000000e+00
- -0.0000000000e+00 -1.4308249289e+00  1.1078707576e+00
-  0.0000000000e+00  1.4308249289e+00  1.1078707576e+00
-</attrib>
-    <attrib name="ionid" datatype="stringArray">
- O H H 
-</attrib>
-  </particleset>
-</qmcsystem>

labs/lab3_advanced_molecules/exercises/ex1_first-run-hartree-fock/opt/h2o.ptcl.xml

@@ -1 +0,0 @@
-../convert/h2o.ptcl.xml

labs/lab3_advanced_molecules/exercises/ex1_first-run-hartree-fock/opt/h2o.wfs.xml

@@ -1 +0,0 @@
-../convert/h2o.wfs.xml

manual/lab_advanced_molecules.tex

@@ -157,7 +157,7 @@ system is -16.9600590022 Ha. To search for the energy in the output file quickly
 use 
 \begin{shaded}
 \begin{verbatim}
-grep "TOTAL ENERGY =" h2o.hf.out
+grep "TOTAL ENERGY =" h2o.hf.output
 \end{verbatim}
 \end{shaded}
 %When the calculation completes,
@@ -171,7 +171,7 @@ As the job runs on VESTA, it is a good time to review section B, which contains
 When the execution of the previous steps is completed, there should be 2 new
 files called h2o.wfs.xml and h2o.ptcl.xml. Now we will use VMC to optimize the 
 Jastrow parameters in the wave-function.  From the top directory, go to
-``ex1\_first-run-hartree-fock/opt''. Link the xml files generated in the previous step
+``ex1\_first-run-hartree-fock/opt''. Copy the xml files generated in the previous step
 to the current directory. This directory should already contain a basic QMCPACK input
 file for an optimization calculation (optm.xml) %and a submission script (submit.csh). 
 Open optm.xml with your favorite text editor and modify the name of the files that contain the