From 9f2b57506b7d991691e8e7b6b81fa84a89c62ae1 Mon Sep 17 00:00:00 2001
From: Francois Gygi <fgygi@ucdavis.edu>
Date: Thu, 5 Dec 2013 21:29:17 +0000
Subject: [PATCH] added utility shell script

git-svn-id: http://qboxcode.org/svn/qb/trunk@1419 cba15fb0-1239-40c8-b417-11db7ca47a34
---
 util/egap.sh           | 17 +++++++++++++++++
 util/get_atomset.sh    |  8 ++++++++
 util/qbox_maxforce.sh  |  9 +++++++++
 util/qbox_replicate.sh | 31 +++++++++++++++++++++++++++++++
 util/qbox_translate.sh | 17 +++++++++++++++++
 util/qbox_xyz.sh       | 39 +++++++++++++++++++++++++++++++++++++++
 util/sample_to_move.sh | 28 ++++++++++++++++++++++++++++
 util/sample_to_sys.sh  | 41 +++++++++++++++++++++++++++++++++++++++++
 8 files changed, 190 insertions(+)
 create mode 100755 util/egap.sh
 create mode 100755 util/get_atomset.sh
 create mode 100755 util/qbox_maxforce.sh
 create mode 100755 util/qbox_replicate.sh
 create mode 100755 util/qbox_translate.sh
 create mode 100755 util/qbox_xyz.sh
 create mode 100755 util/sample_to_move.sh
 create mode 100755 util/sample_to_sys.sh

diff --git a/util/egap.sh b/util/egap.sh
new file mode 100755
index 0000000..6ad47d8
--- /dev/null
+++ b/util/egap.sh
@@ -0,0 +1,17 @@
+#!/bin/bash
+# compute Egap = E(n+1) - E(n)
+# use: egap.sh n file.r
+declare -i nocc=$1
+shift
+declare -i nl=nocc/5+1
+#echo "nl=" $nl
+declare -i nfrac=nocc-5*\(nocc/5\)
+#echo "nfrac=" $nfrac
+
+grep -h -A$nl '<eigenvalues ' ${*}| \
+ awk -v nl=$nl -v nfrac=$nfrac \
+  ' NR%(nl+2)==nl {e[0] = $5;} \
+    NR%(nl+2)==(nl+1) \
+    { e[1]=$1; e[2]=$2; e[3]=$3; e[4]=$4; e[5]=$5; \
+      e_homo = e[nfrac]; e_lumo = e[nfrac+1]; \
+      print "E_HOMO=",e_homo, "E_LUMO=",e_lumo, "Eg=",e_lumo-e_homo}' -
diff --git a/util/get_atomset.sh b/util/get_atomset.sh
new file mode 100755
index 0000000..9b936aa
--- /dev/null
+++ b/util/get_atomset.sh
@@ -0,0 +1,8 @@
+#!/bin/bash
+# get_atomset: extract atomset from a Qbox sample
+#
+# use: get_atomset sample.xml
+#
+nlines=$(grep /atomset -m 1 -n $1 | cut -f1 -d: - )
+head -$nlines $1 
+echo "</fpmd:sample>"
diff --git a/util/qbox_maxforce.sh b/util/qbox_maxforce.sh
new file mode 100755
index 0000000..c7557b2
--- /dev/null
+++ b/util/qbox_maxforce.sh
@@ -0,0 +1,9 @@
+#!/bin/bash
+# get the largest force component in a file of "<force> fx fy fz </force>"
+# use: qbox_maxforce nat file.r
+grep '<force>' $2 | tail -$1 | \
+awk '{
+  if ( mx*mx < $2*$2 ) mx = $2;
+  if ( my*my < $3*$3 ) my = $3;
+  if ( mz*mz < $4*$4 ) mz = $4;
+} END {printf("%9.2e %9.2e %9.2e\n", mx, my, mz)}' - 
diff --git a/util/qbox_replicate.sh b/util/qbox_replicate.sh
new file mode 100755
index 0000000..8831a00
--- /dev/null
+++ b/util/qbox_replicate.sh
@@ -0,0 +1,31 @@
+#!/bin/bash
+#
+# qbox_replicate: replicate the unit cell in the a0,a1,a2 directions.
+# use: qbox_replicate cell.sys n0 n1 n2 > newcell.sys
+#
+if (( $# != 4 ))
+  then echo "use: qbox_replicate cell.sys n0 n1 n2 > newcell.sys"
+  exit
+fi
+gawk -v n0=$2 -v n1=$3 -v n2=$4 \
+    ' / cell/  {a0x=$3;a0y=$4;a0z=$5; \
+               a1x=$6;a1y=$7;a1z=$8; \
+               a2x=$9;a2y=$10;a2z=$11; \
+      print "set cell ", \
+        n0*$3,n0*$4,n0*$5, n1*$6,n1*$7,n1*$8, n2*$9,n2*$10,n2*$11} \
+      /ref_cell/  { \
+      print "set ref_cell ", \
+        n0*$3,n0*$4,n0*$5, n1*$6,n1*$7,n1*$8, n2*$9,n2*$10,n2*$11} \
+      /species/  {print} \
+      /atom/ {x=$4 - (n0-1)*a0x/2 - (n1-1)*a1x/2 - (n2-1)*a2x/2; \
+              y=$5 - (n0-1)*a0y/2 - (n1-1)*a1y/2 - (n2-1)*a2y/2; \
+              z=$6 - (n0-1)*a0z/2 - (n1-1)*a1z/2 - (n2-1)*a2z/2; \
+              for ( i=0; i<n0; i++ )
+              for ( j=0; j<n1; j++ )
+              for ( k=0; k<n2; k++ )
+                printf("atom %s_%d%d%d %s %12.6f %12.6f %12.6f\n", \
+                       $2,i,j,k,$3, \
+                  x+i*a0x+j*a1x+k*a2x, \
+                  y+i*a0y+j*a1y+k*a2y, \
+                  z+i*a0z+j*a1z+k*a2z) \
+             }' $1
diff --git a/util/qbox_translate.sh b/util/qbox_translate.sh
new file mode 100755
index 0000000..db5f665
--- /dev/null
+++ b/util/qbox_translate.sh
@@ -0,0 +1,17 @@
+#!/bin/bash
+# qbox_translate: translate all atoms 
+# use: qbox_replicate cell.sys dx dy dz > newcell.sys
+#
+if (( $# != 4 ))
+  then echo "use: qbox_translate cell.sys dx dy dz > newcell.sys"
+  exit
+fi
+awk -v dx=$2 -v dy=$3 -v dz=$4 \
+    ' /^#/  {print} \
+      / cell/  {print} \
+      /ref_cell/  {print}
+      /species/  {print} \
+      /atom/ {x=$4 + dx; y=$5 + dy; z=$6 + dz; \
+              printf("atom %s %s %12.6f %12.6f %12.6f\n", \
+                       $2,$3,x,y,z) \
+             }' $1
diff --git a/util/qbox_xyz.sh b/util/qbox_xyz.sh
new file mode 100755
index 0000000..e362d1f
--- /dev/null
+++ b/util/qbox_xyz.sh
@@ -0,0 +1,39 @@
+#!/bin/bash
+# qbox_xyz.sh: get atomic positions from an MD simulation in xyz format
+# use: qbox_xyz.sh  mdrun.r > file.xyz
+#
+xsltproc - $1 << EOF
+<?xml version="1.0"?>
+<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
+xmlns:fpmd="http://www.quantum-simulation.org/ns/fpmd/fpmd-1.0">
+<xsl:output method="text" indent="yes"/>
+<xsl:strip-space elements="*"/>
+<xsl:template match="/">
+  <xsl:apply-templates select="//iteration/atomset"/>
+</xsl:template>
+
+<xsl:template match="iteration/atomset">
+  <xsl:value-of select="count(child::atom)"/> <xsl:text>
+</xsl:text>
+<xsl:number count="iteration"/> <xsl:text>
+</xsl:text>
+  <xsl:apply-templates select="atom"/>
+</xsl:template>
+
+<xsl:template match="atom">
+  <xsl:variable name="sym" select="substring(@name,1,2)"/>
+  <xsl:variable name="symbol" select="translate(\$sym,'0123456789_-:.',' ')"/>
+  <xsl:value-of select="\$symbol"/> <xsl:text> </xsl:text>
+  <xsl:variable name="pos" select="normalize-space(position)"/>
+  <xsl:variable name="x" select="substring-before(\$pos,' ')"/>
+  <xsl:variable name="y" select="substring-before(substring-after(\$pos,' '),' ')"/>
+  <xsl:variable name="z" select="substring-after(substring-after(\$pos,' '),' ')"/>
+  <xsl:value-of select="\$x * 0.529177"/> <xsl:text> </xsl:text>
+  <xsl:value-of select="\$y * 0.529177"/> <xsl:text> </xsl:text>
+  <xsl:value-of select="\$z * 0.529177"/> <xsl:text>
+</xsl:text>
+</xsl:template>
+
+<xsl:template match="*"/>
+</xsl:stylesheet>
+EOF
diff --git a/util/sample_to_move.sh b/util/sample_to_move.sh
new file mode 100755
index 0000000..f2f2e4f
--- /dev/null
+++ b/util/sample_to_move.sh
@@ -0,0 +1,28 @@
+#!/bin/bash
+# sample_to_move.sh
+# generate a set of Qbox commands to move atoms to the positions
+# in a given sample.
+# use: sample_to_move.sh sample.xml
+#
+xsltproc - $1 << EOF
+<?xml version="1.0"?>
+<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
+xmlns:fpmd="http://www.quantum-simulation.org/ns/fpmd/fpmd-1.0">
+<xsl:output method="text" indent="yes"/>
+<xsl:strip-space elements="*"/>
+<xsl:template match="/fpmd:sample">
+  <xsl:apply-templates/>
+</xsl:template>
+<xsl:template match="atomset">
+  <xsl:apply-templates/>
+</xsl:template>
+<xsl:template match="atom">
+  <xsl:text>move </xsl:text>
+  <xsl:value-of select="@name"/> 
+  <xsl:text> to </xsl:text>
+  <xsl:value-of select="position"/> <xsl:text>
+</xsl:text>
+</xsl:template>
+<xsl:template match="*"/>
+</xsl:stylesheet>
+EOF
diff --git a/util/sample_to_sys.sh b/util/sample_to_sys.sh
new file mode 100755
index 0000000..7af3b34
--- /dev/null
+++ b/util/sample_to_sys.sh
@@ -0,0 +1,41 @@
+#!/bin/bash
+# sample_to_sys.sh: extract atomic positions from a sample and generate
+# a Qbox input file to create atoms at these positions
+# use: sample_to_sys.sh sample.xml > sample.sys
+#
+xsltproc - $1 << EOF
+<?xml version="1.0"?>
+<xsl:stylesheet version="1.0" xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
+xmlns:fpmd="http://www.quantum-simulation.org/ns/fpmd/fpmd-1.0">
+<xsl:output method="text" indent="yes"/>
+<xsl:strip-space elements="*"/>
+<xsl:template match="/fpmd:sample">
+  <xsl:apply-templates/>
+</xsl:template>
+<xsl:template match="atomset">
+  <xsl:apply-templates/>
+</xsl:template>
+<xsl:template match="unit_cell">
+  <xsl:text>set cell </xsl:text>
+  <xsl:value-of select="@a"/> <xsl:text> </xsl:text>
+  <xsl:value-of select="@b"/> <xsl:text> </xsl:text>
+  <xsl:value-of select="@c"/>  <xsl:text>
+</xsl:text>
+</xsl:template>
+<xsl:template match="species">
+  <xsl:text>species </xsl:text>
+  <xsl:value-of select="@name"/> <xsl:text> </xsl:text>
+  <xsl:value-of select="@href"/> <xsl:text>
+</xsl:text>
+</xsl:template>
+<xsl:template match="atom">
+  <xsl:text>atom </xsl:text>
+  <xsl:value-of select="@name"/> <xsl:text> </xsl:text>
+  <xsl:value-of select="@species"/> <xsl:text> </xsl:text>
+  <xsl:value-of select="position"/>  <xsl:text> </xsl:text> 
+  <xsl:value-of select="velocity"/> <xsl:text> 
+</xsl:text>
+</xsl:template>
+<xsl:template match="*"/>
+</xsl:stylesheet>
+EOF
--
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