added examples

removed polyethylene.xyz
rajak7 · Jan 9, 2019 · dd567c0 · dd567c0
1 parent a67558d
commit dd567c0
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Showing 19 changed files with 1,038 additions and 14 deletions.
diff --git a/examples/1-reaxff/Makefile b/examples/1-reaxff/Makefile
@@ -0,0 +1,10 @@
+set:
+	cp -v ../../init/geninit  .
+	cp -v ../../rxmd .
+	./geninit -i input.xyz -f ffield -o DAT/ -mc 2 3 5 
+
+run:
+	mpirun -np 1 ./rxmd
+
+clean:
+	rm -fv geninit* rxmd DAT/*
diff --git a/examples/1-reaxff/ffield b/examples/1-reaxff/ffield
diff --git a/examples/1-reaxff/input.xyz b/examples/1-reaxff/input.xyz
@@ -0,0 +1,14 @@
+12   "Poly(ethylene),  C.W.Bunn (1939) Trans.Faraday Soc. 35:482-"
+7.40000   4.93000   2.53400    90.000    90.000    90.000
+C       0.038000000    0.935000000    0.250000000
+C       0.962000000    0.065000000    0.750000000
+C       0.462000000    0.435000000    0.750000000
+C       0.538000000    0.565000000    0.250000000
+H       0.197000000    0.970000000    0.250000000
+H       0.803000000    0.030000000    0.750000000
+H       0.303000000    0.470000000    0.750000000
+H       0.697000000    0.530000000    0.250000000
+H       0.018000000    0.722000000    0.250000000
+H       0.982000000    0.278000000    0.750000000
+H       0.482000000    0.222000000    0.750000000
+H       0.518000000    0.778000000    0.250000000
diff --git a/examples/1-reaxff/rxmd.in b/examples/1-reaxff/rxmd.in
@@ -0,0 +1,9 @@
+1                    <mdmod>
+0.25    100         <dt> <ntime_step> 
+300  1.0   100       <treq> <vsfact> <sstep>
+100   10           <fstep>  <pstep>
+1 1 1                <vprocs>
+1  500  1.d-7  1      <isQEq> <NMAXQEq> <QEq_tol> <qstep> 
+1.0  2.0              <Lex_fqs> <Lex_k>
+.false. .false. .false. .false. <isBinary> <isBondFile> <isPDB> <isXYZ>
+1.d-6                <ftol> 
diff --git a/examples/2-reaxff-dc/Makefile b/examples/2-reaxff-dc/Makefile
@@ -0,0 +1,10 @@
+set:
+	cp -v ../../init/geninit  .
+	cp -v ../../rxmd .
+	./geninit -i input.xyz -f ffield -o DAT/ -mc 4 3 5 -v 2 1 1
+
+run:
+	mpirun -np 2 ./rxmd
+
+clean:
+	rm -fv geninit* rxmd DAT/*
diff --git a/examples/2-reaxff-dc/ffield b/examples/2-reaxff-dc/ffield
diff --git a/examples/2-reaxff-dc/input.xyz b/examples/2-reaxff-dc/input.xyz
@@ -0,0 +1,14 @@
+12   "Poly(ethylene),  C.W.Bunn (1939) Trans.Faraday Soc. 35:482-"
+7.40000   4.93000   2.53400    90.000    90.000    90.000
+C       0.038000000    0.935000000    0.250000000
+C       0.962000000    0.065000000    0.750000000
+C       0.462000000    0.435000000    0.750000000
+C       0.538000000    0.565000000    0.250000000
+H       0.197000000    0.970000000    0.250000000
+H       0.803000000    0.030000000    0.750000000
+H       0.303000000    0.470000000    0.750000000
+H       0.697000000    0.530000000    0.250000000
+H       0.018000000    0.722000000    0.250000000
+H       0.982000000    0.278000000    0.750000000
+H       0.482000000    0.222000000    0.750000000
+H       0.518000000    0.778000000    0.250000000
diff --git a/examples/2-reaxff-dc/rxmd.in b/examples/2-reaxff-dc/rxmd.in
@@ -0,0 +1,9 @@
+1                    <mdmod>
+0.25    100         <dt> <ntime_step> 
+300  1.0   100       <treq> <vsfact> <sstep>
+100   10           <fstep>  <pstep>
+2 1 1                <vprocs>
+1  500  1.d-7  1      <isQEq> <NMAXQEq> <QEq_tol> <qstep> 
+1.0  2.0              <Lex_fqs> <Lex_k>
+.false. .false. .false. .false. <isBinary> <isBondFile> <isPDB> <isXYZ>
+1.d-6                <ftol> 
diff --git a/examples/3-reaxpq+/Makefile b/examples/3-reaxpq+/Makefile
@@ -0,0 +1,10 @@
+set:
+	cp -v ../../init/geninit  .
+	cp -v ../../rxmd .
+	./geninit -i input.xyz -f ffield -o DAT/ -mc 2 3 5 
+
+run:
+	mpirun -np 1 ./rxmd --pqeq pqeq1.par
+
+clean:
+	rm -fv geninit* rxmd DAT/*
diff --git a/examples/3-reaxpq+/ffield b/examples/3-reaxpq+/ffield
diff --git a/examples/3-reaxpq+/input.xyz b/examples/3-reaxpq+/input.xyz
@@ -0,0 +1,14 @@
+12   "Poly(ethylene),  C.W.Bunn (1939) Trans.Faraday Soc. 35:482-"
+7.40000   4.93000   2.53400    90.000    90.000    90.000
+C       0.038000000    0.935000000    0.250000000
+C       0.962000000    0.065000000    0.750000000
+C       0.462000000    0.435000000    0.750000000
+C       0.538000000    0.565000000    0.250000000
+H       0.197000000    0.970000000    0.250000000
+H       0.803000000    0.030000000    0.750000000
+H       0.303000000    0.470000000    0.750000000
+H       0.697000000    0.530000000    0.250000000
+H       0.018000000    0.722000000    0.250000000
+H       0.982000000    0.278000000    0.750000000
+H       0.482000000    0.222000000    0.750000000
+H       0.518000000    0.778000000    0.250000000
diff --git a/examples/3-reaxpq+/pqeq1.par b/examples/3-reaxpq+/pqeq1.par
@@ -0,0 +1,15 @@
+################################################################
+#
+# Polarizable Charge Equilibration (PQEq1) Parameter Set
+#
+# contacts:
+# Saber Naserifar, [email protected]
+# William A. Goddard III, [email protected]
+#
+#
+################################################################
+#E P     Xo      Jo        Z        Rc      Rs          Ks
+################################################################ 
+NPARMS 2
+ C 1  5.50813  9.81186 1.000000  0.75900  0.75900    198.84054 
+ H 1  4.72484 15.57338 1.000000  0.37100  0.37100   2037.20061 
diff --git a/examples/3-reaxpq+/rxmd.in b/examples/3-reaxpq+/rxmd.in
@@ -0,0 +1,9 @@
+1                    <mdmod>
+0.25    100         <dt> <ntime_step> 
+300  1.0   100       <treq> <vsfact> <sstep>
+100   10           <fstep>  <pstep>
+1 1 1                <vprocs>
+1  500  1.d-7  1      <isQEq> <NMAXQEq> <QEq_tol> <qstep> 
+1.0  2.0              <Lex_fqs> <Lex_k>
+.false. .false. .false. .false. <isBinary> <isBondFile> <isPDB> <isXYZ>
+1.d-6                <ftol> 
diff --git a/examples/4-reaxpq+-efield/Makefile b/examples/4-reaxpq+-efield/Makefile
@@ -0,0 +1,10 @@
+set:
+	cp -v ../../init/geninit  .
+	cp -v ../../rxmd .
+	./geninit -i input.xyz -f ffield -o DAT/ -mc 2 3 5 
+
+run:
+	mpirun -np 1 ./rxmd --pqeq pqeq1.par -e 1 0.01
+
+clean:
+	rm -fv geninit* rxmd DAT/*