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Merge branch 'master' into optimize-wholemolecules
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@GiovanniBussi
GiovanniBussi committed Mar 14, 2024
2 parents 0511455 + 7b7bedf commit b2d6d98
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Showing 108 changed files with 386 additions and 228 deletions.
2 changes: 1 addition & 1 deletion regtest/adjmat/rt-graph-3/plumed.dat
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Expand Up @@ -16,7 +16,7 @@ cm_cnI: CONTACT_MATRIX GROUPA=cn GROUPB=I SWITCH={RATIONAL R_0=0.65}
cc_cnI: MATRIX_VECTOR_PRODUCT ARG=cm_cnI.w,ones192
mt_cnI: MORE_THAN ARG=cc_cnI SWITCH={RATIONAL R_0=11 NN=12 MM=24}

mm: CUSTOM ARG1=mt_cncn ARG2=mt_cnpb ARG3=mt_cnI FUNC=x*y*z PERIODIC=NO
mm: CUSTOM ARG=mt_cncn,mt_cnpb,mt_cnI FUNC=x*y*z PERIODIC=NO

ff: SUM ARG=mm PERIODIC=NO

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2 changes: 1 addition & 1 deletion regtest/adjmat/rt-graph-4/plumed.dat
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Expand Up @@ -16,7 +16,7 @@ cm_cnI: CONTACT_MATRIX GROUPA=cn GROUPB=I SWITCH={RATIONAL R_0=0.65}
cc_cnI: MATRIX_VECTOR_PRODUCT ARG=cm_cnI.w,ones192
mt_cnI: MORE_THAN ARG=cc_cnI SWITCH={RATIONAL R_0=11 NN=12 MM=24}

mm: CUSTOM ARG1=mt_cncn ARG2=mt_cnpb ARG3=mt_cnI FUNC=x*y*z PERIODIC=NO
mm: CUSTOM ARG=mt_cncn,mt_cnpb,mt_cnI FUNC=x*y*z PERIODIC=NO

ff: SUM ARG=mm PERIODIC=NO

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2 changes: 1 addition & 1 deletion regtest/adjmat/rt-perovskite-nucleation/plumed.dat
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Expand Up @@ -17,7 +17,7 @@ cm_cnI: CONTACT_MATRIX GROUPA=cn GROUPB=I SWITCH={RATIONAL R_0=0.65}
cc_cnI: MATRIX_VECTOR_PRODUCT ARG=cm_cnI.w,ones192
mt_cnI: MORE_THAN ARG=cc_cnI SWITCH={RATIONAL R_0=11 NN=12 MM=24}

mm: CUSTOM ARG1=mt_cncn ARG2=mt_cnpb ARG3=mt_cnI FUNC=x*y*z PERIODIC=NO
mm: CUSTOM ARG=mt_cncn,mt_cnpb,mt_cnI FUNC=x*y*z PERIODIC=NO

ff: SUM ARG=mm PERIODIC=NO

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2 changes: 1 addition & 1 deletion regtest/adjmat/rt45/plumed.dat
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Expand Up @@ -14,7 +14,7 @@ a2: COORD_ANGLES ...
PRINT ARG=a1_wsum FILE=matrix

DUMPDERIVATIVES ARG=a1_sum FILE=deriv FMT=%8.4f
a2b: CUSTOM ARG1=a2_between1 ARG2=a2_denom FUNC=x/y PERIODIC=NO
a2b: CUSTOM ARG=a2_between1,a2_denom FUNC=x/y PERIODIC=NO
PRINT ARG=a1.*,a2.*,a2b FILE=colvar FMT=%8.5f
BIASVALUE ARG=a1_mean
BIASVALUE ARG=a2b
6 changes: 6 additions & 0 deletions regtest/basic/rt2/COLVARN.reference
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@@ -0,0 +1,6 @@
#! FIELDS time d1n d2n d3n
0.000000 1.163 2.690 3.257
0.050000 1.131 3.093 3.312
0.100000 1.098 3.167 3.365
0.150000 1.080 2.800 3.383
0.200000 1.087 2.788 3.377
4 changes: 2 additions & 2 deletions regtest/clusters/rt-dfg2/plumed.dat
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Expand Up @@ -2,11 +2,11 @@ ones: ONES SIZE=1996
cmat: CONTACT_MATRIX GROUP=1-1996 SWITCH={CUBIC D_0=0.34 D_MAX=0.38}
c1: MATRIX_VECTOR_PRODUCT ARG=cmat.w,ones
cf: LESS_THAN ARG=c1 SWITCH={CUBIC D_0=13 D_MAX=13.5}
cf2: CUSTOM ARG1=cf FUNC=x*x PERIODIC=NO
cf2: CUSTOM ARG=cf FUNC=x*x PERIODIC=NO

cmat2: CONTACT_MATRIX GROUP=1-1996 SWITCH={CUBIC D_0=0.34 D_MAX=0.38}
dmat: OUTER_PRODUCT ARG=cf,cf
mat: CUSTOM ARG1=cmat2.w ARG2=dmat FUNC=x*y PERIODIC=NO
mat: CUSTOM ARG=cmat2.w,dmat FUNC=x*y PERIODIC=NO
dfs: DFSCLUSTERING ARG=mat

clust1: CLUSTER_PROPERTIES ARG=cf2 CLUSTERS=dfs CLUSTER=1 SUM
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20 changes: 10 additions & 10 deletions regtest/gridtools/rt-kldiv/KLOhack350insphere_coord.dat
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Expand Up @@ -1059,16 +1059,16 @@ ATOMS700=6981,ZM350
COMPONENTS
...

X_len2: COMBINE ARG1=X_dist.x ARG2=X_dist.y ARG3=X_dist.z POWERS=2,2,2 PERIODIC=NO
X_len: CUSTOM ARG1=X_len2 FUNC=sqrt(x) PERIODIC=NO
X_vectors_x: CUSTOM ARG1=X_dist.x ARG2=X_len FUNC=x/y PERIODIC=NO
X_vectors_y: CUSTOM ARG1=X_dist.y ARG2=X_len FUNC=x/y PERIODIC=NO
X_vectors_z: CUSTOM ARG1=X_dist.z ARG2=X_len FUNC=x/y PERIODIC=NO
Z_len2: COMBINE ARG1=Z_dist.x ARG2=Z_dist.y ARG3=Z_dist.z POWERS=2,2,2 PERIODIC=NO
Z_len: CUSTOM ARG1=Z_len2 FUNC=sqrt(x) PERIODIC=NO
Z_vectors_x: CUSTOM ARG1=Z_dist.x ARG2=Z_len FUNC=x/y PERIODIC=NO
Z_vectors_y: CUSTOM ARG1=Z_dist.y ARG2=Z_len FUNC=x/y PERIODIC=NO
Z_vectors_z: CUSTOM ARG1=Z_dist.z ARG2=Z_len FUNC=x/y PERIODIC=NO
X_len2: COMBINE ARG=X_dist.x,X_dist.y,X_dist.z POWERS=2,2,2 PERIODIC=NO
X_len: CUSTOM ARG=X_len2 FUNC=sqrt(x) PERIODIC=NO
X_vectors_x: CUSTOM ARG=X_dist.x,X_len FUNC=x/y PERIODIC=NO
X_vectors_y: CUSTOM ARG=X_dist.y,X_len FUNC=x/y PERIODIC=NO
X_vectors_z: CUSTOM ARG=X_dist.z,X_len FUNC=x/y PERIODIC=NO
Z_len2: COMBINE ARG=Z_dist.x,Z_dist.y,Z_dist.z POWERS=2,2,2 PERIODIC=NO
Z_len: CUSTOM ARG=Z_len2 FUNC=sqrt(x) PERIODIC=NO
Z_vectors_x: CUSTOM ARG=Z_dist.x,Z_len FUNC=x/y PERIODIC=NO
Z_vectors_y: CUSTOM ARG=Z_dist.y,Z_len FUNC=x/y PERIODIC=NO
Z_vectors_z: CUSTOM ARG=Z_dist.z,Z_len FUNC=x/y PERIODIC=NO

# Insphere for vectors can't use sp because it is half the length needed for Z vectors
sp2: INSPHERE ATOMS=1-6981:20,1-6981:20 CENTER=c1 RADIUS={RATIONAL R_0=0.2 D_0=2.3 NN=10 MM=20 D_MAX=2.7}
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36 changes: 18 additions & 18 deletions regtest/gridtools/rt-kldiv/KLPOShack350insphere_coord.dat
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Expand Up @@ -7,11 +7,11 @@ LABEL=dd_centers
... CONTACT_MATRIX

# Now normalize the orientation vectors
dd_centers_len2: COMBINE ARG1=dd_centers.x ARG2=dd_centers.y ARG3=dd_centers.z POWERS=2,2,2 PERIODIC=NO
dd_centers_len: CUSTOM ARG1=dd_centers_len2 FUNC=sqrt(x) PERIODIC=NO
bonds_x: CUSTOM ARG1=dd_centers.x ARG2=dd_centers_len FUNC=x/y PERIODIC=NO
bonds_y: CUSTOM ARG1=dd_centers.y ARG2=dd_centers_len FUNC=x/y PERIODIC=NO
bonds_z: CUSTOM ARG1=dd_centers.z ARG2=dd_centers_len FUNC=x/y PERIODIC=NO
dd_centers_len2: COMBINE ARG=dd_centers.x,dd_centers.y,dd_centers.z POWERS=2,2,2 PERIODIC=NO
dd_centers_len: CUSTOM ARG=dd_centers_len2 FUNC=sqrt(x) PERIODIC=NO
bonds_x: CUSTOM ARG=dd_centers.x,dd_centers_len FUNC=x/y PERIODIC=NO
bonds_y: CUSTOM ARG=dd_centers.y,dd_centers_len FUNC=x/y PERIODIC=NO
bonds_z: CUSTOM ARG=dd_centers.z,dd_centers_len FUNC=x/y PERIODIC=NO

# Now calculate vectors for OO distances
CONTACT_MATRIX ...
Expand All @@ -24,11 +24,11 @@ LABEL=dd_OO
... CONTACT_MATRIX

# Now normalize the vectors
bonds_OO_len2: COMBINE ARG1=dd_OO.x ARG2=dd_OO.y ARG3=dd_OO.z POWERS=2,2,2 PERIODIC=NO
bonds_OO_len: CUSTOM ARG1=bonds_OO_len2 FUNC=sqrt(x) PERIODIC=NO
bonds_OO_x: CUSTOM ARG1=dd_OO.x ARG2=bonds_OO_len FUNC=x/y PERIODIC=NO
bonds_OO_y: CUSTOM ARG1=dd_OO.y ARG2=bonds_OO_len FUNC=x/y PERIODIC=NO
bonds_OO_z: CUSTOM ARG1=dd_OO.z ARG2=bonds_OO_len FUNC=x/y PERIODIC=NO
bonds_OO_len2: COMBINE ARG=dd_OO.x,dd_OO.y,dd_OO.z POWERS=2,2,2 PERIODIC=NO
bonds_OO_len: CUSTOM ARG=bonds_OO_len2 FUNC=sqrt(x) PERIODIC=NO
bonds_OO_x: CUSTOM ARG=dd_OO.x,bonds_OO_len FUNC=x/y PERIODIC=NO
bonds_OO_y: CUSTOM ARG=dd_OO.y,bonds_OO_len FUNC=x/y PERIODIC=NO
bonds_OO_z: CUSTOM ARG=dd_OO.z,bonds_OO_len FUNC=x/y PERIODIC=NO

# Now calculate vectors for ON distances
CONTACT_MATRIX ...
Expand All @@ -50,19 +50,19 @@ coordmat_2: OUTER_PRODUCT ARG=coord_morethan,coord_morethan
coordmat_3: OUTER_PRODUCT ARG=coord_morethan,coord_morethan

# Now normalize the vectors
bonds_ON_len2: COMBINE ARG1=dd_ON.x ARG2=dd_ON.y ARG3=dd_ON.z POWERS=2,2,2 PERIODIC=NO
bonds_ON_len: CUSTOM ARG1=bonds_ON_len2 FUNC=sqrt(x) PERIODIC=NO
bonds_ON_x: CUSTOM ARG1=dd_ON.x ARG2=bonds_ON_len FUNC=x/y PERIODIC=NO
bonds_ON_y: CUSTOM ARG1=dd_ON.y ARG2=bonds_ON_len FUNC=x/y PERIODIC=NO
bonds_ON_z: CUSTOM ARG1=dd_ON.z ARG2=bonds_ON_len FUNC=x/y PERIODIC=NO
bonds_ON_len2: COMBINE ARG=dd_ON.x,dd_ON.y,dd_ON.z POWERS=2,2,2 PERIODIC=NO
bonds_ON_len: CUSTOM ARG=bonds_ON_len2 FUNC=sqrt(x) PERIODIC=NO
bonds_ON_x: CUSTOM ARG=dd_ON.x,bonds_ON_len FUNC=x/y PERIODIC=NO
bonds_ON_y: CUSTOM ARG=dd_ON.y,bonds_ON_len FUNC=x/y PERIODIC=NO
bonds_ON_z: CUSTOM ARG=dd_ON.z,bonds_ON_len FUNC=x/y PERIODIC=NO

# Building correct weight matrices by element wise multiplication of all weigths
#test: MATHEVAL ARG1=spmat_1 ARG2=coordmat_2 FUNC=x*y PERIODIC=NO
w_centers: MATHEVAL ARG1=dd_centers.w ARG2=coordmat_1 ARG3=spmat_1 FUNC=x*y*z PERIODIC=NO
w_centers: MATHEVAL ARG=dd_centers.w,coordmat_1,spmat_1 FUNC=x*y*z PERIODIC=NO
w_centers_sum: SUM ARG=w_centers PERIODIC=NO
w_OO: MATHEVAL ARG1=dd_OO.w ARG2=coordmat_2 ARG3=spmat_2 FUNC=x*y*z PERIODIC=NO
w_OO: MATHEVAL ARG=dd_OO.w,coordmat_2,spmat_2 FUNC=x*y*z PERIODIC=NO
w_OO_sum: SUM ARG=w_OO PERIODIC=NO
w_ON: MATHEVAL ARG1=dd_ON.w ARG2=coordmat_3 ARG3=spmat_3 FUNC=x*y*z PERIODIC=NO
w_ON: MATHEVAL ARG=dd_ON.w,coordmat_3,spmat_3 FUNC=x*y*z PERIODIC=NO
w_ON_sum: SUM ARG=w_ON PERIODIC=NO
# Now construct the instantaneous histograms
Sppos_u: SPHERICAL_KDE ARG=bonds_x,bonds_y,bonds_z HEIGHTS=w_centers GRID_BIN=400 CONCENTRATION=100.0
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8 changes: 4 additions & 4 deletions regtest/gridtools/rt-spherical-integral/plumed.dat
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Expand Up @@ -5,10 +5,10 @@ lls: SUM ARG=ll PERIODIC=NO

# Calculate directions of bonds
d1c: DISTANCE ATOMS1=2,1 ATOMS2=3,1 ATOMS3=4,1 ATOMS4=5,1 ATOMS5=3,2 ATOMS6=4,2 ATOMS7=5,2 ATOMS8=4,3 ATOMS9=5,3 ATOMS10=5,4 COMPONENTS
d2: COMBINE ARG1=d1c.x ARG2=d1c.y ARG3=d1c.z POWERS=2,2,2 PERIODIC=NO
d1n_x: CUSTOM ARG1=d1c.x ARG2=d2 FUNC=x/sqrt(y) PERIODIC=NO
d1n_y: CUSTOM ARG1=d1c.y ARG2=d2 FUNC=x/sqrt(y) PERIODIC=NO
d1n_z: CUSTOM ARG1=d1c.z ARG2=d2 FUNC=x/sqrt(y) PERIODIC=NO
d2: COMBINE ARG=d1c.x,d1c.y,d1c.z POWERS=2,2,2 PERIODIC=NO
d1n_x: CUSTOM ARG=d1c.x,d2 FUNC=x/sqrt(y) PERIODIC=NO
d1n_y: CUSTOM ARG=d1c.y,d2 FUNC=x/sqrt(y) PERIODIC=NO
d1n_z: CUSTOM ARG=d1c.z,d2 FUNC=x/sqrt(y) PERIODIC=NO

# Now construct histogram
hu: SPHERICAL_KDE ARG=d1n_x,d1n_y,d1n_z HEIGHTS=ll CONCENTRATION=10 GRID_BIN=100
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6 changes: 3 additions & 3 deletions regtest/gridtools/rt-weights-integral/plumed.dat
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@@ -1,10 +1,10 @@
d1: DISTANCE ATOMS1=1,2 ATOMS2=1,3 ATOMS3=1,4 ATOMS4=1,5 ATOMS5=2,3 ATOMS6=2,4 ATOMS7=2,5 ATOMS8=3,4 ATOMS9=3,5 ATOMS10=4,5
d1lt: LESS_THAN ARG=d1 SWITCH={RATIONAL D_0=2.0 R_0=0.5 D_MAX=5.0}
d1lt2: MATHEVAL ARG1=d1lt FUNC=x*x PERIODIC=NO
d1lt2: MATHEVAL ARG=d1lt FUNC=x*x PERIODIC=NO

d1c: DISTANCE ATOMS1=2,1 ATOMS2=3,1 ATOMS3=4,1 ATOMS4=5,1 ATOMS5=3,2 ATOMS6=4,2 ATOMS7=5,2 ATOMS8=4,3 ATOMS9=5,3 ATOMS10=5,4 COMPONENTS
d2: COMBINE ARG1=d1c.x ARG2=d1c.y ARG3=d1c.z POWERS=2,2,2 PERIODIC=NO
aa: MATHEVAL ARG1=d1c.z ARG2=d2 FUNC=acos(x/sqrt(y)) PERIODIC=NO
d2: COMBINE ARG=d1c.x,d1c.y,d1c.z POWERS=2,2,2 PERIODIC=NO
aa: MATHEVAL ARG=d1c.z,d2 FUNC=acos(x/sqrt(y)) PERIODIC=NO

dd0: FIXEDATOM AT=0,0,0
ddx: FIXEDATOM AT=1,0,0
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14 changes: 7 additions & 7 deletions regtest/multicolvar/rt-filters/plumed.dat
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Expand Up @@ -53,45 +53,45 @@ d1: DISTANCE ...
d1_m: MEAN ARG=d1 PERIODIC=NO

d1_lt: LESS_THAN ARG=d1 SWITCH={GAUSSIAN D_0=1.5 R_0=0.00001}
d1_lt_prod: MATHEVAL ARG1=d1_lt ARG2=d1 FUNC=x*y PERIODIC=NO
d1_lt_prod: MATHEVAL ARG=d1_lt,d1 FUNC=x*y PERIODIC=NO
d1_lt_numer: SUM ARG=d1_lt_prod PERIODIC=NO
d1_lt_denom: SUM ARG=d1_lt PERIODIC=NO
d1_ltm: MATHEVAL ARG=d1_lt_numer,d1_lt_denom FUNC=x/y PERIODIC=NO

d1_mt: MORE_THAN ARG=d1 SWITCH={GAUSSIAN D_0=1.5 R_0=0.00001}
d1_mt_prod: MATHEVAL ARG1=d1_mt ARG2=d1 FUNC=x*y PERIODIC=NO
d1_mt_prod: MATHEVAL ARG=d1_mt,d1 FUNC=x*y PERIODIC=NO
d1_mt_numer: SUM ARG=d1_mt_prod PERIODIC=NO
d1_mt_denom: SUM ARG=d1_mt PERIODIC=NO
d1_mtm: MATHEVAL ARG=d1_mt_numer,d1_mt_denom FUNC=x/y PERIODIC=NO

d1_bt1: BETWEEN ARG=d1 LOWER=0 UPPER=3.0 SMEAR=0.0001
d1_bt1_prod: MATHEVAL ARG1=d1_bt1 ARG2=d1 FUNC=x*y PERIODIC=NO
d1_bt1_prod: MATHEVAL ARG=d1_bt1,d1 FUNC=x*y PERIODIC=NO
d1_bt1_numer: SUM ARG=d1_bt1_prod PERIODIC=NO
d1_bt1_denom: SUM ARG=d1_bt1 PERIODIC=NO
d1_bt1m: MATHEVAL ARG=d1_bt1_numer,d1_bt1_denom FUNC=x/y PERIODIC=NO

d1_bt2: BETWEEN ARG=d1 LOWER=3.0 UPPER=10.0 SMEAR=0.0001
d1_bt2_prod: MATHEVAL ARG1=d1_bt2 ARG2=d1 FUNC=x*y PERIODIC=NO
d1_bt2_prod: MATHEVAL ARG=d1_bt2,d1 FUNC=x*y PERIODIC=NO
d1_bt2_numer: SUM ARG=d1_bt2_prod PERIODIC=NO
d1_bt2_denom: SUM ARG=d1_bt2 PERIODIC=NO
d1_bt2m: MATHEVAL ARG=d1_bt2_numer,d1_bt2_denom FUNC=x/y PERIODIC=NO

PRINT ARG=d1_m,d1_ltm,d1_mtm,d1_bt1m,d1_bt2m FILE=colvar FMT=%8.4f

d1_lt1: LESS_THAN ARG=d1 SWITCH={GAUSSIAN D_0=1.5 R_0=0.1}
d1_lt1_prod: MATHEVAL ARG1=d1_lt ARG2=d1 FUNC=x*y PERIODIC=NO
d1_lt1_prod: MATHEVAL ARG=d1_lt,d1 FUNC=x*y PERIODIC=NO
d1_lt1_numer: SUM ARG=d1_lt_prod PERIODIC=NO
d1_lt1_denom: SUM ARG=d1_lt PERIODIC=NO
d1_lt1m: MATHEVAL ARG=d1_lt_numer,d1_lt_denom FUNC=x/y PERIODIC=NO

d1_mt1: MORE_THAN ARG=d1 SWITCH={GAUSSIAN D_0=1.5 R_0=0.1}
d1_mt1_prod: MATHEVAL ARG1=d1_mt ARG2=d1 FUNC=x*y PERIODIC=NO
d1_mt1_prod: MATHEVAL ARG=d1_mt,d1 FUNC=x*y PERIODIC=NO
d1_mt1_numer: SUM ARG=d1_mt_prod PERIODIC=NO
d1_mt1_denom: SUM ARG=d1_mt PERIODIC=NO
d1_mt1m: MATHEVAL ARG=d1_mt_numer,d1_mt_denom FUNC=x/y PERIODIC=NO

d1_bt11: BETWEEN ARG=d1 LOWER=0 UPPER=3.0 SMEAR=0.1
d1_bt11_prod: MATHEVAL ARG1=d1_bt1 ARG2=d1 FUNC=x*y PERIODIC=NO
d1_bt11_prod: MATHEVAL ARG=d1_bt1,d1 FUNC=x*y PERIODIC=NO
d1_bt11_numer: SUM ARG=d1_bt1_prod PERIODIC=NO
d1_bt11_denom: SUM ARG=d1_bt1 PERIODIC=NO
d1_bt11m: MATHEVAL ARG=d1_bt1_numer,d1_bt1_denom FUNC=x/y PERIODIC=NO
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4 changes: 2 additions & 2 deletions regtest/python/rt-symfunc/python-script.py
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Expand Up @@ -72,8 +72,8 @@ def create_plumed_var( p, name, command ):
p.cmd("setLogFile","test.log")
p.cmd("init")
p.cmd("readInputLine","cmat: CONTACT_MATRIX GROUP=1-64 SWITCH={CUSTOM R_0=4.5 D_MAX=4.5 FUNC=0.5*(cos(pi*x)+1)} COMPONENTS")
p.cmd("readInputLine","cmatr: CUSTOM ARG1=cmat.x ARG2=cmat.y ARG3=cmat.z FUNC=sqrt(x*x+y*y+z*z) PERIODIC=NO")
p.cmd("readInputLine","g2_f: CUSTOM ARG1=cmatr ARG2=cmat.w FUNC=y*exp(-(x-3)^2) PERIODIC=NO")
p.cmd("readInputLine","cmatr: CUSTOM ARG=cmat.x,cmat.y,cmat.z FUNC=sqrt(x*x+y*y+z*z) PERIODIC=NO")
p.cmd("readInputLine","g2_f: CUSTOM ARG=cmatr,cmat.w FUNC=y*exp(-(x-3)^2) PERIODIC=NO")
p.cmd("readInputLine","ones: ONES SIZE=64")
t1 = create_plumed_var( p, "beh2_g2", "MATRIX_VECTOR_PRODUCT ARG=g2_f,ones" )
t2 = create_plumed_var( p, "beh3.g4", "GSYMFUNC_THREEBODY WEIGHT=cmat.w ARG=cmat.x,cmat.y,cmat.z FUNCTION1={FUNC=0.25*(cos(pi*sqrt(rjk)/4.5)+1)*exp(-0.1*(rij+rik+rjk))*(1+2*cos(ajik))^2 LABEL=g4}" )
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6 changes: 3 additions & 3 deletions regtest/symfunc/rt-behler/plumed.dat
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@@ -1,7 +1,7 @@
cmat: CONTACT_MATRIX GROUP=1-64 SWITCH={CUSTOM R_0=4.5 D_MAX=4.5 FUNC=0.5*(cos(pi*x)+1)} COMPONENTS
cmatr: CUSTOM ARG1=cmat.x ARG2=cmat.y ARG3=cmat.z FUNC=sqrt(x*x+y*y+z*z) PERIODIC=NO
g2_f: CUSTOM ARG1=cmatr ARG2=cmat.w FUNC=y*exp(-(x-3)^2) PERIODIC=NO
g3_f: CUSTOM ARG1=cmatr ARG2=cmat.w FUNC=y*cos(x) PERIODIC=NO
cmatr: CUSTOM ARG=cmat.x,cmat.y,cmat.z FUNC=sqrt(x*x+y*y+z*z) PERIODIC=NO
g2_f: CUSTOM ARG=cmatr,cmat.w FUNC=y*exp(-(x-3)^2) PERIODIC=NO
g3_f: CUSTOM ARG=cmatr,cmat.w FUNC=y*cos(x) PERIODIC=NO
beh2_g1_ones: ONES SIZE=64
beh2_g1: MATRIX_VECTOR_PRODUCT ARG=cmat.w,beh2_g1_ones
beh2_g2: MATRIX_VECTOR_PRODUCT ARG=g2_f,beh2_g1_ones
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8 changes: 4 additions & 4 deletions regtest/symfunc/rt-behler2/plumed.dat
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Original file line number Diff line number Diff line change
@@ -1,14 +1,14 @@
UNITS LENGTH=Bohr

cmat_hh: CONTACT_MATRIX GROUP=2,3,5,6 SWITCH={CUSTOM R_0=10.0 D_MAX=10 FUNC=tanh(1-x)^3} COMPONENTS
cmat_rh: CUSTOM ARG1=cmat_hh.x ARG2=cmat_hh.y ARG3=cmat_hh.z FUNC=sqrt(x*x+y*y+z*z) PERIODIC=NO
cmat_fh: CUSTOM ARG1=cmat_rh ARG2=cmat_hh.w FUNC=y*exp(-0.01*x*x) PERIODIC=NO
cmat_rh: CUSTOM ARG=cmat_hh.x,cmat_hh.y,cmat_hh.z FUNC=sqrt(x*x+y*y+z*z) PERIODIC=NO
cmat_fh: CUSTOM ARG=cmat_rh,cmat_hh.w FUNC=y*exp(-0.01*x*x) PERIODIC=NO
ones4: ONES SIZE=4
beh_hh: MATRIX_VECTOR_PRODUCT ARG=cmat_fh,ones4

cmat_oo: CONTACT_MATRIX GROUP=1,4 SWITCH={CUSTOM R_0=10.0 D_MAX=10 FUNC=tanh(1-x)^3} COMPONENTS
cmat_or: CUSTOM ARG1=cmat_oo.x ARG2=cmat_oo.y ARG3=cmat_oo.z FUNC=sqrt(x*x+y*y+z*z) PERIODIC=NO
cmat_fo: CUSTOM ARG1=cmat_or ARG2=cmat_oo.w FUNC=y*exp(-0.01*x*x) PERIODIC=NO
cmat_or: CUSTOM ARG=cmat_oo.x,cmat_oo.y,cmat_oo.z FUNC=sqrt(x*x+y*y+z*z) PERIODIC=NO
cmat_fo: CUSTOM ARG=cmat_or,cmat_oo.w FUNC=y*exp(-0.01*x*x) PERIODIC=NO
ones2: ONES SIZE=2
beh_oo: MATRIX_VECTOR_PRODUCT ARG=cmat_fo,ones2

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2 changes: 1 addition & 1 deletion regtest/symfunc/rt-center/plumed.dat
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
c1: COORDINATIONNUMBER SPECIES=1-512 SWITCH={EXP D_0=4.0 R_0=0.5}
cf: MORE_THAN ARG=c1 SWITCH={RATIONAL D_0=2.0 R_0=0.1}
ww: MATHEVAL ARG1=c1 ARG2=cf FUNC=x*y PERIODIC=NO
ww: MATHEVAL ARG=c1,cf FUNC=x*y PERIODIC=NO
cc: CENTER ATOMS=c1 WEIGHTS=ww PHASES

DUMPATOMS ATOMS=cc FILE=cluster-com.xyz PRECISION=5
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2 changes: 1 addition & 1 deletion regtest/symfunc/rt-center3/plumed.dat
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
c1: COORDINATIONNUMBER SPECIES=1-512 SWITCH={EXP D_0=4.0 R_0=0.5}
cf: MORE_THAN ARG=c1 SWITCH={RATIONAL D_0=2.0 R_0=0.1}
ww: MATHEVAL ARG1=c1 ARG2=cf FUNC=x*y PERIODIC=NO
ww: MATHEVAL ARG=c1,cf FUNC=x*y PERIODIC=NO
cc: CENTER ATOMS=c1 WEIGHTS=ww

DUMPATOMS ATOMS=cc FILE=cluster-com.xyz PRECISION=5
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2 changes: 1 addition & 1 deletion regtest/symfunc/rt-combine/plumed.dat
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
c1: COORDINATIONNUMBER SPECIESA=1,2,3 SPECIESB=4-100 SWITCH={RATIONAL R_0=0.5} MEAN
c2: COORDINATIONNUMBER SPECIESA=1,2,3 SPECIESB=4-100 SWITCH={RATIONAL R_0=0.7}
cc: COMBINE ARG1=c1 ARG2=c2 PERIODIC=NO
cc: COMBINE ARG=c1,c2 PERIODIC=NO
cc_mean: MEAN ARG=cc PERIODIC=NO
PRINT ARG=cc FILE=colvar FMT=%8.4f
DUMPATOMS ARG=c1,c2,cc ATOMS=c1 FILE=cc.xyz PRECISION=4
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52 changes: 26 additions & 26 deletions regtest/symfunc/rt-dumpmulti/plumed.dat
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Original file line number Diff line number Diff line change
Expand Up @@ -3,32 +3,32 @@ DUMPATOMS ARG=c ATOMS=c FILE=coordination.xyz PRECISION=4

q6: Q6 SPECIES=1-64 D_0=3.0 R_0=1.5 NN=12 MM=24

q6n_rmn-[-6]: CUSTOM ARG1=q6_sp.rm-n6 ARG2=q6_norm FUNC=x/y PERIODIC=NO
q6n_rmn-[-5]: CUSTOM ARG1=q6_sp.rm-n5 ARG2=q6_norm FUNC=x/y PERIODIC=NO
q6n_rmn-[-4]: CUSTOM ARG1=q6_sp.rm-n4 ARG2=q6_norm FUNC=x/y PERIODIC=NO
q6n_rmn-[-3]: CUSTOM ARG1=q6_sp.rm-n3 ARG2=q6_norm FUNC=x/y PERIODIC=NO
q6n_rmn-[-2]: CUSTOM ARG1=q6_sp.rm-n2 ARG2=q6_norm FUNC=x/y PERIODIC=NO
q6n_rmn-[-1]: CUSTOM ARG1=q6_sp.rm-n1 ARG2=q6_norm FUNC=x/y PERIODIC=NO
q6n_rmn-[0]: CUSTOM ARG1=q6_sp.rm-0 ARG2=q6_norm FUNC=x/y PERIODIC=NO
q6n_rmn-[1]: CUSTOM ARG1=q6_sp.rm-p1 ARG2=q6_norm FUNC=x/y PERIODIC=NO
q6n_rmn-[2]: CUSTOM ARG1=q6_sp.rm-p2 ARG2=q6_norm FUNC=x/y PERIODIC=NO
q6n_rmn-[3]: CUSTOM ARG1=q6_sp.rm-p3 ARG2=q6_norm FUNC=x/y PERIODIC=NO
q6n_rmn-[4]: CUSTOM ARG1=q6_sp.rm-p4 ARG2=q6_norm FUNC=x/y PERIODIC=NO
q6n_rmn-[5]: CUSTOM ARG1=q6_sp.rm-p5 ARG2=q6_norm FUNC=x/y PERIODIC=NO
q6n_rmn-[6]: CUSTOM ARG1=q6_sp.rm-p6 ARG2=q6_norm FUNC=x/y PERIODIC=NO
q6n_imn-[-6]: CUSTOM ARG1=q6_sp.im-n6 ARG2=q6_norm FUNC=x/y PERIODIC=NO
q6n_imn-[-5]: CUSTOM ARG1=q6_sp.im-n5 ARG2=q6_norm FUNC=x/y PERIODIC=NO
q6n_imn-[-4]: CUSTOM ARG1=q6_sp.im-n4 ARG2=q6_norm FUNC=x/y PERIODIC=NO
q6n_imn-[-3]: CUSTOM ARG1=q6_sp.im-n3 ARG2=q6_norm FUNC=x/y PERIODIC=NO
q6n_imn-[-2]: CUSTOM ARG1=q6_sp.im-n2 ARG2=q6_norm FUNC=x/y PERIODIC=NO
q6n_imn-[-1]: CUSTOM ARG1=q6_sp.im-n1 ARG2=q6_norm FUNC=x/y PERIODIC=NO
q6n_imn-[0]: CUSTOM ARG1=q6_sp.im-0 ARG2=q6_norm FUNC=x/y PERIODIC=NO
q6n_imn-[1]: CUSTOM ARG1=q6_sp.im-p1 ARG2=q6_norm FUNC=x/y PERIODIC=NO
q6n_imn-[2]: CUSTOM ARG1=q6_sp.im-p2 ARG2=q6_norm FUNC=x/y PERIODIC=NO
q6n_imn-[3]: CUSTOM ARG1=q6_sp.im-p3 ARG2=q6_norm FUNC=x/y PERIODIC=NO
q6n_imn-[4]: CUSTOM ARG1=q6_sp.im-p4 ARG2=q6_norm FUNC=x/y PERIODIC=NO
q6n_imn-[5]: CUSTOM ARG1=q6_sp.im-p5 ARG2=q6_norm FUNC=x/y PERIODIC=NO
q6n_imn-[6]: CUSTOM ARG1=q6_sp.im-p6 ARG2=q6_norm FUNC=x/y PERIODIC=NO
q6n_rmn-[-6]: CUSTOM ARG=q6_sp.rm-n6,q6_norm FUNC=x/y PERIODIC=NO
q6n_rmn-[-5]: CUSTOM ARG=q6_sp.rm-n5,q6_norm FUNC=x/y PERIODIC=NO
q6n_rmn-[-4]: CUSTOM ARG=q6_sp.rm-n4,q6_norm FUNC=x/y PERIODIC=NO
q6n_rmn-[-3]: CUSTOM ARG=q6_sp.rm-n3,q6_norm FUNC=x/y PERIODIC=NO
q6n_rmn-[-2]: CUSTOM ARG=q6_sp.rm-n2,q6_norm FUNC=x/y PERIODIC=NO
q6n_rmn-[-1]: CUSTOM ARG=q6_sp.rm-n1,q6_norm FUNC=x/y PERIODIC=NO
q6n_rmn-[0]: CUSTOM ARG=q6_sp.rm-0,q6_norm FUNC=x/y PERIODIC=NO
q6n_rmn-[1]: CUSTOM ARG=q6_sp.rm-p1,q6_norm FUNC=x/y PERIODIC=NO
q6n_rmn-[2]: CUSTOM ARG=q6_sp.rm-p2,q6_norm FUNC=x/y PERIODIC=NO
q6n_rmn-[3]: CUSTOM ARG=q6_sp.rm-p3,q6_norm FUNC=x/y PERIODIC=NO
q6n_rmn-[4]: CUSTOM ARG=q6_sp.rm-p4,q6_norm FUNC=x/y PERIODIC=NO
q6n_rmn-[5]: CUSTOM ARG=q6_sp.rm-p5,q6_norm FUNC=x/y PERIODIC=NO
q6n_rmn-[6]: CUSTOM ARG=q6_sp.rm-p6,q6_norm FUNC=x/y PERIODIC=NO
q6n_imn-[-6]: CUSTOM ARG=q6_sp.im-n6,q6_norm FUNC=x/y PERIODIC=NO
q6n_imn-[-5]: CUSTOM ARG=q6_sp.im-n5,q6_norm FUNC=x/y PERIODIC=NO
q6n_imn-[-4]: CUSTOM ARG=q6_sp.im-n4,q6_norm FUNC=x/y PERIODIC=NO
q6n_imn-[-3]: CUSTOM ARG=q6_sp.im-n3,q6_norm FUNC=x/y PERIODIC=NO
q6n_imn-[-2]: CUSTOM ARG=q6_sp.im-n2,q6_norm FUNC=x/y PERIODIC=NO
q6n_imn-[-1]: CUSTOM ARG=q6_sp.im-n1,q6_norm FUNC=x/y PERIODIC=NO
q6n_imn-[0]: CUSTOM ARG=q6_sp.im-0,q6_norm FUNC=x/y PERIODIC=NO
q6n_imn-[1]: CUSTOM ARG=q6_sp.im-p1,q6_norm FUNC=x/y PERIODIC=NO
q6n_imn-[2]: CUSTOM ARG=q6_sp.im-p2,q6_norm FUNC=x/y PERIODIC=NO
q6n_imn-[3]: CUSTOM ARG=q6_sp.im-p3,q6_norm FUNC=x/y PERIODIC=NO
q6n_imn-[4]: CUSTOM ARG=q6_sp.im-p4,q6_norm FUNC=x/y PERIODIC=NO
q6n_imn-[5]: CUSTOM ARG=q6_sp.im-p5,q6_norm FUNC=x/y PERIODIC=NO
q6n_imn-[6]: CUSTOM ARG=q6_sp.im-p6,q6_norm FUNC=x/y PERIODIC=NO

DUMPATOMS ATOMS=q6 ARG=q6_anorm,q6n_rmn-[-6],q6n_rmn-[-5],q6n_rmn-[-4],q6n_rmn-[-3],q6n_rmn-[-2],q6n_rmn-[-1],q6n_rmn-[0],q6n_rmn-[1],q6n_rmn-[2],q6n_rmn-[3],q6n_rmn-[4],q6n_rmn-[5],q6n_rmn-[6],q6n_imn-[-6],q6n_imn-[-5],q6n_imn-[-4],q6n_imn-[-3],q6n_imn-[-2],q6n_imn-[-1],q6n_imn-[0],q6n_imn-[1],q6n_imn-[2],q6n_imn-[3],q6n_imn-[4],q6n_imn-[5],q6n_imn-[6] FILE=q6.xyz PRECISION=4

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6 changes: 3 additions & 3 deletions regtest/symfunc/rt-hexactic/plumed.dat
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Original file line number Diff line number Diff line change
Expand Up @@ -5,14 +5,14 @@ PRINT ARG=hex.mean,bb.* FILE=colvar FMT=%8.4f
# This checks against what is done in LAMMPS
dmat: DISTANCE_MATRIX GROUP=1-400 CUTOFF=3.0 COMPONENTS
neigh: NEIGHBORS ARG=dmat.w NLOWEST=6
harm: CYLINDRICAL_HARMONIC DEGREE=6 ARG1=dmat.x ARG2=dmat.y
harm: CYLINDRICAL_HARMONIC DEGREE=6 ARG=dmat.x,dmat.y
rprod: CUSTOM ARG=neigh,harm.rm FUNC=x*y PERIODIC=NO
iprod: CUSTOM ARG=neigh,harm.im FUNC=x*y PERIODIC=NO
hex2_ones: ONES SIZE=400
hex2_denom: MATRIX_VECTOR_PRODUCT ARG=neigh,hex2_ones
harm_rm: MATRIX_VECTOR_PRODUCT ARG=rprod,hex2_ones
harm_im: MATRIX_VECTOR_PRODUCT ARG=iprod,hex2_ones
hex2_rmn: CUSTOM ARG1=harm_rm ARG2=hex2_denom FUNC=x/y PERIODIC=NO
hex2_imn: CUSTOM ARG1=harm_im ARG2=hex2_denom FUNC=x/y PERIODIC=NO
hex2_rmn: CUSTOM ARG=harm_rm,hex2_denom FUNC=x/y PERIODIC=NO
hex2_imn: CUSTOM ARG=harm_im,hex2_denom FUNC=x/y PERIODIC=NO

DUMPATOMS ATOMS=1-400 ARG=hex2_rmn,hex2_imn,hex2_denom PRECISION=4 FILE=hexparam.xyz
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Found broken examples in automatic/ADAPTIVE_PATH.tmp
Found broken examples in automatic/ANGLES.tmp
Found broken examples in automatic/ANN.tmp
Found broken examples in automatic/AROUND.tmp
Found broken examples in automatic/CAVITY.tmp
Found broken examples in automatic/CLUSTER_DIAMETER.tmp
Found broken examples in automatic/CLUSTER_DISTRIBUTION.tmp
Found broken examples in automatic/CLUSTER_PROPERTIES.tmp
Found broken examples in automatic/CONSTANT.tmp
Found broken examples in automatic/CONTACT_MATRIX.tmp
Found broken examples in automatic/CONVERT_TO_FES.tmp
Found broken examples in automatic/COORDINATIONNUMBER.tmp
Found broken examples in automatic/DFSCLUSTERING.tmp
Found broken examples in automatic/DISTANCE_FROM_CONTOUR.tmp
Found broken examples in automatic/DUMPCUBE.tmp
Found broken examples in automatic/DUMPGRID.tmp
Found broken examples in automatic/EDS.tmp
Found broken examples in automatic/EMMI.tmp
Found broken examples in automatic/ENVIRONMENTSIMILARITY.tmp
Found broken examples in automatic/FIND_CONTOUR.tmp
Found broken examples in automatic/FIND_CONTOUR_SURFACE.tmp
Found broken examples in automatic/FIND_SPHERICAL_CONTOUR.tmp
Found broken examples in automatic/FOURIER_TRANSFORM.tmp
Found broken examples in automatic/FUNCPATHGENERAL.tmp
Found broken examples in automatic/FUNCPATHMSD.tmp
Found broken examples in automatic/FUNNEL.tmp
Found broken examples in automatic/FUNNEL_PS.tmp
Found broken examples in automatic/GHBFIX.tmp
Found broken examples in automatic/GPROPERTYMAP.tmp
Found broken examples in automatic/HBOND_MATRIX.tmp
Found broken examples in automatic/HISTOGRAM.tmp
Found broken examples in automatic/INCLUDE.tmp
Found broken examples in automatic/INCYLINDER.tmp
Found broken examples in automatic/INENVELOPE.tmp
Found broken examples in automatic/INSPHERE.tmp
Found broken examples in automatic/INTERPOLATE_GRID.tmp
Found broken examples in automatic/LOCAL_AVERAGE.tmp
Found broken examples in automatic/LOCAL_Q3.tmp
Found broken examples in automatic/LOCAL_Q4.tmp
Found broken examples in automatic/LOCAL_Q6.tmp
Found broken examples in automatic/MAZE_OPTIMIZER_BIAS.tmp
Found broken examples in automatic/MAZE_RANDOM_ACCELERATION_MD.tmp
Found broken examples in automatic/MAZE_SIMULATED_ANNEALING.tmp
Found broken examples in automatic/MAZE_STEERED_MD.tmp
Found broken examples in automatic/MULTICOLVARDENS.tmp
Found broken examples in automatic/OUTPUT_CLUSTER.tmp
Found broken examples in automatic/PAMM.tmp
Found broken examples in automatic/PARABETARMSD.tmp
Found broken examples in automatic/PATH.tmp
Found broken examples in automatic/PCAVARS.tmp
Found broken examples in automatic/PIV.tmp
Found broken examples in automatic/PLUMED.tmp
Found broken examples in automatic/PYCVINTERFACE.tmp
Found broken examples in automatic/PYTHONFUNCTION.tmp
Found broken examples in automatic/QUATERNION.tmp
Found broken examples in automatic/REWEIGHT_BIAS.tmp
Found broken examples in automatic/REWEIGHT_METAD.tmp
Found broken examples in automatic/SPRINT.tmp
Found broken examples in automatic/TETRAHEDRALPORE.tmp
Found broken examples in automatic/TORSION.tmp
Found broken examples in automatic/TORSIONS.tmp
Found broken examples in automatic/WHAM_HISTOGRAM.tmp
Found broken examples in automatic/WHAM_WEIGHTS.tmp
Found broken examples in AnalysisPP.md
Found broken examples in CollectiveVariablesPP.md
Found broken examples in MiscelaneousPP.md

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