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GiovanniBussiGiovanniBussi
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Merge branch 'master' into optimize-wholemolecules
2 parents 0511455 + 7b7bedf commit b2d6d98

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‎regtest/adjmat/rt-graph-3/plumed.dat

+1-1
Original file line numberDiff line numberDiff line change
@@ -16,7 +16,7 @@ cm_cnI: CONTACT_MATRIX GROUPA=cn GROUPB=I SWITCH={RATIONAL R_0=0.65}
1616
cc_cnI: MATRIX_VECTOR_PRODUCT ARG=cm_cnI.w,ones192
1717
mt_cnI: MORE_THAN ARG=cc_cnI SWITCH={RATIONAL R_0=11 NN=12 MM=24}
1818

19-
mm: CUSTOM ARG1=mt_cncn ARG2=mt_cnpb ARG3=mt_cnI FUNC=x*y*z PERIODIC=NO
19+
mm: CUSTOM ARG=mt_cncn,mt_cnpb,mt_cnI FUNC=x*y*z PERIODIC=NO
2020

2121
ff: SUM ARG=mm PERIODIC=NO
2222

‎regtest/adjmat/rt-graph-4/plumed.dat

+1-1
Original file line numberDiff line numberDiff line change
@@ -16,7 +16,7 @@ cm_cnI: CONTACT_MATRIX GROUPA=cn GROUPB=I SWITCH={RATIONAL R_0=0.65}
1616
cc_cnI: MATRIX_VECTOR_PRODUCT ARG=cm_cnI.w,ones192
1717
mt_cnI: MORE_THAN ARG=cc_cnI SWITCH={RATIONAL R_0=11 NN=12 MM=24}
1818

19-
mm: CUSTOM ARG1=mt_cncn ARG2=mt_cnpb ARG3=mt_cnI FUNC=x*y*z PERIODIC=NO
19+
mm: CUSTOM ARG=mt_cncn,mt_cnpb,mt_cnI FUNC=x*y*z PERIODIC=NO
2020

2121
ff: SUM ARG=mm PERIODIC=NO
2222

‎regtest/adjmat/rt-perovskite-nucleation/plumed.dat

+1-1
Original file line numberDiff line numberDiff line change
@@ -17,7 +17,7 @@ cm_cnI: CONTACT_MATRIX GROUPA=cn GROUPB=I SWITCH={RATIONAL R_0=0.65}
1717
cc_cnI: MATRIX_VECTOR_PRODUCT ARG=cm_cnI.w,ones192
1818
mt_cnI: MORE_THAN ARG=cc_cnI SWITCH={RATIONAL R_0=11 NN=12 MM=24}
1919

20-
mm: CUSTOM ARG1=mt_cncn ARG2=mt_cnpb ARG3=mt_cnI FUNC=x*y*z PERIODIC=NO
20+
mm: CUSTOM ARG=mt_cncn,mt_cnpb,mt_cnI FUNC=x*y*z PERIODIC=NO
2121

2222
ff: SUM ARG=mm PERIODIC=NO
2323

‎regtest/adjmat/rt45/plumed.dat

+1-1
Original file line numberDiff line numberDiff line change
@@ -14,7 +14,7 @@ a2: COORD_ANGLES ...
1414
PRINT ARG=a1_wsum FILE=matrix
1515

1616
DUMPDERIVATIVES ARG=a1_sum FILE=deriv FMT=%8.4f
17-
a2b: CUSTOM ARG1=a2_between1 ARG2=a2_denom FUNC=x/y PERIODIC=NO
17+
a2b: CUSTOM ARG=a2_between1,a2_denom FUNC=x/y PERIODIC=NO
1818
PRINT ARG=a1.*,a2.*,a2b FILE=colvar FMT=%8.5f
1919
BIASVALUE ARG=a1_mean
2020
BIASVALUE ARG=a2b

‎regtest/basic/rt2/COLVARN.reference

+6
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,6 @@
1+
#! FIELDS time d1n d2n d3n
2+
0.000000 1.163 2.690 3.257
3+
0.050000 1.131 3.093 3.312
4+
0.100000 1.098 3.167 3.365
5+
0.150000 1.080 2.800 3.383
6+
0.200000 1.087 2.788 3.377

‎regtest/clusters/rt-dfg2/plumed.dat

+2-2
Original file line numberDiff line numberDiff line change
@@ -2,11 +2,11 @@ ones: ONES SIZE=1996
22
cmat: CONTACT_MATRIX GROUP=1-1996 SWITCH={CUBIC D_0=0.34 D_MAX=0.38}
33
c1: MATRIX_VECTOR_PRODUCT ARG=cmat.w,ones
44
cf: LESS_THAN ARG=c1 SWITCH={CUBIC D_0=13 D_MAX=13.5}
5-
cf2: CUSTOM ARG1=cf FUNC=x*x PERIODIC=NO
5+
cf2: CUSTOM ARG=cf FUNC=x*x PERIODIC=NO
66

77
cmat2: CONTACT_MATRIX GROUP=1-1996 SWITCH={CUBIC D_0=0.34 D_MAX=0.38}
88
dmat: OUTER_PRODUCT ARG=cf,cf
9-
mat: CUSTOM ARG1=cmat2.w ARG2=dmat FUNC=x*y PERIODIC=NO
9+
mat: CUSTOM ARG=cmat2.w,dmat FUNC=x*y PERIODIC=NO
1010
dfs: DFSCLUSTERING ARG=mat
1111

1212
clust1: CLUSTER_PROPERTIES ARG=cf2 CLUSTERS=dfs CLUSTER=1 SUM

‎regtest/gridtools/rt-kldiv/KLOhack350insphere_coord.dat

+10-10
Original file line numberDiff line numberDiff line change
@@ -1059,16 +1059,16 @@ ATOMS700=6981,ZM350
10591059
COMPONENTS
10601060
...
10611061

1062-
X_len2: COMBINE ARG1=X_dist.x ARG2=X_dist.y ARG3=X_dist.z POWERS=2,2,2 PERIODIC=NO
1063-
X_len: CUSTOM ARG1=X_len2 FUNC=sqrt(x) PERIODIC=NO
1064-
X_vectors_x: CUSTOM ARG1=X_dist.x ARG2=X_len FUNC=x/y PERIODIC=NO
1065-
X_vectors_y: CUSTOM ARG1=X_dist.y ARG2=X_len FUNC=x/y PERIODIC=NO
1066-
X_vectors_z: CUSTOM ARG1=X_dist.z ARG2=X_len FUNC=x/y PERIODIC=NO
1067-
Z_len2: COMBINE ARG1=Z_dist.x ARG2=Z_dist.y ARG3=Z_dist.z POWERS=2,2,2 PERIODIC=NO
1068-
Z_len: CUSTOM ARG1=Z_len2 FUNC=sqrt(x) PERIODIC=NO
1069-
Z_vectors_x: CUSTOM ARG1=Z_dist.x ARG2=Z_len FUNC=x/y PERIODIC=NO
1070-
Z_vectors_y: CUSTOM ARG1=Z_dist.y ARG2=Z_len FUNC=x/y PERIODIC=NO
1071-
Z_vectors_z: CUSTOM ARG1=Z_dist.z ARG2=Z_len FUNC=x/y PERIODIC=NO
1062+
X_len2: COMBINE ARG=X_dist.x,X_dist.y,X_dist.z POWERS=2,2,2 PERIODIC=NO
1063+
X_len: CUSTOM ARG=X_len2 FUNC=sqrt(x) PERIODIC=NO
1064+
X_vectors_x: CUSTOM ARG=X_dist.x,X_len FUNC=x/y PERIODIC=NO
1065+
X_vectors_y: CUSTOM ARG=X_dist.y,X_len FUNC=x/y PERIODIC=NO
1066+
X_vectors_z: CUSTOM ARG=X_dist.z,X_len FUNC=x/y PERIODIC=NO
1067+
Z_len2: COMBINE ARG=Z_dist.x,Z_dist.y,Z_dist.z POWERS=2,2,2 PERIODIC=NO
1068+
Z_len: CUSTOM ARG=Z_len2 FUNC=sqrt(x) PERIODIC=NO
1069+
Z_vectors_x: CUSTOM ARG=Z_dist.x,Z_len FUNC=x/y PERIODIC=NO
1070+
Z_vectors_y: CUSTOM ARG=Z_dist.y,Z_len FUNC=x/y PERIODIC=NO
1071+
Z_vectors_z: CUSTOM ARG=Z_dist.z,Z_len FUNC=x/y PERIODIC=NO
10721072

10731073
# Insphere for vectors can't use sp because it is half the length needed for Z vectors
10741074
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}

‎regtest/gridtools/rt-kldiv/KLPOShack350insphere_coord.dat

+18-18
Original file line numberDiff line numberDiff line change
@@ -7,11 +7,11 @@ LABEL=dd_centers
77
... CONTACT_MATRIX
88

99
# Now normalize the orientation vectors
10-
dd_centers_len2: COMBINE ARG1=dd_centers.x ARG2=dd_centers.y ARG3=dd_centers.z POWERS=2,2,2 PERIODIC=NO
11-
dd_centers_len: CUSTOM ARG1=dd_centers_len2 FUNC=sqrt(x) PERIODIC=NO
12-
bonds_x: CUSTOM ARG1=dd_centers.x ARG2=dd_centers_len FUNC=x/y PERIODIC=NO
13-
bonds_y: CUSTOM ARG1=dd_centers.y ARG2=dd_centers_len FUNC=x/y PERIODIC=NO
14-
bonds_z: CUSTOM ARG1=dd_centers.z ARG2=dd_centers_len FUNC=x/y PERIODIC=NO
10+
dd_centers_len2: COMBINE ARG=dd_centers.x,dd_centers.y,dd_centers.z POWERS=2,2,2 PERIODIC=NO
11+
dd_centers_len: CUSTOM ARG=dd_centers_len2 FUNC=sqrt(x) PERIODIC=NO
12+
bonds_x: CUSTOM ARG=dd_centers.x,dd_centers_len FUNC=x/y PERIODIC=NO
13+
bonds_y: CUSTOM ARG=dd_centers.y,dd_centers_len FUNC=x/y PERIODIC=NO
14+
bonds_z: CUSTOM ARG=dd_centers.z,dd_centers_len FUNC=x/y PERIODIC=NO
1515

1616
# Now calculate vectors for OO distances
1717
CONTACT_MATRIX ...
@@ -24,11 +24,11 @@ LABEL=dd_OO
2424
... CONTACT_MATRIX
2525

2626
# Now normalize the vectors
27-
bonds_OO_len2: COMBINE ARG1=dd_OO.x ARG2=dd_OO.y ARG3=dd_OO.z POWERS=2,2,2 PERIODIC=NO
28-
bonds_OO_len: CUSTOM ARG1=bonds_OO_len2 FUNC=sqrt(x) PERIODIC=NO
29-
bonds_OO_x: CUSTOM ARG1=dd_OO.x ARG2=bonds_OO_len FUNC=x/y PERIODIC=NO
30-
bonds_OO_y: CUSTOM ARG1=dd_OO.y ARG2=bonds_OO_len FUNC=x/y PERIODIC=NO
31-
bonds_OO_z: CUSTOM ARG1=dd_OO.z ARG2=bonds_OO_len FUNC=x/y PERIODIC=NO
27+
bonds_OO_len2: COMBINE ARG=dd_OO.x,dd_OO.y,dd_OO.z POWERS=2,2,2 PERIODIC=NO
28+
bonds_OO_len: CUSTOM ARG=bonds_OO_len2 FUNC=sqrt(x) PERIODIC=NO
29+
bonds_OO_x: CUSTOM ARG=dd_OO.x,bonds_OO_len FUNC=x/y PERIODIC=NO
30+
bonds_OO_y: CUSTOM ARG=dd_OO.y,bonds_OO_len FUNC=x/y PERIODIC=NO
31+
bonds_OO_z: CUSTOM ARG=dd_OO.z,bonds_OO_len FUNC=x/y PERIODIC=NO
3232

3333
# Now calculate vectors for ON distances
3434
CONTACT_MATRIX ...
@@ -50,19 +50,19 @@ coordmat_2: OUTER_PRODUCT ARG=coord_morethan,coord_morethan
5050
coordmat_3: OUTER_PRODUCT ARG=coord_morethan,coord_morethan
5151

5252
# Now normalize the vectors
53-
bonds_ON_len2: COMBINE ARG1=dd_ON.x ARG2=dd_ON.y ARG3=dd_ON.z POWERS=2,2,2 PERIODIC=NO
54-
bonds_ON_len: CUSTOM ARG1=bonds_ON_len2 FUNC=sqrt(x) PERIODIC=NO
55-
bonds_ON_x: CUSTOM ARG1=dd_ON.x ARG2=bonds_ON_len FUNC=x/y PERIODIC=NO
56-
bonds_ON_y: CUSTOM ARG1=dd_ON.y ARG2=bonds_ON_len FUNC=x/y PERIODIC=NO
57-
bonds_ON_z: CUSTOM ARG1=dd_ON.z ARG2=bonds_ON_len FUNC=x/y PERIODIC=NO
53+
bonds_ON_len2: COMBINE ARG=dd_ON.x,dd_ON.y,dd_ON.z POWERS=2,2,2 PERIODIC=NO
54+
bonds_ON_len: CUSTOM ARG=bonds_ON_len2 FUNC=sqrt(x) PERIODIC=NO
55+
bonds_ON_x: CUSTOM ARG=dd_ON.x,bonds_ON_len FUNC=x/y PERIODIC=NO
56+
bonds_ON_y: CUSTOM ARG=dd_ON.y,bonds_ON_len FUNC=x/y PERIODIC=NO
57+
bonds_ON_z: CUSTOM ARG=dd_ON.z,bonds_ON_len FUNC=x/y PERIODIC=NO
5858

5959
# Building correct weight matrices by element wise multiplication of all weigths
6060
#test: MATHEVAL ARG1=spmat_1 ARG2=coordmat_2 FUNC=x*y PERIODIC=NO
61-
w_centers: MATHEVAL ARG1=dd_centers.w ARG2=coordmat_1 ARG3=spmat_1 FUNC=x*y*z PERIODIC=NO
61+
w_centers: MATHEVAL ARG=dd_centers.w,coordmat_1,spmat_1 FUNC=x*y*z PERIODIC=NO
6262
w_centers_sum: SUM ARG=w_centers PERIODIC=NO
63-
w_OO: MATHEVAL ARG1=dd_OO.w ARG2=coordmat_2 ARG3=spmat_2 FUNC=x*y*z PERIODIC=NO
63+
w_OO: MATHEVAL ARG=dd_OO.w,coordmat_2,spmat_2 FUNC=x*y*z PERIODIC=NO
6464
w_OO_sum: SUM ARG=w_OO PERIODIC=NO
65-
w_ON: MATHEVAL ARG1=dd_ON.w ARG2=coordmat_3 ARG3=spmat_3 FUNC=x*y*z PERIODIC=NO
65+
w_ON: MATHEVAL ARG=dd_ON.w,coordmat_3,spmat_3 FUNC=x*y*z PERIODIC=NO
6666
w_ON_sum: SUM ARG=w_ON PERIODIC=NO
6767
# Now construct the instantaneous histograms
6868
Sppos_u: SPHERICAL_KDE ARG=bonds_x,bonds_y,bonds_z HEIGHTS=w_centers GRID_BIN=400 CONCENTRATION=100.0

‎regtest/gridtools/rt-spherical-integral/plumed.dat

+4-4
Original file line numberDiff line numberDiff line change
@@ -5,10 +5,10 @@ lls: SUM ARG=ll PERIODIC=NO
55

66
# Calculate directions of bonds
77
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
8-
d2: COMBINE ARG1=d1c.x ARG2=d1c.y ARG3=d1c.z POWERS=2,2,2 PERIODIC=NO
9-
d1n_x: CUSTOM ARG1=d1c.x ARG2=d2 FUNC=x/sqrt(y) PERIODIC=NO
10-
d1n_y: CUSTOM ARG1=d1c.y ARG2=d2 FUNC=x/sqrt(y) PERIODIC=NO
11-
d1n_z: CUSTOM ARG1=d1c.z ARG2=d2 FUNC=x/sqrt(y) PERIODIC=NO
8+
d2: COMBINE ARG=d1c.x,d1c.y,d1c.z POWERS=2,2,2 PERIODIC=NO
9+
d1n_x: CUSTOM ARG=d1c.x,d2 FUNC=x/sqrt(y) PERIODIC=NO
10+
d1n_y: CUSTOM ARG=d1c.y,d2 FUNC=x/sqrt(y) PERIODIC=NO
11+
d1n_z: CUSTOM ARG=d1c.z,d2 FUNC=x/sqrt(y) PERIODIC=NO
1212

1313
# Now construct histogram
1414
hu: SPHERICAL_KDE ARG=d1n_x,d1n_y,d1n_z HEIGHTS=ll CONCENTRATION=10 GRID_BIN=100

‎regtest/gridtools/rt-weights-integral/plumed.dat

+3-3
Original file line numberDiff line numberDiff line change
@@ -1,10 +1,10 @@
11
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
22
d1lt: LESS_THAN ARG=d1 SWITCH={RATIONAL D_0=2.0 R_0=0.5 D_MAX=5.0}
3-
d1lt2: MATHEVAL ARG1=d1lt FUNC=x*x PERIODIC=NO
3+
d1lt2: MATHEVAL ARG=d1lt FUNC=x*x PERIODIC=NO
44

55
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
6-
d2: COMBINE ARG1=d1c.x ARG2=d1c.y ARG3=d1c.z POWERS=2,2,2 PERIODIC=NO
7-
aa: MATHEVAL ARG1=d1c.z ARG2=d2 FUNC=acos(x/sqrt(y)) PERIODIC=NO
6+
d2: COMBINE ARG=d1c.x,d1c.y,d1c.z POWERS=2,2,2 PERIODIC=NO
7+
aa: MATHEVAL ARG=d1c.z,d2 FUNC=acos(x/sqrt(y)) PERIODIC=NO
88

99
dd0: FIXEDATOM AT=0,0,0
1010
ddx: FIXEDATOM AT=1,0,0

‎regtest/multicolvar/rt-filters/plumed.dat

+7-7
Original file line numberDiff line numberDiff line change
@@ -53,45 +53,45 @@ d1: DISTANCE ...
5353
d1_m: MEAN ARG=d1 PERIODIC=NO
5454

5555
d1_lt: LESS_THAN ARG=d1 SWITCH={GAUSSIAN D_0=1.5 R_0=0.00001}
56-
d1_lt_prod: MATHEVAL ARG1=d1_lt ARG2=d1 FUNC=x*y PERIODIC=NO
56+
d1_lt_prod: MATHEVAL ARG=d1_lt,d1 FUNC=x*y PERIODIC=NO
5757
d1_lt_numer: SUM ARG=d1_lt_prod PERIODIC=NO
5858
d1_lt_denom: SUM ARG=d1_lt PERIODIC=NO
5959
d1_ltm: MATHEVAL ARG=d1_lt_numer,d1_lt_denom FUNC=x/y PERIODIC=NO
6060

6161
d1_mt: MORE_THAN ARG=d1 SWITCH={GAUSSIAN D_0=1.5 R_0=0.00001}
62-
d1_mt_prod: MATHEVAL ARG1=d1_mt ARG2=d1 FUNC=x*y PERIODIC=NO
62+
d1_mt_prod: MATHEVAL ARG=d1_mt,d1 FUNC=x*y PERIODIC=NO
6363
d1_mt_numer: SUM ARG=d1_mt_prod PERIODIC=NO
6464
d1_mt_denom: SUM ARG=d1_mt PERIODIC=NO
6565
d1_mtm: MATHEVAL ARG=d1_mt_numer,d1_mt_denom FUNC=x/y PERIODIC=NO
6666

6767
d1_bt1: BETWEEN ARG=d1 LOWER=0 UPPER=3.0 SMEAR=0.0001
68-
d1_bt1_prod: MATHEVAL ARG1=d1_bt1 ARG2=d1 FUNC=x*y PERIODIC=NO
68+
d1_bt1_prod: MATHEVAL ARG=d1_bt1,d1 FUNC=x*y PERIODIC=NO
6969
d1_bt1_numer: SUM ARG=d1_bt1_prod PERIODIC=NO
7070
d1_bt1_denom: SUM ARG=d1_bt1 PERIODIC=NO
7171
d1_bt1m: MATHEVAL ARG=d1_bt1_numer,d1_bt1_denom FUNC=x/y PERIODIC=NO
7272

7373
d1_bt2: BETWEEN ARG=d1 LOWER=3.0 UPPER=10.0 SMEAR=0.0001
74-
d1_bt2_prod: MATHEVAL ARG1=d1_bt2 ARG2=d1 FUNC=x*y PERIODIC=NO
74+
d1_bt2_prod: MATHEVAL ARG=d1_bt2,d1 FUNC=x*y PERIODIC=NO
7575
d1_bt2_numer: SUM ARG=d1_bt2_prod PERIODIC=NO
7676
d1_bt2_denom: SUM ARG=d1_bt2 PERIODIC=NO
7777
d1_bt2m: MATHEVAL ARG=d1_bt2_numer,d1_bt2_denom FUNC=x/y PERIODIC=NO
7878

7979
PRINT ARG=d1_m,d1_ltm,d1_mtm,d1_bt1m,d1_bt2m FILE=colvar FMT=%8.4f
8080

8181
d1_lt1: LESS_THAN ARG=d1 SWITCH={GAUSSIAN D_0=1.5 R_0=0.1}
82-
d1_lt1_prod: MATHEVAL ARG1=d1_lt ARG2=d1 FUNC=x*y PERIODIC=NO
82+
d1_lt1_prod: MATHEVAL ARG=d1_lt,d1 FUNC=x*y PERIODIC=NO
8383
d1_lt1_numer: SUM ARG=d1_lt_prod PERIODIC=NO
8484
d1_lt1_denom: SUM ARG=d1_lt PERIODIC=NO
8585
d1_lt1m: MATHEVAL ARG=d1_lt_numer,d1_lt_denom FUNC=x/y PERIODIC=NO
8686

8787
d1_mt1: MORE_THAN ARG=d1 SWITCH={GAUSSIAN D_0=1.5 R_0=0.1}
88-
d1_mt1_prod: MATHEVAL ARG1=d1_mt ARG2=d1 FUNC=x*y PERIODIC=NO
88+
d1_mt1_prod: MATHEVAL ARG=d1_mt,d1 FUNC=x*y PERIODIC=NO
8989
d1_mt1_numer: SUM ARG=d1_mt_prod PERIODIC=NO
9090
d1_mt1_denom: SUM ARG=d1_mt PERIODIC=NO
9191
d1_mt1m: MATHEVAL ARG=d1_mt_numer,d1_mt_denom FUNC=x/y PERIODIC=NO
9292

9393
d1_bt11: BETWEEN ARG=d1 LOWER=0 UPPER=3.0 SMEAR=0.1
94-
d1_bt11_prod: MATHEVAL ARG1=d1_bt1 ARG2=d1 FUNC=x*y PERIODIC=NO
94+
d1_bt11_prod: MATHEVAL ARG=d1_bt1,d1 FUNC=x*y PERIODIC=NO
9595
d1_bt11_numer: SUM ARG=d1_bt1_prod PERIODIC=NO
9696
d1_bt11_denom: SUM ARG=d1_bt1 PERIODIC=NO
9797
d1_bt11m: MATHEVAL ARG=d1_bt1_numer,d1_bt1_denom FUNC=x/y PERIODIC=NO

‎regtest/python/rt-symfunc/python-script.py

+2-2
Original file line numberDiff line numberDiff line change
@@ -72,8 +72,8 @@ def create_plumed_var( p, name, command ):
7272
p.cmd("setLogFile","test.log")
7373
p.cmd("init")
7474
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")
75-
p.cmd("readInputLine","cmatr: CUSTOM ARG1=cmat.x ARG2=cmat.y ARG3=cmat.z FUNC=sqrt(x*x+y*y+z*z) PERIODIC=NO")
76-
p.cmd("readInputLine","g2_f: CUSTOM ARG1=cmatr ARG2=cmat.w FUNC=y*exp(-(x-3)^2) PERIODIC=NO")
75+
p.cmd("readInputLine","cmatr: CUSTOM ARG=cmat.x,cmat.y,cmat.z FUNC=sqrt(x*x+y*y+z*z) PERIODIC=NO")
76+
p.cmd("readInputLine","g2_f: CUSTOM ARG=cmatr,cmat.w FUNC=y*exp(-(x-3)^2) PERIODIC=NO")
7777
p.cmd("readInputLine","ones: ONES SIZE=64")
7878
t1 = create_plumed_var( p, "beh2_g2", "MATRIX_VECTOR_PRODUCT ARG=g2_f,ones" )
7979
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}" )

‎regtest/symfunc/rt-behler/plumed.dat

+3-3
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
cmat: CONTACT_MATRIX GROUP=1-64 SWITCH={CUSTOM R_0=4.5 D_MAX=4.5 FUNC=0.5*(cos(pi*x)+1)} COMPONENTS
2-
cmatr: CUSTOM ARG1=cmat.x ARG2=cmat.y ARG3=cmat.z FUNC=sqrt(x*x+y*y+z*z) PERIODIC=NO
3-
g2_f: CUSTOM ARG1=cmatr ARG2=cmat.w FUNC=y*exp(-(x-3)^2) PERIODIC=NO
4-
g3_f: CUSTOM ARG1=cmatr ARG2=cmat.w FUNC=y*cos(x) PERIODIC=NO
2+
cmatr: CUSTOM ARG=cmat.x,cmat.y,cmat.z FUNC=sqrt(x*x+y*y+z*z) PERIODIC=NO
3+
g2_f: CUSTOM ARG=cmatr,cmat.w FUNC=y*exp(-(x-3)^2) PERIODIC=NO
4+
g3_f: CUSTOM ARG=cmatr,cmat.w FUNC=y*cos(x) PERIODIC=NO
55
beh2_g1_ones: ONES SIZE=64
66
beh2_g1: MATRIX_VECTOR_PRODUCT ARG=cmat.w,beh2_g1_ones
77
beh2_g2: MATRIX_VECTOR_PRODUCT ARG=g2_f,beh2_g1_ones

‎regtest/symfunc/rt-behler2/plumed.dat

+4-4
Original file line numberDiff line numberDiff line change
@@ -1,14 +1,14 @@
11
UNITS LENGTH=Bohr
22

33
cmat_hh: CONTACT_MATRIX GROUP=2,3,5,6 SWITCH={CUSTOM R_0=10.0 D_MAX=10 FUNC=tanh(1-x)^3} COMPONENTS
4-
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
5-
cmat_fh: CUSTOM ARG1=cmat_rh ARG2=cmat_hh.w FUNC=y*exp(-0.01*x*x) PERIODIC=NO
4+
cmat_rh: CUSTOM ARG=cmat_hh.x,cmat_hh.y,cmat_hh.z FUNC=sqrt(x*x+y*y+z*z) PERIODIC=NO
5+
cmat_fh: CUSTOM ARG=cmat_rh,cmat_hh.w FUNC=y*exp(-0.01*x*x) PERIODIC=NO
66
ones4: ONES SIZE=4
77
beh_hh: MATRIX_VECTOR_PRODUCT ARG=cmat_fh,ones4
88

99
cmat_oo: CONTACT_MATRIX GROUP=1,4 SWITCH={CUSTOM R_0=10.0 D_MAX=10 FUNC=tanh(1-x)^3} COMPONENTS
10-
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
11-
cmat_fo: CUSTOM ARG1=cmat_or ARG2=cmat_oo.w FUNC=y*exp(-0.01*x*x) PERIODIC=NO
10+
cmat_or: CUSTOM ARG=cmat_oo.x,cmat_oo.y,cmat_oo.z FUNC=sqrt(x*x+y*y+z*z) PERIODIC=NO
11+
cmat_fo: CUSTOM ARG=cmat_or,cmat_oo.w FUNC=y*exp(-0.01*x*x) PERIODIC=NO
1212
ones2: ONES SIZE=2
1313
beh_oo: MATRIX_VECTOR_PRODUCT ARG=cmat_fo,ones2
1414

‎regtest/symfunc/rt-center/plumed.dat

+1-1
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
c1: COORDINATIONNUMBER SPECIES=1-512 SWITCH={EXP D_0=4.0 R_0=0.5}
22
cf: MORE_THAN ARG=c1 SWITCH={RATIONAL D_0=2.0 R_0=0.1}
3-
ww: MATHEVAL ARG1=c1 ARG2=cf FUNC=x*y PERIODIC=NO
3+
ww: MATHEVAL ARG=c1,cf FUNC=x*y PERIODIC=NO
44
cc: CENTER ATOMS=c1 WEIGHTS=ww PHASES
55

66
DUMPATOMS ATOMS=cc FILE=cluster-com.xyz PRECISION=5

‎regtest/symfunc/rt-center3/plumed.dat

+1-1
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
c1: COORDINATIONNUMBER SPECIES=1-512 SWITCH={EXP D_0=4.0 R_0=0.5}
22
cf: MORE_THAN ARG=c1 SWITCH={RATIONAL D_0=2.0 R_0=0.1}
3-
ww: MATHEVAL ARG1=c1 ARG2=cf FUNC=x*y PERIODIC=NO
3+
ww: MATHEVAL ARG=c1,cf FUNC=x*y PERIODIC=NO
44
cc: CENTER ATOMS=c1 WEIGHTS=ww
55

66
DUMPATOMS ATOMS=cc FILE=cluster-com.xyz PRECISION=5

‎regtest/symfunc/rt-combine/plumed.dat

+1-1
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
c1: COORDINATIONNUMBER SPECIESA=1,2,3 SPECIESB=4-100 SWITCH={RATIONAL R_0=0.5} MEAN
22
c2: COORDINATIONNUMBER SPECIESA=1,2,3 SPECIESB=4-100 SWITCH={RATIONAL R_0=0.7}
3-
cc: COMBINE ARG1=c1 ARG2=c2 PERIODIC=NO
3+
cc: COMBINE ARG=c1,c2 PERIODIC=NO
44
cc_mean: MEAN ARG=cc PERIODIC=NO
55
PRINT ARG=cc FILE=colvar FMT=%8.4f
66
DUMPATOMS ARG=c1,c2,cc ATOMS=c1 FILE=cc.xyz PRECISION=4

‎regtest/symfunc/rt-dumpmulti/plumed.dat

+26-26
Original file line numberDiff line numberDiff line change
@@ -3,32 +3,32 @@ DUMPATOMS ARG=c ATOMS=c FILE=coordination.xyz PRECISION=4
33

44
q6: Q6 SPECIES=1-64 D_0=3.0 R_0=1.5 NN=12 MM=24
55

6-
q6n_rmn-[-6]: CUSTOM ARG1=q6_sp.rm-n6 ARG2=q6_norm FUNC=x/y PERIODIC=NO
7-
q6n_rmn-[-5]: CUSTOM ARG1=q6_sp.rm-n5 ARG2=q6_norm FUNC=x/y PERIODIC=NO
8-
q6n_rmn-[-4]: CUSTOM ARG1=q6_sp.rm-n4 ARG2=q6_norm FUNC=x/y PERIODIC=NO
9-
q6n_rmn-[-3]: CUSTOM ARG1=q6_sp.rm-n3 ARG2=q6_norm FUNC=x/y PERIODIC=NO
10-
q6n_rmn-[-2]: CUSTOM ARG1=q6_sp.rm-n2 ARG2=q6_norm FUNC=x/y PERIODIC=NO
11-
q6n_rmn-[-1]: CUSTOM ARG1=q6_sp.rm-n1 ARG2=q6_norm FUNC=x/y PERIODIC=NO
12-
q6n_rmn-[0]: CUSTOM ARG1=q6_sp.rm-0 ARG2=q6_norm FUNC=x/y PERIODIC=NO
13-
q6n_rmn-[1]: CUSTOM ARG1=q6_sp.rm-p1 ARG2=q6_norm FUNC=x/y PERIODIC=NO
14-
q6n_rmn-[2]: CUSTOM ARG1=q6_sp.rm-p2 ARG2=q6_norm FUNC=x/y PERIODIC=NO
15-
q6n_rmn-[3]: CUSTOM ARG1=q6_sp.rm-p3 ARG2=q6_norm FUNC=x/y PERIODIC=NO
16-
q6n_rmn-[4]: CUSTOM ARG1=q6_sp.rm-p4 ARG2=q6_norm FUNC=x/y PERIODIC=NO
17-
q6n_rmn-[5]: CUSTOM ARG1=q6_sp.rm-p5 ARG2=q6_norm FUNC=x/y PERIODIC=NO
18-
q6n_rmn-[6]: CUSTOM ARG1=q6_sp.rm-p6 ARG2=q6_norm FUNC=x/y PERIODIC=NO
19-
q6n_imn-[-6]: CUSTOM ARG1=q6_sp.im-n6 ARG2=q6_norm FUNC=x/y PERIODIC=NO
20-
q6n_imn-[-5]: CUSTOM ARG1=q6_sp.im-n5 ARG2=q6_norm FUNC=x/y PERIODIC=NO
21-
q6n_imn-[-4]: CUSTOM ARG1=q6_sp.im-n4 ARG2=q6_norm FUNC=x/y PERIODIC=NO
22-
q6n_imn-[-3]: CUSTOM ARG1=q6_sp.im-n3 ARG2=q6_norm FUNC=x/y PERIODIC=NO
23-
q6n_imn-[-2]: CUSTOM ARG1=q6_sp.im-n2 ARG2=q6_norm FUNC=x/y PERIODIC=NO
24-
q6n_imn-[-1]: CUSTOM ARG1=q6_sp.im-n1 ARG2=q6_norm FUNC=x/y PERIODIC=NO
25-
q6n_imn-[0]: CUSTOM ARG1=q6_sp.im-0 ARG2=q6_norm FUNC=x/y PERIODIC=NO
26-
q6n_imn-[1]: CUSTOM ARG1=q6_sp.im-p1 ARG2=q6_norm FUNC=x/y PERIODIC=NO
27-
q6n_imn-[2]: CUSTOM ARG1=q6_sp.im-p2 ARG2=q6_norm FUNC=x/y PERIODIC=NO
28-
q6n_imn-[3]: CUSTOM ARG1=q6_sp.im-p3 ARG2=q6_norm FUNC=x/y PERIODIC=NO
29-
q6n_imn-[4]: CUSTOM ARG1=q6_sp.im-p4 ARG2=q6_norm FUNC=x/y PERIODIC=NO
30-
q6n_imn-[5]: CUSTOM ARG1=q6_sp.im-p5 ARG2=q6_norm FUNC=x/y PERIODIC=NO
31-
q6n_imn-[6]: CUSTOM ARG1=q6_sp.im-p6 ARG2=q6_norm FUNC=x/y PERIODIC=NO
6+
q6n_rmn-[-6]: CUSTOM ARG=q6_sp.rm-n6,q6_norm FUNC=x/y PERIODIC=NO
7+
q6n_rmn-[-5]: CUSTOM ARG=q6_sp.rm-n5,q6_norm FUNC=x/y PERIODIC=NO
8+
q6n_rmn-[-4]: CUSTOM ARG=q6_sp.rm-n4,q6_norm FUNC=x/y PERIODIC=NO
9+
q6n_rmn-[-3]: CUSTOM ARG=q6_sp.rm-n3,q6_norm FUNC=x/y PERIODIC=NO
10+
q6n_rmn-[-2]: CUSTOM ARG=q6_sp.rm-n2,q6_norm FUNC=x/y PERIODIC=NO
11+
q6n_rmn-[-1]: CUSTOM ARG=q6_sp.rm-n1,q6_norm FUNC=x/y PERIODIC=NO
12+
q6n_rmn-[0]: CUSTOM ARG=q6_sp.rm-0,q6_norm FUNC=x/y PERIODIC=NO
13+
q6n_rmn-[1]: CUSTOM ARG=q6_sp.rm-p1,q6_norm FUNC=x/y PERIODIC=NO
14+
q6n_rmn-[2]: CUSTOM ARG=q6_sp.rm-p2,q6_norm FUNC=x/y PERIODIC=NO
15+
q6n_rmn-[3]: CUSTOM ARG=q6_sp.rm-p3,q6_norm FUNC=x/y PERIODIC=NO
16+
q6n_rmn-[4]: CUSTOM ARG=q6_sp.rm-p4,q6_norm FUNC=x/y PERIODIC=NO
17+
q6n_rmn-[5]: CUSTOM ARG=q6_sp.rm-p5,q6_norm FUNC=x/y PERIODIC=NO
18+
q6n_rmn-[6]: CUSTOM ARG=q6_sp.rm-p6,q6_norm FUNC=x/y PERIODIC=NO
19+
q6n_imn-[-6]: CUSTOM ARG=q6_sp.im-n6,q6_norm FUNC=x/y PERIODIC=NO
20+
q6n_imn-[-5]: CUSTOM ARG=q6_sp.im-n5,q6_norm FUNC=x/y PERIODIC=NO
21+
q6n_imn-[-4]: CUSTOM ARG=q6_sp.im-n4,q6_norm FUNC=x/y PERIODIC=NO
22+
q6n_imn-[-3]: CUSTOM ARG=q6_sp.im-n3,q6_norm FUNC=x/y PERIODIC=NO
23+
q6n_imn-[-2]: CUSTOM ARG=q6_sp.im-n2,q6_norm FUNC=x/y PERIODIC=NO
24+
q6n_imn-[-1]: CUSTOM ARG=q6_sp.im-n1,q6_norm FUNC=x/y PERIODIC=NO
25+
q6n_imn-[0]: CUSTOM ARG=q6_sp.im-0,q6_norm FUNC=x/y PERIODIC=NO
26+
q6n_imn-[1]: CUSTOM ARG=q6_sp.im-p1,q6_norm FUNC=x/y PERIODIC=NO
27+
q6n_imn-[2]: CUSTOM ARG=q6_sp.im-p2,q6_norm FUNC=x/y PERIODIC=NO
28+
q6n_imn-[3]: CUSTOM ARG=q6_sp.im-p3,q6_norm FUNC=x/y PERIODIC=NO
29+
q6n_imn-[4]: CUSTOM ARG=q6_sp.im-p4,q6_norm FUNC=x/y PERIODIC=NO
30+
q6n_imn-[5]: CUSTOM ARG=q6_sp.im-p5,q6_norm FUNC=x/y PERIODIC=NO
31+
q6n_imn-[6]: CUSTOM ARG=q6_sp.im-p6,q6_norm FUNC=x/y PERIODIC=NO
3232

3333
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
3434

‎regtest/symfunc/rt-hexactic/plumed.dat

+3-3
Original file line numberDiff line numberDiff line change
@@ -5,14 +5,14 @@ PRINT ARG=hex.mean,bb.* FILE=colvar FMT=%8.4f
55
# This checks against what is done in LAMMPS
66
dmat: DISTANCE_MATRIX GROUP=1-400 CUTOFF=3.0 COMPONENTS
77
neigh: NEIGHBORS ARG=dmat.w NLOWEST=6
8-
harm: CYLINDRICAL_HARMONIC DEGREE=6 ARG1=dmat.x ARG2=dmat.y
8+
harm: CYLINDRICAL_HARMONIC DEGREE=6 ARG=dmat.x,dmat.y
99
rprod: CUSTOM ARG=neigh,harm.rm FUNC=x*y PERIODIC=NO
1010
iprod: CUSTOM ARG=neigh,harm.im FUNC=x*y PERIODIC=NO
1111
hex2_ones: ONES SIZE=400
1212
hex2_denom: MATRIX_VECTOR_PRODUCT ARG=neigh,hex2_ones
1313
harm_rm: MATRIX_VECTOR_PRODUCT ARG=rprod,hex2_ones
1414
harm_im: MATRIX_VECTOR_PRODUCT ARG=iprod,hex2_ones
15-
hex2_rmn: CUSTOM ARG1=harm_rm ARG2=hex2_denom FUNC=x/y PERIODIC=NO
16-
hex2_imn: CUSTOM ARG1=harm_im ARG2=hex2_denom FUNC=x/y PERIODIC=NO
15+
hex2_rmn: CUSTOM ARG=harm_rm,hex2_denom FUNC=x/y PERIODIC=NO
16+
hex2_imn: CUSTOM ARG=harm_im,hex2_denom FUNC=x/y PERIODIC=NO
1717

1818
DUMPATOMS ATOMS=1-400 ARG=hex2_rmn,hex2_imn,hex2_denom PRECISION=4 FILE=hexparam.xyz

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