Project ID: plumID:23.017
Source: QM-MM_MD/8atomsCV/plumed.dat
Originally used with PLUMED version: 2.9
Stable: zipped raw stdout - zipped raw stderr - stderr
Master: zipped raw stdout - zipped raw stderr - stderr
Click on the labels of the actions for more information on what each action computes
UNITSThis command sets the internal units for the code. More details LENGTHthe units of lengths=A
The UNITS action with label calculates somethinga_1_1The COORDINATION action with label a_1_1 calculates the following quantities:| Quantity | Type | Description |
| a_1_1 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=3026 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3026 R_0The r_0 parameter of the switching function=1.6 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10
a_1_1: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=3026 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3026 R_0The r_0 parameter of the switching function=1.6 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10 D_0 The d_0 parameter of the switching function=0.0
a_1_2The COORDINATION action with label a_1_2 calculates the following quantities:| Quantity | Type | Description |
| a_1_2 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=3026 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3027 R_0The r_0 parameter of the switching function=1.6 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10
a_1_2: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=3026 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3027 R_0The r_0 parameter of the switching function=1.6 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10 D_0 The d_0 parameter of the switching function=0.0
a_1_3The COORDINATION action with label a_1_3 calculates the following quantities:| Quantity | Type | Description |
| a_1_3 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=3026 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3605 R_0The r_0 parameter of the switching function=1.6 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10
a_1_3: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=3026 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3605 R_0The r_0 parameter of the switching function=1.6 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10 D_0 The d_0 parameter of the switching function=0.0
a_1_4The COORDINATION action with label a_1_4 calculates the following quantities:| Quantity | Type | Description |
| a_1_4 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=3026 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3606 R_0The r_0 parameter of the switching function=1.6 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10
a_1_4: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=3026 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3606 R_0The r_0 parameter of the switching function=1.6 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10 D_0 The d_0 parameter of the switching function=0.0
a_1_5The COORDINATION action with label a_1_5 calculates the following quantities:| Quantity | Type | Description |
| a_1_5 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=3026 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3607 R_0The r_0 parameter of the switching function=1.4 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10
a_1_5: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=3026 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3607 R_0The r_0 parameter of the switching function=1.4 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10 D_0 The d_0 parameter of the switching function=0.0
a_1_6The COORDINATION action with label a_1_6 calculates the following quantities:| Quantity | Type | Description |
| a_1_6 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=3026 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7689 R_0The r_0 parameter of the switching function=1.8 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10
a_1_6: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=3026 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7689 R_0The r_0 parameter of the switching function=1.8 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10 D_0 The d_0 parameter of the switching function=0.0
a_1_7The COORDINATION action with label a_1_7 calculates the following quantities:| Quantity | Type | Description |
| a_1_7 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=3026 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7699 R_0The r_0 parameter of the switching function=1.6 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10
a_1_7: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=3026 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7699 R_0The r_0 parameter of the switching function=1.6 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10 D_0 The d_0 parameter of the switching function=0.0
a_1_8The COORDINATION action with label a_1_8 calculates the following quantities:| Quantity | Type | Description |
| a_1_8 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=3026 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7700 R_0The r_0 parameter of the switching function=1.8 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10
a_1_8: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=3026 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7700 R_0The r_0 parameter of the switching function=1.8 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10 D_0 The d_0 parameter of the switching function=0.0
a_2_1The CUSTOM action with label a_2_1 calculates the following quantities:| Quantity | Type | Description |
| a_2_1 | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=a_1_2 FUNCthe function you wish to evaluate=x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
a_2_2The COORDINATION action with label a_2_2 calculates the following quantities:| Quantity | Type | Description |
| a_2_2 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=3027 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3027 R_0The r_0 parameter of the switching function=1.6 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10
a_2_2: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=3027 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3027 R_0The r_0 parameter of the switching function=1.6 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10 D_0 The d_0 parameter of the switching function=0.0
a_2_3The COORDINATION action with label a_2_3 calculates the following quantities:| Quantity | Type | Description |
| a_2_3 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=3027 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3605 R_0The r_0 parameter of the switching function=1.6 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10
a_2_3: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=3027 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3605 R_0The r_0 parameter of the switching function=1.6 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10 D_0 The d_0 parameter of the switching function=0.0
a_2_4The COORDINATION action with label a_2_4 calculates the following quantities:| Quantity | Type | Description |
| a_2_4 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=3027 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3606 R_0The r_0 parameter of the switching function=1.6 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10
a_2_4: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=3027 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3606 R_0The r_0 parameter of the switching function=1.6 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10 D_0 The d_0 parameter of the switching function=0.0
a_2_5The COORDINATION action with label a_2_5 calculates the following quantities:| Quantity | Type | Description |
| a_2_5 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=3027 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3607 R_0The r_0 parameter of the switching function=1.4 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10
a_2_5: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=3027 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3607 R_0The r_0 parameter of the switching function=1.4 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10 D_0 The d_0 parameter of the switching function=0.0
a_2_6The COORDINATION action with label a_2_6 calculates the following quantities:| Quantity | Type | Description |
| a_2_6 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=3027 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7689 R_0The r_0 parameter of the switching function=1.8 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10
a_2_6: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=3027 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7689 R_0The r_0 parameter of the switching function=1.8 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10 D_0 The d_0 parameter of the switching function=0.0
a_2_7The COORDINATION action with label a_2_7 calculates the following quantities:| Quantity | Type | Description |
| a_2_7 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=3027 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7699 R_0The r_0 parameter of the switching function=1.6 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10
a_2_7: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=3027 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7699 R_0The r_0 parameter of the switching function=1.6 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10 D_0 The d_0 parameter of the switching function=0.0
a_2_8The COORDINATION action with label a_2_8 calculates the following quantities:| Quantity | Type | Description |
| a_2_8 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=3027 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7700 R_0The r_0 parameter of the switching function=1.8 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10
a_2_8: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=3027 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7700 R_0The r_0 parameter of the switching function=1.8 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10 D_0 The d_0 parameter of the switching function=0.0
a_3_1The CUSTOM action with label a_3_1 calculates the following quantities:| Quantity | Type | Description |
| a_3_1 | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=a_1_3 FUNCthe function you wish to evaluate=x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
a_3_2The CUSTOM action with label a_3_2 calculates the following quantities:| Quantity | Type | Description |
| a_3_2 | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=a_2_3 FUNCthe function you wish to evaluate=x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
a_3_3The COORDINATION action with label a_3_3 calculates the following quantities:| Quantity | Type | Description |
| a_3_3 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=3605 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3605 R_0The r_0 parameter of the switching function=1.6 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10
a_3_3: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=3605 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3605 R_0The r_0 parameter of the switching function=1.6 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10 D_0 The d_0 parameter of the switching function=0.0
a_3_4The COORDINATION action with label a_3_4 calculates the following quantities:| Quantity | Type | Description |
| a_3_4 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=3605 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3606 R_0The r_0 parameter of the switching function=1.6 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10
a_3_4: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=3605 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3606 R_0The r_0 parameter of the switching function=1.6 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10 D_0 The d_0 parameter of the switching function=0.0
a_3_5The COORDINATION action with label a_3_5 calculates the following quantities:| Quantity | Type | Description |
| a_3_5 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=3605 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3607 R_0The r_0 parameter of the switching function=1.4 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10
a_3_5: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=3605 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3607 R_0The r_0 parameter of the switching function=1.4 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10 D_0 The d_0 parameter of the switching function=0.0
a_3_6The COORDINATION action with label a_3_6 calculates the following quantities:| Quantity | Type | Description |
| a_3_6 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=3605 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7689 R_0The r_0 parameter of the switching function=1.8 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10
a_3_6: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=3605 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7689 R_0The r_0 parameter of the switching function=1.8 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10 D_0 The d_0 parameter of the switching function=0.0
a_3_7The COORDINATION action with label a_3_7 calculates the following quantities:| Quantity | Type | Description |
| a_3_7 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=3605 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7699 R_0The r_0 parameter of the switching function=1.6 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10
a_3_7: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=3605 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7699 R_0The r_0 parameter of the switching function=1.6 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10 D_0 The d_0 parameter of the switching function=0.0
a_3_8The COORDINATION action with label a_3_8 calculates the following quantities:| Quantity | Type | Description |
| a_3_8 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=3605 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7700 R_0The r_0 parameter of the switching function=1.8 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10
a_3_8: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=3605 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7700 R_0The r_0 parameter of the switching function=1.8 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10 D_0 The d_0 parameter of the switching function=0.0
a_4_1The CUSTOM action with label a_4_1 calculates the following quantities:| Quantity | Type | Description |
| a_4_1 | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=a_1_4 FUNCthe function you wish to evaluate=x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
a_4_2The CUSTOM action with label a_4_2 calculates the following quantities:| Quantity | Type | Description |
| a_4_2 | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=a_2_4 FUNCthe function you wish to evaluate=x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
a_4_3The CUSTOM action with label a_4_3 calculates the following quantities:| Quantity | Type | Description |
| a_4_3 | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=a_3_4 FUNCthe function you wish to evaluate=x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
a_4_4The COORDINATION action with label a_4_4 calculates the following quantities:| Quantity | Type | Description |
| a_4_4 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=3606 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3606 R_0The r_0 parameter of the switching function=1.6 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10
a_4_4: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=3606 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3606 R_0The r_0 parameter of the switching function=1.6 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10 D_0 The d_0 parameter of the switching function=0.0
a_4_5The COORDINATION action with label a_4_5 calculates the following quantities:| Quantity | Type | Description |
| a_4_5 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=3606 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3607 R_0The r_0 parameter of the switching function=1.4 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10
a_4_5: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=3606 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3607 R_0The r_0 parameter of the switching function=1.4 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10 D_0 The d_0 parameter of the switching function=0.0
a_4_6The COORDINATION action with label a_4_6 calculates the following quantities:| Quantity | Type | Description |
| a_4_6 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=3606 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7689 R_0The r_0 parameter of the switching function=1.8 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10
a_4_6: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=3606 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7689 R_0The r_0 parameter of the switching function=1.8 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10 D_0 The d_0 parameter of the switching function=0.0
a_4_7The COORDINATION action with label a_4_7 calculates the following quantities:| Quantity | Type | Description |
| a_4_7 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=3606 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7699 R_0The r_0 parameter of the switching function=1.6 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10
a_4_7: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=3606 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7699 R_0The r_0 parameter of the switching function=1.6 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10 D_0 The d_0 parameter of the switching function=0.0
a_4_8The COORDINATION action with label a_4_8 calculates the following quantities:| Quantity | Type | Description |
| a_4_8 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=3606 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7700 R_0The r_0 parameter of the switching function=1.8 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10
a_4_8: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=3606 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7700 R_0The r_0 parameter of the switching function=1.8 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10 D_0 The d_0 parameter of the switching function=0.0
a_5_1The CUSTOM action with label a_5_1 calculates the following quantities:| Quantity | Type | Description |
| a_5_1 | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=a_1_5 FUNCthe function you wish to evaluate=x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
a_5_2The CUSTOM action with label a_5_2 calculates the following quantities:| Quantity | Type | Description |
| a_5_2 | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=a_2_5 FUNCthe function you wish to evaluate=x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
a_5_3The CUSTOM action with label a_5_3 calculates the following quantities:| Quantity | Type | Description |
| a_5_3 | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=a_3_5 FUNCthe function you wish to evaluate=x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
a_5_4The CUSTOM action with label a_5_4 calculates the following quantities:| Quantity | Type | Description |
| a_5_4 | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=a_4_5 FUNCthe function you wish to evaluate=x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
a_5_5The COORDINATION action with label a_5_5 calculates the following quantities:| Quantity | Type | Description |
| a_5_5 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=3607 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3607 R_0The r_0 parameter of the switching function=1.2 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10
a_5_5: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=3607 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=3607 R_0The r_0 parameter of the switching function=1.2 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10 D_0 The d_0 parameter of the switching function=0.0
a_5_6The COORDINATION action with label a_5_6 calculates the following quantities:| Quantity | Type | Description |
| a_5_6 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=3607 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7689 R_0The r_0 parameter of the switching function=1.2 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10
a_5_6: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=3607 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7689 R_0The r_0 parameter of the switching function=1.2 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10 D_0 The d_0 parameter of the switching function=0.0
a_5_7The COORDINATION action with label a_5_7 calculates the following quantities:| Quantity | Type | Description |
| a_5_7 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=3607 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7699 R_0The r_0 parameter of the switching function=1.4 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10
a_5_7: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=3607 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7699 R_0The r_0 parameter of the switching function=1.4 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10 D_0 The d_0 parameter of the switching function=0.0
a_5_8The COORDINATION action with label a_5_8 calculates the following quantities:| Quantity | Type | Description |
| a_5_8 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=3607 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7700 R_0The r_0 parameter of the switching function=1.2 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10
a_5_8: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=3607 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7700 R_0The r_0 parameter of the switching function=1.2 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10 D_0 The d_0 parameter of the switching function=0.0
a_6_1The CUSTOM action with label a_6_1 calculates the following quantities:| Quantity | Type | Description |
| a_6_1 | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=a_1_6 FUNCthe function you wish to evaluate=x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
a_6_2The CUSTOM action with label a_6_2 calculates the following quantities:| Quantity | Type | Description |
| a_6_2 | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=a_2_6 FUNCthe function you wish to evaluate=x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
a_6_3The CUSTOM action with label a_6_3 calculates the following quantities:| Quantity | Type | Description |
| a_6_3 | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=a_3_6 FUNCthe function you wish to evaluate=x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
a_6_4The CUSTOM action with label a_6_4 calculates the following quantities:| Quantity | Type | Description |
| a_6_4 | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=a_4_6 FUNCthe function you wish to evaluate=x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
a_6_5The CUSTOM action with label a_6_5 calculates the following quantities:| Quantity | Type | Description |
| a_6_5 | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=a_5_6 FUNCthe function you wish to evaluate=x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
a_6_6The COORDINATION action with label a_6_6 calculates the following quantities:| Quantity | Type | Description |
| a_6_6 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=7689 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7689 R_0The r_0 parameter of the switching function=1.7 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10
a_6_6: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=7689 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7689 R_0The r_0 parameter of the switching function=1.7 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10 D_0 The d_0 parameter of the switching function=0.0
a_6_7The COORDINATION action with label a_6_7 calculates the following quantities:| Quantity | Type | Description |
| a_6_7 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=7689 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7699 R_0The r_0 parameter of the switching function=1.8 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10
a_6_7: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=7689 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7699 R_0The r_0 parameter of the switching function=1.8 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10 D_0 The d_0 parameter of the switching function=0.0
a_6_8The COORDINATION action with label a_6_8 calculates the following quantities:| Quantity | Type | Description |
| a_6_8 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=7689 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7700 R_0The r_0 parameter of the switching function=1.7 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10
a_6_8: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=7689 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7700 R_0The r_0 parameter of the switching function=1.7 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10 D_0 The d_0 parameter of the switching function=0.0
a_7_1The CUSTOM action with label a_7_1 calculates the following quantities:| Quantity | Type | Description |
| a_7_1 | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=a_1_7 FUNCthe function you wish to evaluate=x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
a_7_2The CUSTOM action with label a_7_2 calculates the following quantities:| Quantity | Type | Description |
| a_7_2 | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=a_2_7 FUNCthe function you wish to evaluate=x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
a_7_3The CUSTOM action with label a_7_3 calculates the following quantities:| Quantity | Type | Description |
| a_7_3 | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=a_3_7 FUNCthe function you wish to evaluate=x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
a_7_4The CUSTOM action with label a_7_4 calculates the following quantities:| Quantity | Type | Description |
| a_7_4 | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=a_4_7 FUNCthe function you wish to evaluate=x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
a_7_5The CUSTOM action with label a_7_5 calculates the following quantities:| Quantity | Type | Description |
| a_7_5 | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=a_5_7 FUNCthe function you wish to evaluate=x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
a_7_6The CUSTOM action with label a_7_6 calculates the following quantities:| Quantity | Type | Description |
| a_7_6 | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=a_6_7 FUNCthe function you wish to evaluate=x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
a_7_7The COORDINATION action with label a_7_7 calculates the following quantities:| Quantity | Type | Description |
| a_7_7 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=7699 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7699 R_0The r_0 parameter of the switching function=1.6 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10
a_7_7: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=7699 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7699 R_0The r_0 parameter of the switching function=1.6 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10 D_0 The d_0 parameter of the switching function=0.0
a_7_8The COORDINATION action with label a_7_8 calculates the following quantities:| Quantity | Type | Description |
| a_7_8 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=7699 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7700 R_0The r_0 parameter of the switching function=1.8 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10
a_7_8: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=7699 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7700 R_0The r_0 parameter of the switching function=1.8 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10 D_0 The d_0 parameter of the switching function=0.0
a_8_1The CUSTOM action with label a_8_1 calculates the following quantities:| Quantity | Type | Description |
| a_8_1 | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=a_1_8 FUNCthe function you wish to evaluate=x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
a_8_2The CUSTOM action with label a_8_2 calculates the following quantities:| Quantity | Type | Description |
| a_8_2 | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=a_2_8 FUNCthe function you wish to evaluate=x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
a_8_3The CUSTOM action with label a_8_3 calculates the following quantities:| Quantity | Type | Description |
| a_8_3 | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=a_3_8 FUNCthe function you wish to evaluate=x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
a_8_4The CUSTOM action with label a_8_4 calculates the following quantities:| Quantity | Type | Description |
| a_8_4 | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=a_4_8 FUNCthe function you wish to evaluate=x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
a_8_5The CUSTOM action with label a_8_5 calculates the following quantities:| Quantity | Type | Description |
| a_8_5 | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=a_5_8 FUNCthe function you wish to evaluate=x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
a_8_6The CUSTOM action with label a_8_6 calculates the following quantities:| Quantity | Type | Description |
| a_8_6 | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=a_6_8 FUNCthe function you wish to evaluate=x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
a_8_7The CUSTOM action with label a_8_7 calculates the following quantities:| Quantity | Type | Description |
| a_8_7 | scalar | an arbitrary function |
: CUSTOMCalculate a combination of variables using a custom expression. More details ARGthe values input to this function=a_7_8 FUNCthe function you wish to evaluate=x PERIODICif the output of your function is periodic then you should specify the periodicity of the function=NO
a_8_8The COORDINATION action with label a_8_8 calculates the following quantities:| Quantity | Type | Description |
| a_8_8 | scalar | the value of the coordination |
: COORDINATIONCalculate coordination numbers. This action has hidden defaults. More details GROUPAFirst list of atoms=7700 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7700 R_0The r_0 parameter of the switching function=1.7 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10
a_8_8: COORDINATIONCalculate coordination numbers. This action uses the defaults shown here. More details GROUPAFirst list of atoms=7700 GROUPBSecond list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)=7700 R_0The r_0 parameter of the switching function=1.7 NN The n parameter of the switching function =6 MM The m parameter of the switching function; 0 implies 2*NN=10 D_0 The d_0 parameter of the switching function=0.0
cvThe PYTORCH_MODEL action with label cv calculates the following quantities:| Quantity | Type | Description |
| cv.node-0 | scalar | Model outputs This is the 0th of these quantities |
: PYTORCH_MODELLoad a PyTorch model compiled with TorchScript. More details FILEFilename of the PyTorch compiled model=08_cv.pt ARGthe labels of the values from which the function is calculated=,a_1_1,a_1_2,a_1_3,a_1_4,a_1_5,a_1_6,a_1_7,a_1_8,a_2_1,a_2_2,a_2_3,a_2_4,a_2_5,a_2_6,a_2_7,a_2_8,a_3_1,a_3_2,a_3_3,a_3_4,a_3_5,a_3_6,a_3_7,a_3_8,a_4_1,a_4_2,a_4_3,a_4_4,a_4_5,a_4_6,a_4_7,a_4_8,a_5_1,a_5_2,a_5_3,a_5_4,a_5_5,a_5_6,a_5_7,a_5_8,a_6_1,a_6_2,a_6_3,a_6_4,a_6_5,a_6_6,a_6_7,a_6_8,a_7_1,a_7_2,a_7_3,a_7_4,a_7_5,a_7_6,a_7_7,a_7_8,a_8_1,a_8_2,a_8_3,a_8_4,a_8_5,a_8_6,a_8_7,a_8_8
opesThe OPES_METAD_EXPLORE action with label opes calculates the following quantities:| Quantity | Type | Description |
| opes.bias | scalar | the instantaneous value of the bias potential |
| opes.rct | scalar | estimate of c(t). log(exp(beta V)/beta, should become flat as the simulation converges. Do NOT use for reweighting |
| opes.zed | scalar | estimate of Z_n. should become flat once no new CV-space region is explored |
| opes.neff | scalar | effective sample size |
| opes.nker | scalar | total number of compressed kernels used to represent the bias |
: OPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. This action has hidden defaults. More details ...
ARGthe labels of the scalars on which the bias will act=cv.*
PACEthe frequency for kernel deposition=100
BARRIERthe free energy barrier to be overcome=50
TEMP temperature=300.0
...
opes: OPES_METAD_EXPLOREOn-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode. This action uses the defaults shown here. More details ...
ARGthe labels of the scalars on which the bias will act=cv.*
PACEthe frequency for kernel deposition=100
BARRIERthe free energy barrier to be overcome=50
TEMP temperature=300.0
SIGMA the initial widths of the kernels, divided by the square root of gamma=ADAPTIVE COMPRESSION_THRESHOLD merge kernels if closer than this threshold, in units of sigma=1 FILE a file in which the list of all deposited kernels is stored=KERNELS
...
PRINTPrint quantities to a file. More details ARGthe labels of the values that you would like to print to the file=cv.*,opes.* FILEthe name of the file on which to output these quantities=colvar STRIDE the frequency with which the quantities of interest should be output=1
