From d9b3659be70adc223e34f788ab76ee526e9bd806 Mon Sep 17 00:00:00 2001
From: Zhuohan_Lao <zlao@mit.edu>
Date: Sat, 30 Sep 2023 00:54:40 -0400
Subject: [PATCH] deformation

---
 openNucleome/.whole_nucleus_model.py.swp      | Bin 0 -> 16384 bytes
 openNucleome/whole_nucleus_model.py           |   8 +++--
 .../HFF_100KB/NuclearDeformation/README.md    |   2 +-
 .../NuclearDeformation/simulation.ipynb       |  31 +++++++++++++-----
 .../SphericalNucleus/simulation.ipynb         |   2 +-
 5 files changed, 30 insertions(+), 13 deletions(-)
 create mode 100644 openNucleome/.whole_nucleus_model.py.swp

diff --git a/openNucleome/.whole_nucleus_model.py.swp b/openNucleome/.whole_nucleus_model.py.swp
new file mode 100644
index 0000000000000000000000000000000000000000..865495aed61e2f683f020d23e4420d5bb28dec60
GIT binary patch
literal 16384
zcmeHOOKc@a742jQgoHpu1W7<h#W>1)9=+H8Oon(K8jwFTkt5q<#vX&144ra!J-^2N
zOLz5n97M7SA`4bXK_DVN5(pM7BC<+0AZ7(91c3+=JCIng0HjEP6@hcBsz2{zO!!Da
z>XweXyFRyWox1h8_qBItcUITgf<15Hy3?}0^_{!LPk#A<6SsZrChPG*9uIgF@R%}>
zzPy2(bmwNf^JlyBb7#6|&)VK$WUsGo+vis<*Qz~H37lCG*}jaEnTv^tHgY!*aVTcu
z`pdx}4ulg?UY<E&?1{im4r}6?$A*E1fj7j!9oFgjxml_*b@GGku6NgG=Nl5#6mA%3
z7-$%17-$%17-$%17-$%182CSAKqj|XPeSjTjqW?<e$&YP@8()H=^r1-f8FGN%A|i|
zB>!(F|GY_meI);cd7m-&Wuri$he>X34Fe4W4Fe4W4Fe4W4Fe4W4Fe4W4Fe4W4Fe4W
z{{{oxv#i_UWIss(0Q~-6`2W9omu3AB_&V@3kOTX`4)8GWQQ&^y_wTf<9|7M4o&tPe
z0Bi$mz|Zcmte1cma6cg5VOariCvXDz_3f7R3UC8>4tN@P2)F>;2fTQjWxW7A11tfH
z!25xpzumH425tZua29y&R?GT6@Ht=$xCER4{`xlb1^5B*J>V<Amw^np2e=#f^II*;
z16<%Ez+Y~GJm3$&kAbfN>%batFK`d=>RT-97r=|a3qS}g0N+M1;}BQ?9t8dfZl42)
z<0pvc<|-Iq=E_9Sx5GGa<Y6M%Id<hLo5CwouYS~z(~wI)j;x^yZX6~&mGw#{DHM@B
zrt*d(W61+F7Ko^=6mSQrlf;=%EoIYeN*9Roa95-(?la`GUBSJ~D)k_J#_QTV!KW-<
zC3SOU$u1>d@vlx#7BE_jojS+xdp$Km*Hj+)lDTnoO{5ug>@YbH%oBZ{2a@?=5~osl
z3{qIp7^{)T{EYEvFOz8;cG$tdcL(gi4+8WFtuX0_B4b&|g8<zH<w|-))CVjInacw=
z57aQ&meL1*sF;sNSPIFaJw)YDZ>FbvWu>W9xN+(!`4bfd*MdVkBAbMdGhB^;%EMr4
z!&xXB8Ly-4YCJzX%%ljB8HV<jdTvjTh$q7!R;dhz*2eP%KM-w`?j&3eYIXcR>j!+#
z2}QUIUPMoKpm=q5<H&=oD6xZ>d-A$$2Ru}%9p+I-&b9nVwkji0eHjvo>O=2kx9TdP
z5HxlAP_@i&wOUo@7_M!Y5S1XilH8B{Xip7{QgT<w10gT~iE#bC?=mRrM_kW>$_fhg
zSsTU$0Uef#$8tXv9!9-vnp#^_YBL$D=2DvCWWt9L<hmJ6GI}?y6ohrycAA4lKXQZI
z6GK%#%r5XCL#DVsp2^xPdUEuXgo@B1?pS*_j)S9hCWdH)No&#$6vttl;fpmj)rh=~
z(T&JcpRC1!-%+gX2O{fW+Igl^6=}uL{BzQ}<yG>y$x|K*i8Y|&b~zPXYG#Z*ANbH1
z!zq1CUyN<v-^)`qd$URhvIZI!tRc)*A{<>^EnS_`d^*F{2E$UUcc@c^Id8;~s1J8J
z0Yjc;s4+Kd&$3f2w|SW3PN`0YMWwP$Rbzh}W%bh%im4~e&qP4^JRL1eb27J=F0O5V
za(!`Q!&$z#v9-OpvF+?r<=kG}x%klH%B71{#>S%RG4)!@re#lx1cKBGNRMo)dZx8a
zc)5#(RV}}5DpgsMlCj6JE<k|3Phmc}w1<Fp(Z{n-yHR^?W<t$c&q#r)pKOMKui1su
za}SU<wTuyk%HE94>~-Q@G0gG|>Z2m{K+Uoq_R~S{(MQ7k(Q=ZoYdpwl_not6rz;z&
z28y-&Sg_>LGiA#U%?_dXV~W>F%}PG0UFz_eTFd2l9M|rJR1-e4!o!5-AnZMp9IV$H
z$FAciX$+Io+O-V{b2E>SKGWkw%-VA`b@b?t>B2^qxb36IDznGi7$&<u(34ssv!$zC
z6}pys$Dc{d!m6JC{^NRSP~X(*1uD;&{-(C9pVk)x$DyUeam+eUS4-JP$JqKgSm_+j
zA=M;OgV?D}Z(~q;`!Cv9jaZzgT7{0@?CI!+B?N;u;IP|b$D#euX3P4hr_ObYJ%%Rh
zDN8*zkHt#B3{W4dvq(kOW2aH7{{BFR>2Hk#zsJsCuia!@Xoi;P9{Ugk)LtL#ur;;U
z_1J=5W@#J9N(0Yu9*XGXgoTNYr?fm|%JlL~LIF?DrmQ?jQ9rse?$VvM3z>3t6KS{H
zP&js>@<n9bYAc})q@F|cklxssip{{T)TFPfmj~%OeKgJ7fYyOR%}i}!!-i09zq_2)
z2`pS{o2yaIqX>s(buPxL`B*L@SC|vA*$U03LgT9&tbf^!8Pdn7FxzbG`lxCMHd&@e
z<``Rygvm5Sz-UcXGmd#?3RK(_CD4DPnl+^wuYX-WUZ_*FSlURAeOsG=ZUY-*Q7yqS
zm<HW4+90cV{B#B{#Ux{F$Pi%7N$3@caak0OMRG{FQBq{WzU02G_8Fw-!^zYEoKbNA
zrAq1~I;nup)H*v(Kc`*Oaaf@f&Sw&-k=mgw^8d-Fy$?Pw`TsM<GkYGseIK|BcnN;|
z=YbXA75MPa0NcQOf%gD^f*=1o;Jd)Hz#i~E;9lUj@Zo<2JPUjkApbrG9tK{9AAbYb
z2f9E9xE1&*eEBZ{r+}M*8}Q-305IS+`0CFCTYwF`3cbGwJOz;7PW_kynyX=;VW454
zVc<V!pg3Tr0$T}U0p%H}JUUW|gf^D;$zp5N0U2{f67WS4Q(C^fve;qjaI)56h#W0%
zUOrj5QiA;WA(>TEI7I5u%U0QX6<xzWlEv`0DTau1fbn4U;c5?FW1Mzap;pzJ(%J0e
zO1iyi-t0Xgi|3`o4fxva7BsEJV?=-uPa)ETp3X5<=*`-JOQMfMF^+A=ccUu$zwQji
zCB>;GmA=SEMy5>1*nFm?ZDx}^I0}5WdaUKe`EDRupB*xoVoZ)7P%ZIzGEBKQ4HL_`
z$N!r=(44HXFxjrD49@UVG-q&Oq6<B-G|xLC4TM}RQ}xU&d_n}$*~ZR!OI4jvdyOK;
z*ZgR#e&t7-$*ml4^IS?V<rc1G(GK}*n6~9SrSNwqBpr{*y)j{P6$nT4b9ikccdMKR
zjHiO}YupbwERO2O3AsXuBNX;l3#k=JdRZ6`h$382X!tKW@#LfWeRv9Ga|qreD60Z?
z<Z@DXs-?1u+!Tz|qkF^4XSFaE0d&36jf6DfTqe164pJXcM_b+6@I*cl23zpCd4Tvr
zYG=h`wJ_^g;&e5&RZtQ$9zVFKNV{`Agv;AHXiY0x>&;X&72P1(w)iy@<t#gbD3c0(
z#)#8#PYn^IlHZLO*JLs>NEr@vR_cs}FuCVB+Hb{=LlW@>bhzyy;6$lTzpq?&^{jmH
zs<UcCqS~eRIw}Aer2u+9N`Uc=N2^nESzo;zC7^PTM`frSCB*jx53~yECj;~g5db-q
zLNh<5JytcOidFrkbfQG%VP(JwxB_KF;Ngc3_ex8%*t&Y9HB_{9wVV-@UUg)W3`0dB
zq$)fjrKEF`ka9o@F=gqRlnH&EBnv8=I0FfrP^l(zl+feljn=3M8y&CXg^kvLuzvur
C*%vtg

literal 0
HcmV?d00001

diff --git a/openNucleome/whole_nucleus_model.py b/openNucleome/whole_nucleus_model.py
index f9abe7d..a5c42a0 100644
--- a/openNucleome/whole_nucleus_model.py
+++ b/openNucleome/whole_nucleus_model.py
@@ -284,7 +284,7 @@ def add_lamina_potential(self, flag, chr_lam_param):
         if flag['lam-lam']:
             self.chr_system.addForce(self.lamina_model.add_lam_lam(22))
         if flag['squeeze_nucleus']:
-            self.chr_system.addForce(self.lamina_model.add_squeeze_nucleus(23))
+            self.chr_system.addForce(self.lamina_model.add_squeeze_nucleus(23, k = flag['strength']))
 
     def load_default_settings(self):
         '''
@@ -305,7 +305,7 @@ def load_default_settings(self):
         self.add_nucleolus_potential(dict_nuc_ff, chr_nuc_param)
         self.add_lamina_potential(dict_lam_ff, chr_lam_param)
 
-    def load_customized_settings(self, force_field):
+    def load_customized_settings(self, force_field, k = 1.0):
         '''
         Load customized force field settings
 
@@ -313,11 +313,13 @@ def load_customized_settings(self, force_field):
         ----------
         force_field (Pandas Dataframe, required) :
             Store the flag of all the potentials and the parameter file names
+        k (float, required) :
+            The strength of force squeezing the nucleus (Default: 1.0)
         '''
         dict_chrom_ff = {'bond':force_field.loc['chromosome']['bond'], 'angle':force_field.loc['chromosome']['angle'], 'softcore':force_field.loc['chromosome']['softcore'], 'ideal':force_field.loc['chromosome']['ideal'], 'compt':force_field.loc['chromosome']['compt'], 'inter':force_field.loc['chromosome']['inter']}
         dict_spec_ff = {'spec-spec':force_field.loc['speckle']['spec-spec'], 'spec-chrom':force_field.loc['speckle']['spec-chrom']}
         dict_nuc_ff = {'nuc-nuc':force_field.loc['nucleolus']['nuc-nuc'], 'nuc-spec':force_field.loc['nucleolus']['nuc-spec'], 'nuc-chrom':force_field.loc['nucleolus']['nuc-chrom']}
-        dict_lam_ff = {'lam-chrom':force_field.loc['lamina']['lam-chrom'], 'hard-wall':force_field.loc['lamina']['hard-wall'], 'lam-lam':self.flag_membrane, 'squeeze_nucleus':self.flag_membrane}
+        dict_lam_ff = {'lam-chrom':force_field.loc['lamina']['lam-chrom'], 'hard-wall':force_field.loc['lamina']['hard-wall'], 'lam-lam':self.flag_membrane, 'squeeze_nucleus':self.flag_membrane, 'strength': k}
         ideal_param_file = force_field.loc['chromosome']['ideal_param_file']
         compt_param_file = force_field.loc['chromosome']['compt_param_file']
         interchr_param_file = force_field.loc['chromosome']['interchr_param_file']
diff --git a/tutorials/HFF_100KB/NuclearDeformation/README.md b/tutorials/HFF_100KB/NuclearDeformation/README.md
index f6620ce..332cabc 100644
--- a/tutorials/HFF_100KB/NuclearDeformation/README.md
+++ b/tutorials/HFF_100KB/NuclearDeformation/README.md
@@ -1,6 +1,6 @@
 ## NuclearDeformation 
 
-This folder provides tutorials for setting up and performing simulations of the HFF nucleus at the 100KB resolution with the presence of various nuclear landmarks, including nuclear lamina, speckles, and nucleoli. Different from the sphere situation, we applied a force to squeeze the nucleus.
+This folder provides tutorials for setting up and performing simulations of the HFF nucleus at the 100KB resolution with the presence of various nuclear landmarks, including nuclear lamina, speckles, and nucleoli. Different from the sphere nucleus situation, we applied a force to squeeze the nucleus.
 
 - simulation.ipynb: The jupyter notebook showing how to create a system and run a simulation
 
diff --git a/tutorials/HFF_100KB/NuclearDeformation/simulation.ipynb b/tutorials/HFF_100KB/NuclearDeformation/simulation.ipynb
index 2bbec39..9d7e829 100644
--- a/tutorials/HFF_100KB/NuclearDeformation/simulation.ipynb
+++ b/tutorials/HFF_100KB/NuclearDeformation/simulation.ipynb
@@ -31,7 +31,8 @@
    "id": "0987436b-c228-4ba7-baa9-28e21b3a63ed",
    "metadata": {},
    "source": [
-    "## Important parameters"
+    "## Important parameters\n",
+    "We defined the important parameters in the next block. First, we set the transition probability between dP particles and P particles as 0.2, and the transition frequency as 4000. When creating the system, we set type 6, 7 as the dP and P particles, respectively, so we kept using 6, 7 here. In this example, we ran a simulation with total length of 3,000,000 steps, and output one configuration and the energy every 2000 steps."
    ]
   },
   {
@@ -55,7 +56,12 @@
    "id": "8e0e9ef8-97a2-488e-ba82-5fdfe446b9b3",
    "metadata": {},
    "source": [
-    "## Initialize the system"
+    "## Initialize the system\n",
+    "We first set up an example \"model\" of class \"OpenNucleome\" with the conserved temperature, damping coefficient, timestep, and the mass scale. In this folder, we also included the initial configuration \"human.pdb\" used for the simulation and created a system according to the initial configuration.\n",
+    "\n",
+    "Because during the simulations, we would transit the dP speckle and P speckle particles, here, we logged the start index and end index of speckle particle, and computed the number of speckle particles.\n",
+    "\n",
+    "In this example, we moved all the lamina beads, and would consider the dynamics of the membrane, and that is why we set \"True\" (on) for membrane dynamics. Consequently, we need to designate the bonds between specific lamina beads, so we included a text file, which logs all the pairs linked by the bonds, for the variable \"membrane_bond\"."
    ]
   },
   {
@@ -70,7 +76,6 @@
     "# Generate new elements and construct topology as well; membrane_dynamics: True for including lamina dynamics, False for excluding lamina dynamics; membrane_bond: A file contains the lamina bond when membrane_dynamics is on.\n",
     "model.create_system(PDB_file, membrane_dynamics = True, membrane_bond = 'lamina_bond.txt') \n",
     "\n",
-    "index_spec_spec_potential = 6\n",
     "start_spec_index = model.N_chr_nuc+1\n",
     "end_spec_index = model.N_chr_nuc_spec+1\n",
     "N_spec = start_spec_index-end_spec_index"
@@ -81,7 +86,12 @@
    "id": "07c89f5c-7839-45ae-8b98-186d5600b42e",
    "metadata": {},
    "source": [
-    "## Add the force field"
+    "## Add the force field\n",
+    "Different from the sphere nucleus situation, we used a csv file to log all the flags of interactions between chromosomes and chromosomes, or chromosomes and nuclear landmarks. \n",
+    "\n",
+    "The column from \"bond\" to \"lam_squeeze\" is boolen, which means the switches of the corresponding interactions. For example, if the spec-chrom is True, it means in the simulation, the interaction between speckle and chromosome will be present; if the inter is False, it means we exclude the interchromosomal interactions between chromosome. Remember some potentials require the corresponding parameter files, such as ideal requires ideal_param_file and spec-chrom requires the chr_spec_param, so if you turn those potentials on, you should also include the corresponding parameter files.\n",
+    "\n",
+    "In this example, we turn every interaction on, and set the strength of force squeezing the nucleus as 1.0 (k) when loading the customized force field. The users can set their specific strengths."
    ]
   },
   {
@@ -277,10 +287,14 @@
    ],
    "source": [
     "# Add the customized force field\n",
-    "# In this customized setting, I logged all the flags for different interactions (True means on, False means off, and NaN means N/A) and all the corresponding files required for interactions. \n",
+    "# In this customized setting, I logged all the flags for different interactions\n",
+    "# (True means on, False means off, and NaN means N/A)\n",
+    "# and all the corresponding files required for interactions. \n",
     "force_field = pd.read_csv('input.csv', sep=' ', header=0, index_col=0)\n",
-    "force_field\n",
-    "model.load_customized_settings(force_field)"
+    "model.load_customized_settings(force_field, k = 1.0)\n",
+    "\n",
+    "index_spec_spec_potential = 6\n",
+    "force_field"
    ]
   },
   {
@@ -288,7 +302,8 @@
    "id": "6c942879-33b9-4ddd-92bf-0ebae07561cb",
    "metadata": {},
    "source": [
-    "## Perform simulation, in this example, total step = 3,000,000, output to dcd every 2000 steps, and output the energy (similar to thermo in lammps) every 2000 steps"
+    "## Perform the simulation\n",
+    "We first created the simulation with a specific Platform, and here, we used \"CUDA\" but users can also use \"CPU\", \"Reference\", and \"OpenCL\" according to their hardware. Before the simulation, we minimized the energy to make the system much more reasonable and stable. After randomly setting velocity, we started our simulation with a total length of 3,000,000 steps and output the configuration and energy every 2000 steps, and change the speckle types every 4000 steps as we mentioned in the previous blocks."
    ]
   },
   {
diff --git a/tutorials/HFF_100KB/SphericalNucleus/simulation.ipynb b/tutorials/HFF_100KB/SphericalNucleus/simulation.ipynb
index a659b4d..4c4ed91 100644
--- a/tutorials/HFF_100KB/SphericalNucleus/simulation.ipynb
+++ b/tutorials/HFF_100KB/SphericalNucleus/simulation.ipynb
@@ -114,7 +114,7 @@
    "metadata": {},
    "source": [
     "## Perform the simulation\n",
-    "We first created the simulation with a specific Platform, and here, we used \"CUDA\" but users can also use \"CPU\", \"Reference\", and \"OpenCL\" according to their hardware. Before the simulation, we minimized the energy to make the system much more reasonable and stable. After randomly setting velocity, we started our simulation with a total length of 3,000,000 steps and output the configuration and energy every 2000 steps, and change the speckle types every 4000 steps as we mentioned in the previous blocks"
+    "We first created the simulation with a specific Platform, and here, we used \"CUDA\" but users can also use \"CPU\", \"Reference\", and \"OpenCL\" according to their hardware. Before the simulation, we minimized the energy to make the system much more reasonable and stable. After randomly setting velocity, we started our simulation with a total length of 3,000,000 steps and output the configuration and energy every 2000 steps, and change the speckle types every 4000 steps as we mentioned in the previous blocks."
    ]
   },
   {